From l.m.timmermans at students.uu.nl  Fri Mar  1 16:49:58 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Fri, 1 Mar 2013 22:49:58 +0100
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
Message-ID: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>

On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
> Greetings,
>
> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>
> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>
> Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetw!
>  ork::RandomFactory -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA::ESEfinder -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameSubs -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::interpro -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::berkeleydb -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::entrezgene -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tinyseq -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::chadoxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (opt!
>  ional_features -> Bio::SeqIO::game::gameWriter -> requires) [Validatio
> n: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::FileCache -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::bsml_sax -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Primer3 -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::HtSNP -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Compatible -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Taxonomy::entrez -> requires) [Validation: 1.2], Expected a ma!
>  p structure from string or file. (optional_features -> Bio::SeqIO::agave -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::TagHaplotype -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::SeqFeature::Store::FeatureFileLoader -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::Protein* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::blastxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::EUtilities -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Draw::Cladogram -> requires) [Validation: 1!
>  .2], Expected a map structure from string or file. (optional_features
> -> Bio::Tools::SeqPattern -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tigrxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Collection -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Draw::Pictogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::Writer::BSMLResultWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::HIVQuery -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::TreeIO::svggraph -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::eutils -> requires) [Validation: 1.2], Expected a map structure from string or file. (opti!
>  onal_features -> Bio::PhyloNetwork -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern::BackTranslate -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::GenBank -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Variation::IO::xml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::GraphViz -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Annotated -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::NCBIHelper -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::HIV -> requires) [Validation: 1.2], Expected a map structure from string or file. (!
>  optional_features -> Bio::Tools::Analysis::DNA* -> requires) [Validati
> on: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Run::RemoteBlast -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::excel -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::ClusterIO::dbsnp -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Microarray::Tools::ReseqChip -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::soap -> requires) [Validation: 1.2]
> at /usr/local/lib/perl5/5.10.1/Module/Build/Base.pm line 4559
>
> Could not create MYMETA files
> Creating new 'Build' script for 'BioPerl' version '1.006001'

What versions of Module::Build and CPAN::Meta are you using?

> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.

Yeah, 1.6.1 equals 1.006001. See also
http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
Do note that it is no longer the lastest release, latest is 1.6.901
and a new release is expected on a short notice.

Leon


From cjfields at illinois.edu  Fri Mar  1 18:11:39 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 1 Mar 2013 23:11:39 +0000
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
	<CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6E70B5F7@CHIMBX5.ad.uillinois.edu>

On Mar 1, 2013, at 3:49 PM, Leon Timmermans <l.m.timmermans at students.uu.nl>
 wrote:

> On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
>> Greetings,
>> 
>> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>> 
>> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>> ?.
> 
>> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.
> 
> Yeah, 1.6.1 equals 1.006001. See also
> http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
> Do note that it is no longer the lastest release, latest is 1.6.901
> and a new release is expected on a short notice.
> 
> Leon

Yup, hoping to work on it tonight and tomorrow.  Travis-CI indicates all normal tests are passing, I'll run through a few remaining ones.  Some we can't address directly; there are a number of warnings popping up I can't do anything about (they originate from Graph).

chris

From pcantalupo at gmail.com  Sat Mar  2 12:28:15 2013
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Sat, 2 Mar 2013 12:28:15 -0500
Subject: [Bioperl-l] Fix for Bug #3376 broke somewhere else
In-Reply-To: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
References: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
Message-ID: <CAJqbkv5-cXLh_cMa3rWoOVv7PijY2Orq=Smvqd3Xij887iVhMg@mail.gmail.com>

Hi Francisco,

Nice catch. Please submit a new bug report for this and reference bug
3376. Please provide a minimal hmmer output file, a script and the
expected output. Then, I'll look into it and fix the bug.

Thank you,

Paul

Paul Cantalupo
University of Pittsburgh


On Thu, Feb 28, 2013 at 10:36 AM, Francisco J. Ossand?n
<fossandonc at hotmail.com> wrote:
> Hi,
> I was re-checking Bug #3302 using the Bio::SearchIO modules of the
> repository and found that now it can't parse a Hmmer2 file that was
> previously fine. After tracking the problem, I discovered that a change in a
> regular expression to fix another bug broke the parse.
>
> The fix for the Bug #3376 consisted in adding an extra condition to omit
> lines where end of domain indicator is split across lines
> (https://redmine.open-bio.org/issues/3376):
> TEST: domain 1 of 1, from 8 to 97: score 184.7, E = 2.5e-56
>                    *->svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDn
>                       sv+qqqq+  +    +vtAiAiAigYRYRYRAv Wn GsLs G nDn
>         Test     8    SVYQQQQGGSA----MVTAIAIAIGYRYRYRAVVWNKGSLSTGTNDN 50
>
>                    DnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr<-
>                    DnDq +d LYtiYYsvtv +ss+p q+v+HHHaH+asstkiiiki P
>         Test    51 DNDQAAD-LYTIYYSVTVSASSWPGQSVTHHHAHPASSTKIIIKIAPS   97
>
>                    *
>
>         Test     -   -
> This case is characterized by the 2 dashes in the line...
>
> So the expression added in hmmer2.pm - ?next_result?
> (https://github.com/bioperl/bioperl-live/commit/142e5d79e3a6593db32bf0af9904
> 8f47d01bd3f2):
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\-\s+\-\s*$/ ) ### <--- This regex was
> designed for bug 3376
>                         {
>                             next;
>                         }
>
> But the expression used is too broad because it uses the "^.+" just before
> the 2 dashes, and it broke these lines parsing, where is full of dashes:
>                    KyACrqCdtiVQAPaPakpIErGiptaGLLArvlVSKyaEHlPLYRQsEI
>
>   lcl|gi|340     - -------------------------------------------------- -
>
>                    yaRqGVeiaRstLadWVgrtgarLaPLvdALaeyVLkeGklHADeTPVqV
>                          +i  s L   V++ + r
>   lcl|gi|340 60938 ------AIMISGLIHGVSARCLRF-------------------------- 60955
>
> I think a reasonable fix that still fixes the original bug and restore the
> function for this case is to add an extra \s+ in the regex just before the
> first dash, so the expression makes sure that the first dash is the one that
> comes AFTER the description (and is replacing the usual coordinate number)
> and is not the last of an alignment or a series of dashes like the one
> above:
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\s+\-\s+\-\s*$/ ) ### <--- Tweaked regex
>                         {
>                             next;
>                         }
> I tested it and it works fine, hope you find the fix acceptable.
>
> Cheers,
>
> --
> Francisco J. Ossandon
> Bioinformatician.
> Ph.D. Candidate, University Andres Bello.
> Center for Bioinformatics and Genome Biology,
> Fundacion Ciencia para la Vida.
> Santiago, Chile.
> www.cienciavida.cl/CBGB.htm
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From hlapp at drycafe.net  Sun Mar  3 12:53:34 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sun, 3 Mar 2013 12:53:34 -0500
Subject: [Bioperl-l] GSoC 2013 is ON
Message-ID: <F68E8168-80A5-4681-9912-8655998A9F40@drycafe.net>

Forwarding on behalf of Pjotr Prins, who just volunteered to serve as OBF's GSoC admin for this year.

~~~

Game on! GSoC 2013 is ON. I am running with the OBF project
administration this year for the Google Summer of code (GSoC). 
First and foremost I want to thank Robert Buels and others for making
OBF/GSoC a success in the previous three years! This year, Robert, Chris
Fields and Hilmar Lapp will act as backup administrators.

The deadline for the OBF application for GSoC2013 as a mentoring
organisation is Friday March 29! See

 http://www.google-melange.com/gsoc/events/google/gsoc2013

Similar to previous years, each Bio* project needs to update and add project
ideas on the project's individual OBF wiki page and create links from the main
OBF page at

 http://www.open-bio.org/wiki/Google_Summer_of_Code

(we will update the main information on that page soon).

So, for each of the OBF projects that wants to do GSoC again this
year:

1. Update the list of project ideas on your project's GSoC page (BioPython,
  BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done
  or no longer relevant, etc. For an example see

    http://bioruby.open-bio.org/wiki/Google_Summer_of_Code

2. Update the final list of project ideas on the main OBF GSoC page
  to match.

    http://www.open-bio.org/wiki/Google_Summer_of_Code

3. Register with gsoc at lists.open-bio.org

4. Announce it on that list when you are ready :)

Anyone can submit a project idea! Former GSoC students are especially
encouraged to contribute ideas to the mailing lists.

Please have the updates done by Friday March 22nd. The number and quality of
the project ideas are part of the evaluation process for whether OBF is
accepted as a Summer of Code organisation again this year, so let's come up
with some good ones!

Pj. (Pjotr Prins)

Important dates: 

 * March 22nd: Finalise project ideas
 * March 29th: Deadline OBF mentoring organisation submission to Google

http://www.open-bio.org/wiki/Google_Summer_of_Code


From carandraug+dev at gmail.com  Sun Mar  3 20:58:41 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 01:58:41 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <512B3DCB.7050008@uni-wuerzburg.de>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
Message-ID: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>

On 25 February 2013 10:32, Andreas Leimbach
<andreas.leimbach at uni-wuerzburg.de> wrote:
> On 25.2.13 11:08, Carn? Draug wrote:
>>
>> I'm writing a perl module to write a description of the variance
>> between 2 sequences as described on
>> http://www.hgvs.org/mutnomen/recs-prot.html
>>
>> Basically, given 2 sequences, would returns something like "p.Lys2del
>> p.His25_Met26insGln" if those are the differences. It also accounts
>> for the existence of - characters on the sequences that may come from
>> their alignment.
>>
>> My question is, where on the project tree should I place the module?
>>
>> Also, is there something already written that would convert from 1 to
>> 3 letter code?
>>
> for your last question:
> You can convert aa strings from one to three letter code with
> 'Bio::SeqUtils'.

Thank you. I have never used Bio::SeqUtils. Not only does solve my
problem, but also seems to be the right place to insert my code.

If no one objects, I'll add a new method to Bio::SeqUtils named
"describe_mutation".

Carn?


From cjfields at illinois.edu  Sun Mar  3 22:45:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 03:45:45 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 7:58 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 25 February 2013 10:32, Andreas Leimbach
> <andreas.leimbach at uni-wuerzburg.de> wrote:
>> On 25.2.13 11:08, Carn? Draug wrote:
>>> 
>>> I'm writing a perl module to write a description of the variance
>>> between 2 sequences as described on
>>> http://www.hgvs.org/mutnomen/recs-prot.html
>>> 
>>> Basically, given 2 sequences, would returns something like "p.Lys2del
>>> p.His25_Met26insGln" if those are the differences. It also accounts
>>> for the existence of - characters on the sequences that may come from
>>> their alignment.
>>> 
>>> My question is, where on the project tree should I place the module?
>>> 
>>> Also, is there something already written that would convert from 1 to
>>> 3 letter code?
>>> 
>> for your last question:
>> You can convert aa strings from one to three letter code with
>> 'Bio::SeqUtils'.
> 
> Thank you. I have never used Bio::SeqUtils. Not only does solve my
> problem, but also seems to be the right place to insert my code.
> 
> If no one objects, I'll add a new method to Bio::SeqUtils named
> "describe_mutation".
> 
> Carn?

I'm fine with that; at some point it might be worth thinking about whether we need to organize the various *Utils modules a bit better.  As most of these export methods, they would be good targets for reorganization at some point (maybe into a general Bio::Utils namespace).

chris


From carandraug+dev at gmail.com  Sun Mar  3 23:15:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 04:15:51 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>

On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
> [...] at some point it might be worth thinking about whether we need to
> organize the various *Utils modules a bit better.  As most of these export
> methods, they would be good targets for reorganization at some point
> (maybe into a general Bio::Utils namespace).

Do you mean placing all of them into a separate Util distribution? I
think it makes more sense to keep them close to what they deal with.

If it's just moving them all into Bio::Utils:: may be a good idea. At
the moment there's not much of a model for their naming. I found these
ones (am I missing anything that does not have Utils on the name?)

Bio/Coordinate/Utils.pm
Bio/SeqUtils.pm
Bio/Search/SearchUtils.pm
Bio/Search/BlastUtils.pm
Bio/Search/Tiling/MapTileUtils.pm

Also, only the last one seems to export anything.

Carn?


From cjfields at illinois.edu  Sun Mar  3 23:50:15 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 04:50:15 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> [...] at some point it might be worth thinking about whether we need to
>> organize the various *Utils modules a bit better.  As most of these export
>> methods, they would be good targets for reorganization at some point
>> (maybe into a general Bio::Utils namespace).
> 
> Do you mean placing all of them into a separate Util distribution? I
> think it makes more sense to keep them close to what they deal with.

No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

> If it's just moving them all into Bio::Utils:: may be a good idea. At
> the moment there's not much of a model for their naming. I found these
> ones (am I missing anything that does not have Utils on the name?)
> 
> Bio/Coordinate/Utils.pm
> Bio/SeqUtils.pm
> Bio/Search/SearchUtils.pm
> Bio/Search/BlastUtils.pm
> Bio/Search/Tiling/MapTileUtils.pm
> 
> Also, only the last one seems to export anything.
> 
> Carn?


A few mentioned above.  I don't think they have to be object classes, their entire purpose is to add functionality, so a full-blown class is probably a bit overkill (no one is likely to override their behavior).  

I could also see subdividing these up: DNA, RNA, and protein specific methods as well (for instance the 1->3 letter amino acid conversions, which would never be used on DNA).  It just depends how fine-grained we want to get.  

chris

From cjfields at illinois.edu  Tue Mar  5 09:46:34 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 5 Mar 2013 14:46:34 +0000
Subject: [Bioperl-l] Quick update on BioPerl release
In-Reply-To: <511C14AA.9030107@gmail.com>
References: <118F034CF4C3EF48A96F86CE585B94BF6CE24CF5@CHIMBX5.ad.uillinois.edu>
	<511C14AA.9030107@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F79C09@CHIMBX5.ad.uillinois.edu>

Just a note to keep everyone updated: the upcoming BioPerl release hasn't dropped off my (our) radar, but it will slip probably to the beginning of next week, likely Sunday-Monday CST.  There are a couple of changes/fixes that I would like to see going in (namely the recent HMMER fixes on master among others), and not insignificantly I've been tied up with a few $job-related tasks that have eaten up my time.

chris

On Feb 13, 2013, at 4:33 PM, Florent Angly <florent.angly at gmail.com> wrote:

> On 14/02/13 01:18, Fields, Christopher J wrote:
>> I*highly*  recommend using X.Y versioning for simplicity (e.g. no more 3-point versions)
> Yes, I support the X.Y versioning as well.
> Florent
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From clarsen at vecna.com  Tue Mar  5 15:55:05 2013
From: clarsen at vecna.com (Chris Larsen)
Date: Tue, 5 Mar 2013 15:55:05 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
	->1.6.1) ?
Message-ID: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>

Hello BioPerl-l,

Issue with partial codon translation. 

At our bioinformatics resource center we are using BioPerl to translate partial sequences to amino acids. This is necessary in the case of certain virus GenBank files, which are typically untranslated from polyprotein into their final mature peptide format, and no amino acid sequence is given in the source file. We need to make one from our mat_peptide generator. However our developers are finding that in their migration from BioPerl 1.6.0 to 1.6.1, the final amino acid generated from a partial nucleotide sequence is now being dropped, and this is resulting in several hundred files being altered relative to legacy. Here is an example:

In the hepC virus genome : AB014488

The nucleotide sequence (only) is given:

caagctgtca tggacatggt ggcgggggcc cactggggag tcctagcggg ccttgcctac
tattccatgg tggggaactg ggctaaggtt ttgattgtga tgctactctt cgccggcgtt
gacgggcata cccgcgtgac ggggggggtg caaggccacg tcacctctac actcacgtcc
ctctttagac ctggggcgtc ccagaaaatt cagcttgtaa acaccaatgg cagttggcac
atcaacagga ctgccctgaa ctgcaatgac tccctccaaa ctgggttcct tgccgcgctg
ttctacacac acaagttcaa cgcgtccgga tgcccggagc gcatggccag ctgccgctcc
attgacaagt tcgaccaggg atggggtccc atcacttatg cccaacctga caactcggac
cagaggccgt attgctggca ctatgcacct cgacagtgtg gtatcgtacc cgcgtcgcag
gtgtgcggtc cagtgtattg cttcacccca agccctgttg tggtggggac gaccgatcgt
tccggtgccc ctacgtataa ctgggg

where this ends in the partial codon of 'gg'. (Dont bother, this is 188 and 2/3 aa). A biologist might know that this terminus is always going to be a Glycine, G, since the third position is irrelevant, and so we would like to extend the partial codon into another amino acid in the last 'E2' protein encoded by this genome fragment. It's not sequenced but we can infer. The viral proteins are so short, it really matters! We want that G (and SPTAVRL). However the newer BioPerl version is not giving us the last amino acid. The functionality appears to be turned off, or a default argument was changed?  Issue with -complete ?

Sorry, not good quite enough in (bio)perl to find the solution myself. Only know it is not working now, and am trying to prevent the DBA from stabbing me in the neck with a spork because 4% of the records are now diff in the new pipeline. (Partial seqs, exactly 2 of 3 bp,  non-stop terminus in the available CDS). They are not telling me that errors don't occur within a string, only at the terminus, in viral polyproteins, and only when is not a stop codon. Ergo, color me confused.

I believe this is being handled by:

Bio::Tools::CodonTable and $obj->translate().

where the docs state the method:

"Returns a string of one letter amino acid codes from 
           nucleotide sequence input. The imput (sic) can be of any length. 
(...)
if the codon is two nucleotides long and if by adding
               an a third character 'N', it codes for a single amino
               acid (with exceptions above), return that, otherwise
               return empty string."

But I defer to the much larger bioperl-l wisdom. Sorry for the complexity. The options for them seem to be to continue using the 1.6.0 version to generate the longer better string, and 1.6.1 for everything else; but I'd rather the DBA team just uses one version of BioPerl. They could also update their version to 1.6.9. But, migrating a whole industrial pipeline to a new version for a production system also isnt trivial, so rather than hoping blindly for the fix in v1.6.9, I am asking here if the functionality works for others, and for which versions, and if its truly a bug, or has been fixed or changed, and as of what version. It would be great if one tiny piece could be replaced and the whole problem vanishes...But we may find it is our problem too. 

Hoping we just have to turn on this changed functionality, but we also want to see the issue documented. Cannot find the solution in BIO's docs. Sorry Brian!

I just want all the extra [SPTAVRLG] we can get. Any guidance I will graciously convey back to the team and try to work it out.

Thanks,

Chris

PS: Chris F and Amir discuss : highly related issue: http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html

"why should CodonTable::translate() automatically 'complete' the translation for incomplete codons by default?  I would consider this a bug."
 
-- 

Christopher Larsen, Ph.D.
Sr. Scientist / Grants Manager
Vecna Medical
Phone: (240) 965-4525
Fax: (240) 547-6133

clarsen at vecna dot com
http://vecna.com

Better Technology, Better World (TM)

The contents of this message may be privileged and confidential. Therefore, if this message has been received in error, please delete it. Your receipt of this message is not intended to waive any applicable privilege. Please do not disseminate this message without the permission of the author.








From Amir_Karger at hms.harvard.edu  Wed Mar  6 13:18:13 2013
From: Amir_Karger at hms.harvard.edu (Karger, Amir)
Date: Wed, 6 Mar 2013 13:18:13 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>
Message-ID: <CD5CF244.51003%amir_karger@hms.harvard.edu>

On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:

>Hello BioPerl-l,
>
>A biologist might know that this terminus is always going to be a
>Glycine, G, since the third position is irrelevant, and so we would like
>to extend the partial codon into another amino acid in the last 'E2'
>protein encoded by this genome fragment. It's not sequenced but we can
>infer. The viral proteins are so short, it really matters! We want that G
>(and SPTAVRL). However the newer BioPerl version is not giving us the
>last amino acid. The functionality appears to be turned off, or a default
>argument was changed?  Issue with -complete ?
>
>
>
>PS: Chris F and Amir discuss : highly related issue:
>http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>
>"why should CodonTable::translate() automatically 'complete' the
>translation for incomplete codons by default?  I would consider this a
>bug."

I guess one man's bug is another man's feature.

Sorry to have ruined your pipeline.

-Amir



From cjfields at illinois.edu  Wed Mar  6 14:19:23 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 6 Mar 2013 19:19:23 +0000
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <CD5CF244.51003%amir_karger@hms.harvard.edu>
References: <CD5CF244.51003%amir_karger@hms.harvard.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D8FF30@CHIMBX5.ad.uillinois.edu>

On Mar 6, 2013, at 12:18 PM, "Karger, Amir" <Amir_Karger at hms.harvard.edu> wrote:

> On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:
> 
>> Hello BioPerl-l,
>> 
>> A biologist might know that this terminus is always going to be a
>> Glycine, G, since the third position is irrelevant, and so we would like
>> to extend the partial codon into another amino acid in the last 'E2'
>> protein encoded by this genome fragment. It's not sequenced but we can
>> infer. The viral proteins are so short, it really matters! We want that G
>> (and SPTAVRL). However the newer BioPerl version is not giving us the
>> last amino acid. The functionality appears to be turned off, or a default
>> argument was changed?  Issue with -complete ?
>> 
>> 
>> 
>> PS: Chris F and Amir discuss : highly related issue:
>> http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>> 
>> "why should CodonTable::translate() automatically 'complete' the
>> translation for incomplete codons by default?  I would consider this a
>> bug."
> 
> I guess one man's bug is another man's feature.
> 
> Sorry to have ruined your pipeline.
> 
> -Amir

Chris, Amir,

Just a note: BioPerl is now at 1.6.901 on CPAN (released in 2011) and will be at 1.6.902 sometime next week.  

IIRC (and from back-reading in that thread), the problem was one of consistency, namely that translate() from PrimarySeqI and CodonTable act differently, and that to intuit what is the 'correct' thing to do in this case was possibly wrong from the PrimarySeqI end.  We went the route of least magic and least surprise, namely to return just the translated sequence w/o guessing whether the sequence in question is complete.  

So in my opinion, the old behavior was a bug, and the new behavior is more consistent.  The magic way is still there, though; pass in '-complete => 1'.  I can check that, just in case, to make sure it works.

chris



From a0071251 at nus.edu.sg  Thu Mar  7 00:24:06 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 13:24:06 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
Message-ID: <BBEBCF29-53C3-4BCD-AE6C-33B42D8F5933@nus.edu.sg>



Dear BioPerl,


I have encountered failed tests while installing Bioperl-1.6.901 from CPAN.
i downloaded BioPerl-1.6.901.tar and ran 'tar xvfz BioPerl-1.6.901.tar'
It gave me a message saying 'tar: Error exit delayed from previous errors.' but i moved on to install using 'perl Build.PL'
it gave me a message saying that some files are missing. I just moved on again and eventually when i ran './Build test', it told me that 32//55 test programs failed and 1/2436 subtests failed.
you will find a detailed report of the errors in the attached file.

Please take a look and let me know where i have gone wrong.
I am suspecting that the problem started when i extracted .tar file, but i have no idea how to correct that.

Your help will be much appreciated.
Thank you for your time and help.


Sincerely,
Ah Jung


-------------- next part --------------
A non-text attachment was scrubbed...
Name: error_from_Bioperl_installation
Type: application/octet-stream
Size: 126548 bytes
Desc: error_from_Bioperl_installation
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0001.obj>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ATT00001.txt
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0001.txt>

From a0071251 at nus.edu.sg  Thu Mar  7 01:15:58 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 14:15:58 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
	(continued)
Message-ID: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>



Dear BioPerl,

I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
Hope this helps to clarify the problem further.

Thank you,
Ah Jung

-------------- next part --------------
A non-text attachment was scrubbed...
Name: error2
Type: application/octet-stream
Size: 71030 bytes
Desc: error2
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/363ab81b/attachment-0001.obj>

From scott at scottcain.net  Thu Mar  7 11:01:37 2013
From: scott at scottcain.net (Scott Cain)
Date: Thu, 7 Mar 2013 11:01:37 -0500
Subject: [Bioperl-l] Failed ./Build test while installing
	Bioperl-1.6.901 (continued)
In-Reply-To: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
References: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
Message-ID: <CA+JTaoxRxE5RtZuYwaW1OAG=G+TxkCQO3WC+OpCx7kzKKYoxCA@mail.gmail.com>

Hi Ah Jung,

The first problem you reported was because you didn't download the
whole tar file (the were a warning message that it was truncated, and
then messages that there were files missing); you just needed to
download it again.

For this message, you have this the first time cpan tries to install a module:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/Library/Perl/5.12/darwin-thread-multi-2level'
Do not have write permissions on '/Library/Perl/5.12/darwin-thread-multi-2level'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

When running cpan, you need to either run it as root (ie, "sudo cpan")
or configure it to use a local directory where you do have write
permission.  The former is probably easier, whereas the latter is
probably better.

Scott


On Thu, Mar 7, 2013 at 1:15 AM, Jeon Ah Jung <a0071251 at nus.edu.sg> wrote:
>
>
> Dear BioPerl,
>
> I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
> Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
> Hope this helps to clarify the problem further.
>
> Thank you,
> Ah Jung
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

From liyc1989 at gmail.com  Thu Mar  7 17:52:18 2013
From: liyc1989 at gmail.com (yichao li)
Date: Thu, 7 Mar 2013 17:52:18 -0500
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
Message-ID: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>

Hi,

            In the SYSNOPSIS, it says:

my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
  for my $feat ($in->next_feature) {
    # do something with $feat (a Bio::SeqFeature::Annotated object)
  }

  my $out = Bio::FeatureIO(-format=>'bed');
  for my $feat ($seq->get_seqFeatures) {
    $out->write_feature($feat);
  }

Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
'file.bed');*

If not, an error will occur.


------------------------------------
Best wishes,
Yichao
Ohio University Bioinformatics Lab
Phone: (740)-591-1289

From ragowthaman at gmail.com  Fri Mar  8 14:41:38 2013
From: ragowthaman at gmail.com (gowtham)
Date: Fri, 8 Mar 2013 11:41:38 -0800
Subject: [Bioperl-l] Writing alignment objects read via Bio::DB::Sam
Message-ID: <CAMvwBZnuEYHCFqOwyGuTPs9CZRxWhsGhJfpSzQ_Mrm4CO5mMJA@mail.gmail.com>

Hi Every One,
I'm using Bio::DB::Sam->new(-bam='') method to read a bam file. And I am
able to query individual values of each alignment record. For example
'XM','AS', and 'AS' tags, or alignment start end positions etc. After
filtering these records for some values (eg, mismatches), i would like to
write them back into a "SAM" (preferable BAM) format.

I am not able to find a method that writes the record. Can someone help me
with this?

Though, I am able to open a new bam file for  writing using
Bio::DB::Bam->open(my.bam, 'w'), I dont know how to convert the SAM
alignment i read from (Bio::DB::SAM) to be written using this.

write1() does not accept alignment object read by Bio::DB::SAM, it accepts
objects read only by Bio::DB::BAM.


Thanks very much in advance,
Gowthaman
-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).

From witch.of.agnessi at gmail.com  Fri Mar  8 20:24:01 2013
From: witch.of.agnessi at gmail.com (witch.of.agnessi at gmail.com)
Date: Fri, 8 Mar 2013 17:24:01 -0800 (PST)
Subject: [Bioperl-l] How to find 'is_a'/'part_of' relationship using
	GO::Termfinder
Message-ID: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>

Hello All,

I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
 node. I wonder How I can extract the type of relationship,
like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
any better way to do this in Bioperl?

Thanks in advance


 

From antony.vincent.1 at ulaval.ca  Fri Mar  8 22:56:59 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Fri, 8 Mar 2013 19:56:59 -0800 (PST)
Subject: [Bioperl-l]  sh: 1: Syntax error: "(" unexpected
Message-ID: <35154292.post@talk.nabble.com>


Hi!

I'm trying to use emboss program (water or needle) with a bioperl script. I
got this error when I try the script: sh: 1: Syntax error: "(" unexpected

Here is the script:

#!/usr/bin/perl 

 # get an EMBOSS factory
  use Bio::Factory::EMBOSS;
  use Bio::AlignIO;
  use Bio::SeqIO;
  $f = Bio::Factory::EMBOSS -> new();
  # get an EMBOSS application  object from the factory
  $water = $f->program('water');
    $inputfilename = "krt1.fasta";
    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
                             '-format' => 'fasta');

    $inputfilename2 = "krt2.fasta";
    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
                             '-format' => 'fasta');
  # here is an example of running the application -
  # water can compare 1 sequence against 1 or more sequences
  # in a database using Smith-Waterman
  #this would be a list of seqs to compare 
                       # (could be just 1)
  my $wateroutfile = 'out.water';
  $water->run({-sequences => $seq_to_test,
               -seqall    => \@seqs_to_check,
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => $wateroutfile});
  # now you might want to get the alignment
  
  my $alnin = Bio::AlignIO->new(-format => 'emboss',
                                       -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }

Have you an idea of what can do this error?

Thanks!
-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From l.m.timmermans at students.uu.nl  Sat Mar  9 08:43:54 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Sat, 9 Mar 2013 14:43:54 +0100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>

On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected

The error suggests the script is interpreted by the shell instead of
perl. Are you sure the hashbang (#!) is the absolute first thing in
the file. No whitespace or BOM character in the front?

Leon

From carandraug+dev at gmail.com  Sat Mar  9 09:03:50 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:03:50 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>

On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>  wrote:
>
>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> [...] at some point it might be worth thinking about whether we need to
>>> organize the various *Utils modules a bit better.  As most of these export
>>> methods, they would be good targets for reorganization at some point
>>> (maybe into a general Bio::Utils namespace).
>>
>> Do you mean placing all of them into a separate Util distribution? I
>> think it makes more sense to keep them close to what they deal with.
>
> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

How would you define exportable? I usually don't like the idea of
having functions exported by default. Specially since it's so easy for
the user to load them themselves.

Carn?


From carandraug+dev at gmail.com  Sat Mar  9 09:47:08 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:47:08 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
	Bio::DB::EUtilities ?
Message-ID: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>

Hi

I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
module, part of bioperl-live, seems to be re-implementing pieces of
Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

According to Bio::DB::Biblio::eutils documentation, it should not be
used directly, instead should be used through Bio::DB::Biblio. This
means that it could be replaced by Bio::DB::EUtilities without any
disturbance (other than adding a dependency and as long as users have
been respecting the recommendations).

Carn?


From cjfields at illinois.edu  Sat Mar  9 10:07:20 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:07:20 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate
	of	Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
> module, part of bioperl-live, seems to be re-implementing pieces of
> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.

> According to Bio::DB::Biblio::eutils documentation, it should not be
> used directly, instead should be used through Bio::DB::Biblio. This
> means that it could be replaced by Bio::DB::EUtilities without any
> disturbance (other than adding a dependency and as long as users have
> been respecting the recommendations).
> 
> Carn?

Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

chris

From cjfields at illinois.edu  Sat Mar  9 10:05:33 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:05:33 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94D74@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:03 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>> wrote:
>> 
>>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> [...] at some point it might be worth thinking about whether we need to
>>>> organize the various *Utils modules a bit better.  As most of these export
>>>> methods, they would be good targets for reorganization at some point
>>>> (maybe into a general Bio::Utils namespace).
>>> 
>>> Do you mean placing all of them into a separate Util distribution? I
>>> think it makes more sense to keep them close to what they deal with.
>> 
>> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?
> 
> How would you define exportable? I usually don't like the idea of
> having functions exported by default. Specially since it's so easy for
> the user to load them themselves.
> 
> Carn?

Yes, I agree (no export by default).

chris

From carandraug+dev at gmail.com  Sat Mar  9 16:20:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 21:20:51 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>

On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>> module, part of bioperl-live, seems to be re-implementing pieces of
>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>
> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>
>> According to Bio::DB::Biblio::eutils documentation, it should not be
>> used directly, instead should be used through Bio::DB::Biblio. This
>> means that it could be replaced by Bio::DB::EUtilities without any
>> disturbance (other than adding a dependency and as long as users have
>> been respecting the recommendations).
>>
>> Carn?
>
> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

So I was looking at this but seems that would cause an issue with
circular dependency. Not at module level, but at distribution level
(Bio-Eutilities is dependent on bioperl-live and bioperl-live
dependent on Bio-EUtilities because of Bio::DB::Biblio).

This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
Could this be done and a separate distribution created for it? None of
the empty repositories seems fitting for it.

Carn?


From cjfields at illinois.edu  Sat Mar  9 17:06:41 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 22:06:41 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>


On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>>> module, part of bioperl-live, seems to be re-implementing pieces of
>>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>> 
>> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>> 
>>> According to Bio::DB::Biblio::eutils documentation, it should not be
>>> used directly, instead should be used through Bio::DB::Biblio. This
>>> means that it could be replaced by Bio::DB::EUtilities without any
>>> disturbance (other than adding a dependency and as long as users have
>>> been respecting the recommendations).
>>> 
>>> Carn?
>> 
>> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).
> 
> So I was looking at this but seems that would cause an issue with
> circular dependency. Not at module level, but at distribution level
> (Bio-Eutilities is dependent on bioperl-live and bioperl-live
> dependent on Bio-EUtilities because of Bio::DB::Biblio).
> 
> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
> Could this be done and a separate distribution created for it? None of
> the empty repositories seems fitting for it.
> 
> Carn?

Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

chris




From carandraug+dev at gmail.com  Sat Mar  9 22:06:02 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 10 Mar 2013 03:06:02 +0000
Subject: [Bioperl-l] graphics of gene distribution through a genome interval
Message-ID: <CAPOrs_1BwNeGLse000t6rmNEhneP_svosM2KYhMO+8OO6JrZ-w@mail.gmail.com>

Hi everyone

I was wondering if anyone knows any tools to produce this type of
diagram? http://picpaste.com/1fqB4e8h.png It a piece of genome with
some gene positions marked. And it has nice "zoom-in boxes" around
some more cluttered regions. I've seen these more than once but do not
know how to generate one. Could someone give me a pointer?

Thanks,
Carn?


From antony.vincent.1 at ulaval.ca  Sun Mar 10 09:17:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 06:17:09 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From Russell.Smithies at agresearch.co.nz  Sun Mar 10 16:30:36 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 11 Mar 2013 09:30:36 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>

I'll get in first and say it's best to 'use strict', and 'use warnings'  ;-)

Perhaps some of the params to water have changed? It looks like it wants filenames, not objects.
I get the same errors with your code - which I think is coming from water.

If I do this it seems to work OK:
---------------------------------------
#!/usr/bin/perl

# get an EMBOSS factory
use Bio::Factory::EMBOSS;
use Bio::AlignIO;
use Bio::SeqIO;

use strict;
use warnings;

my $f = Bio::Factory::EMBOSS -> new();
# get an EMBOSS application  object from the factory
my $water = $f->program('water');
my $wateroutfile = 'out.water';
$water->run({  -verbose => 1,
               -asequence => 'krt1.fasta',
               -bsequence => 'krt2.fasta',
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => 'out.water'});
------------------------------------------------


illustrious$ cat out.water
########################################
# Program: water
# Rundate: Mon 11 Mar 2013 09:29:36
# Commandline: water
#    -gapopen 10.0
#    -gapextend 0.5
#    -outfile out.water
#    -asequence krt1.fasta
#    -verbose 1
#    -bsequence krt2.fasta
#    -auto
# Align_format: srspair
# Report_file: out.water
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: K2C1_HUMAN
# 2: K22E_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     436/667 (65.4%)
# Similarity:   499/667 (74.8%)
# Gaps:          78/667 (11.7%)
# Score: 2023.5
#
#
#=======================================

K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR     45
                     ||.|.|.:|..|.||     |||||||.:....||:|||
K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------     39

K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG     91
                      .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA     86

K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG    130
                     ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG    136

K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR    179
                     | ||||.|||         ||||.||::||||||||||::|||||.||::
K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ    177

K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP    229
                     ||||||:|||:|||||||||||||||||||||||||||::..||..||||
K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP    227

K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN    279
                     .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA    277

K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ    329
                     |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS    327

K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE    379
                     :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE    377

K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA    429
                     ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA    427

K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI    479
                     |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI    477

K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG    521
                     ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG    525

K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS    568
                        ||||.||.|||||||...||.||.||| ||.        |||| |||
K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS    565

K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR    616
                     |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG    610

K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
                     |..|||    |||||||
K22E_HUMAN       611 GYGSGG----GGSSSVK    623


#---------------------------------------
#---------------------------------------



--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Monday, 11 March 2013 2:17 a.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From antony.vincent.1 at ulaval.ca  Sun Mar 10 17:59:51 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 14:59:51 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
	<35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
Message-ID: <35158468.post@talk.nabble.com>


That's works! Thanks a lot!

Smithies, Russell wrote:
> 
> I'll get in first and say it's best to 'use strict', and 'use warnings' 
> ;-)
> 
> Perhaps some of the params to water have changed? It looks like it wants
> filenames, not objects.
> I get the same errors with your code - which I think is coming from water.
> 
> If I do this it seems to work OK:
> ---------------------------------------
> #!/usr/bin/perl
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> 
> use strict;
> use warnings;
> 
> my $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> my $water = $f->program('water');
> my $wateroutfile = 'out.water';
> $water->run({  -verbose => 1,
>                -asequence => 'krt1.fasta',
>                -bsequence => 'krt2.fasta',
>                -gapopen   => '10.0',
>                -gapextend => '0.5',
>                -outfile   => 'out.water'});
> ------------------------------------------------
> 
> 
> illustrious$ cat out.water
> ########################################
> # Program: water
> # Rundate: Mon 11 Mar 2013 09:29:36
> # Commandline: water
> #    -gapopen 10.0
> #    -gapextend 0.5
> #    -outfile out.water
> #    -asequence krt1.fasta
> #    -verbose 1
> #    -bsequence krt2.fasta
> #    -auto
> # Align_format: srspair
> # Report_file: out.water
> ########################################
> 
> #=======================================
> #
> # Aligned_sequences: 2
> # 1: K2C1_HUMAN
> # 2: K22E_HUMAN
> # Matrix: EBLOSUM62
> # Gap_penalty: 10.0
> # Extend_penalty: 0.5
> #
> # Length: 667
> # Identity:     436/667 (65.4%)
> # Similarity:   499/667 (74.8%)
> # Gaps:          78/667 (11.7%)
> # Score: 2023.5
> #
> #
> #=======================================
> 
> K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR    
> 45
>                      ||.|.|.:|..|.||     |||||||.:....||:|||
> K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------    
> 39
> 
> K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG    
> 91
>                       .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
> K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA    
> 86
> 
> K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG   
> 130
>                      ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
> K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG   
> 136
> 
> K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR   
> 179
>                      | ||||.|||         ||||.||::||||||||||::|||||.||::
> K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ   
> 177
> 
> K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP   
> 229
>                      ||||||:|||:|||||||||||||||||||||||||||::..||..||||
> K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP   
> 227
> 
> K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN   
> 279
>                      .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
> K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA   
> 277
> 
> K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ   
> 329
>                      |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
> K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS   
> 327
> 
> K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE   
> 379
>                      :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
> K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE   
> 377
> 
> K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA   
> 429
>                      ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
> K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA   
> 427
> 
> K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI   
> 479
>                      |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
> K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI   
> 477
> 
> K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG   
> 521
>                      ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
> K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG   
> 525
> 
> K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS   
> 568
>                         ||||.||.|||||||...||.||.||| ||.        |||| |||
> K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS   
> 565
> 
> K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR   
> 616
>                      |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
> K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG   
> 610
> 
> K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
>                      |..|||    |||||||
> K22E_HUMAN       611 GYGSGG----GGSSSVK    623
> 
> 
> #---------------------------------------
> #---------------------------------------
> 
> 
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Monday, 11 March 2013 2:17 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it
> like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this
> why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl
>>> script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context:
> http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35158468.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From liamelbourne at me.com  Sat Mar  9 04:18:34 2013
From: liamelbourne at me.com (Liam Elbourne)
Date: Sat, 09 Mar 2013 20:18:34 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <7A059EB2-147A-4B26-B321-DEB40D1693EC@me.com>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
>  use Bio::Factory::EMBOSS;
>  use Bio::AlignIO;
>  use Bio::SeqIO;
>  $f = Bio::Factory::EMBOSS -> new();
>  # get an EMBOSS application  object from the factory
>  $water = $f->program('water');
>    $inputfilename = "krt1.fasta";
>    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                             '-format' => 'fasta');
> 
>    $inputfilename2 = "krt2.fasta";
>    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                             '-format' => 'fasta');
>  # here is an example of running the application -
>  # water can compare 1 sequence against 1 or more sequences
>  # in a database using Smith-Waterman
>  #this would be a list of seqs to compare 
>                       # (could be just 1)
>  my $wateroutfile = 'out.water';
>  $water->run({-sequences => $seq_to_test,
>               -seqall    => \@seqs_to_check,
>               -gapopen   => '10.0',
>               -gapextend => '0.5',
>               -outfile   => $wateroutfile});
>  # now you might want to get the alignment
> 
>  my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                       -file   => $wateroutfile);
> 
>  while ( my $aln = $alnin->next_aln ) {
>      # process the alignment -- these will be Bio::SimpleAlign objects
>  }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From antony.vincent.1 at ulaval.ca  Sat Mar  9 13:24:43 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 10:24:43 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From liam.elbourne at mq.edu.au  Sat Mar  9 06:39:44 2013
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Sat, 9 Mar 2013 22:39:44 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <0C3E5EF2-9A20-4C33-94B7-93F242E69704@mq.edu.au>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> $water = $f->program('water');
>   $inputfilename = "krt1.fasta";
>   $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                            '-format' => 'fasta');
> 
>   $inputfilename2 = "krt2.fasta";
>   @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                            '-format' => 'fasta');
> # here is an example of running the application -
> # water can compare 1 sequence against 1 or more sequences
> # in a database using Smith-Waterman
> #this would be a list of seqs to compare 
>                      # (could be just 1)
> my $wateroutfile = 'out.water';
> $water->run({-sequences => $seq_to_test,
>              -seqall    => \@seqs_to_check,
>              -gapopen   => '10.0',
>              -gapextend => '0.5',
>              -outfile   => $wateroutfile});
> # now you might want to get the alignment
> 
> my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                      -file   => $wateroutfile);
> 
> while ( my $aln = $alnin->next_aln ) {
>     # process the alignment -- these will be Bio::SimpleAlign objects
> }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 235 bytes
Desc: Message signed with OpenPGP using GPGMail
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130309/0fd852ec/attachment.bin>

From antony.vincent.1 at ulaval.ca  Sat Mar  9 21:59:26 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 18:59:26 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From sidd.basu at gmail.com  Mon Mar 11 13:16:45 2013
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Mon, 11 Mar 2013 12:16:45 -0500
Subject: [Bioperl-l] Re: How to find 'is_a'/'part_of' relationship
	using	GO::Termfinder
In-Reply-To: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
References: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
Message-ID: <513e1181.aade320a.5bee.ffff87da@mx.google.com>

Hi, 

On Fri, 08 Mar 2013, witch.of.agnessi at gmail.com wrote:

> Hello All,
> 
> I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
>  node. I wonder How I can extract the type of relationship,
> like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
> any better way to do this in Bioperl?

You could use the Bioperl's ontology module in this case. For example,  here is how
you could start with ...

1. Parse gene_ontology obo file with Bio::OntologyIO
https://metacpan.org/module/Bio::OntologyIO

2. Once you get the ontology object(Bio::Ontology::Ontology), you could
use the *find_terms*
https://metacpan.org/module/Bio::Ontology::Ontology#find_terms
to get your term objects.

3. Then use the graph lookup methods
   such as *get_relationships*, get_child_terms, get_parent_terms,
   get_ancestor_terms that takes a term and relationship objects to extract
   whatever connection you are looking for. 

Hope this helps, 
-siddhartha


   


> 
> Thanks in advance
> 
> 
>  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From Russell.Smithies at agresearch.co.nz  Mon Mar 11 14:09:56 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 12 Mar 2013 07:09:56 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>

I suspect that there's several versions of water and the parameters have changed.
This is the version I'm using and I can reproduce the errors:

intrepid$ water -h
Smith-Waterman local alignment of sequences
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -gapopen            float      [10.0 for any sequence] The gap open penalty
                                  is the score taken away when a gap is
                                  created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value assumes you are using the EBLOSUM62
                                  matrix for protein sequences, and the
                                  EDNAFULL matrix for nucleotide sequences.
                                  (Number from 0.000 to 100.000)
   -gapextend          float      [0.5 for any sequence] The gap extension
                                  penalty is added to the standard gap penalty
                                  for each base or residue in the gap. This
                                  is how long gaps are penalized. Usually you
                                  will expect a few long gaps rather than many
                                  short gaps, so the gap extension penalty
                                  should be lower than the gap penalty. An
                                  exception is where one or both sequences are
                                  single reads with possible sequencing
                                  errors in which case you would expect many
                                  single base gaps. You can get this result by
                                  setting the gap open penalty to zero (or
                                  very low) and using the gap extension
                                  penalty to control gap scoring. (Number from
                                  0.000 to 10.000)
  [-outfile]           align      [*.water] Output alignment file name
                                  (default -aformat srspair)

   Additional (Optional) qualifiers:
   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.

   Advanced (Unprompted) qualifiers:
   -[no]brief          boolean    [Y] Brief identity and similarity

   General qualifiers:
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Sunday, 10 March 2013 3:59 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From cjfields at illinois.edu  Mon Mar 11 16:57:59 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 11 Mar 2013 20:57:59 +0000
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
References: <35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D96D47@CHIMBX5.ad.uillinois.edu>

I think the EMBOSS code checks the ACD file for whatever version of EMBOSS is installed, parses the parameters out of that, and uses those for input.  I don't remember if it accepts a Bio::Seq as input (I don't recall it doing so), but if it does then we should file that as a bug.

chris

On Mar 11, 2013, at 1:09 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> I suspect that there's several versions of water and the parameters have changed.
> This is the version I'm using and I can reproduce the errors:
> 
> intrepid$ water -h
> Smith-Waterman local alignment of sequences
> Version: EMBOSS:6.5.0.0
> 
>   Standard (Mandatory) qualifiers:
>  [-asequence]         sequence   Sequence filename and optional format, or
>                                  reference (input USA)
>  [-bsequence]         seqall     Sequence(s) filename and optional format, or
>                                  reference (input USA)
>   -gapopen            float      [10.0 for any sequence] The gap open penalty
>                                  is the score taken away when a gap is
>                                  created. The best value depends on the
>                                  choice of comparison matrix. The default
>                                  value assumes you are using the EBLOSUM62
>                                  matrix for protein sequences, and the
>                                  EDNAFULL matrix for nucleotide sequences.
>                                  (Number from 0.000 to 100.000)
>   -gapextend          float      [0.5 for any sequence] The gap extension
>                                  penalty is added to the standard gap penalty
>                                  for each base or residue in the gap. This
>                                  is how long gaps are penalized. Usually you
>                                  will expect a few long gaps rather than many
>                                  short gaps, so the gap extension penalty
>                                  should be lower than the gap penalty. An
>                                  exception is where one or both sequences are
>                                  single reads with possible sequencing
>                                  errors in which case you would expect many
>                                  single base gaps. You can get this result by
>                                  setting the gap open penalty to zero (or
>                                  very low) and using the gap extension
>                                  penalty to control gap scoring. (Number from
>                                  0.000 to 10.000)
>  [-outfile]           align      [*.water] Output alignment file name
>                                  (default -aformat srspair)
> 
>   Additional (Optional) qualifiers:
>   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
>                                  This is the scoring matrix file used when
>                                  comparing sequences. By default it is the
>                                  file 'EBLOSUM62' (for proteins) or the file
>                                  'EDNAFULL' (for nucleic sequences). These
>                                  files are found in the 'data' directory of
>                                  the EMBOSS installation.
> 
>   Advanced (Unprompted) qualifiers:
>   -[no]brief          boolean    [Y] Brief identity and similarity
> 
>   General qualifiers:
>   -help               boolean    Report command line options and exit. More
>                                  information on associated and general
>                                  qualifiers can be found with -help -verbose
> 
> 
> --Russell
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Sunday, 10 March 2013 3:59 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From bosborne11 at verizon.net  Tue Mar 12 11:04:36 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 12 Mar 2013 11:04:36 -0400
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
In-Reply-To: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
References: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
Message-ID: <C262A6D6-3967-4290-90FF-738A1A8CCC3F@verizon.net>

Yichao,

Fixed. Thank you for pointing that out.

Brian O.


On Mar 7, 2013, at 5:52 PM, yichao li <liyc1989 at gmail.com> wrote:

> Hi,
> 
>            In the SYSNOPSIS, it says:
> 
> my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
>  for my $feat ($in->next_feature) {
>    # do something with $feat (a Bio::SeqFeature::Annotated object)
>  }
> 
>  my $out = Bio::FeatureIO(-format=>'bed');
>  for my $feat ($seq->get_seqFeatures) {
>    $out->write_feature($feat);
>  }
> 
> Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
> 'file.bed');*
> 
> If not, an error will occur.
> 
> 
> ------------------------------------
> Best wishes,
> Yichao
> Ohio University Bioinformatics Lab
> Phone: (740)-591-1289
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From carandraug+dev at gmail.com  Tue Mar 12 18:43:05 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 12 Mar 2013 22:43:05 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>

On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>> Could this be done and a separate distribution created for it? None of
>> the empty repositories seems fitting for it.
>>
>
> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

Could you (or some other admin) prepare a separate Bio-biblio
repository? I'm splitting them now and need a repo to push into.

Thanks,
Carn?


From cjfields at illinois.edu  Tue Mar 12 19:42:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 12 Mar 2013 23:42:11 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>

Done:

https://github.com/bioperl/Bio-Biblio

chris

On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>> Could this be done and a separate distribution created for it? None of
>>> the empty repositories seems fitting for it.
>>> 
>> 
>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
> 
> Could you (or some other admin) prepare a separate Bio-biblio
> repository? I'm splitting them now and need a repo to push into.
> 
> Thanks,
> Carn?



From therealsisterdot at gmail.com  Mon Mar 11 06:31:42 2013
From: therealsisterdot at gmail.com (sisterdot)
Date: Mon, 11 Mar 2013 03:31:42 -0700 (PDT)
Subject: [Bioperl-l] parsing psiblast + ?
Message-ID: <97a3d346-c5dd-41f4-b71d-042cc92f7ee9@googlegroups.com>

hey hey, 

i am using perl v5.10.0 and Bio::SearchIO 1.006901

i would like to use psiblast 2.2.27 + (instead of blastpgp), but parsing 
via  
new Bio::SearchIO(-format => "blast",-file => "$file")
doesn't seem to work well- individual iterations are interpreted as 
separate results.

Bio::SearchIO doesn't seem to really understand "psiblast +" default 
pairwise output, or am i mistaken?
if i am not mistaken, are there alternatives in Bioperl for parsing 
"psiblast +" with the default "-outfmt 0"?

thanks a lot
sis

From scott at scottcain.net  Wed Mar 13 22:51:55 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 13 Mar 2013 22:51:55 -0400
Subject: [Bioperl-l] Early registration for GMOD meeting closes in one week
Message-ID: <CA+JTaozZFOWKcsZ0bDqUS1mD_E2kWLUGi_1bA+bGj6GKb9eJdg@mail.gmail.com>

Hello,

The GMOD meeting is in Cambridge, England on April 5-6 (right before
the Biocurator meeting) and early registration closes March 21 (in one
week).  It is shaping up to be a good meeting with several interesting
talks scheduled.  Please try to make it!  For more information on the
meeting, see the meeting page:

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

and to save some money on your registration, go to

  http://gmod2013.eventbrite.com/

before March 21 to register.

If you'd like to give a talk at the meeting please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

From carandraug+dev at gmail.com  Thu Mar 14 19:55:27 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 14 Mar 2013 23:55:27 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>

On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>> Could this be done and a separate distribution created for it? None of
>>>> the empty repositories seems fitting for it.
>>>>
>>>
>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>
>> Could you (or some other admin) prepare a separate Bio-biblio
>> repository? I'm splitting them now and need a repo to push into.
>>
>
> Done:
>
> https://github.com/bioperl/Bio-Biblio

Thanks, I'm trying to prepare a release of the Bio-biblio distribution
soon. I'd like to do a 1.7 release first. One with minimal changes
compared to the current bioperl-live. Could someone give me
co-maintenance of the Bio::Biblio namespace? Or should I just prepare
everything for the release and wait for someone else to just accept
it? Also, the Bio-biblio distribution also has modules on the
Bio::DB::biblio namespace.

Carn?


From carandraug+dev at gmail.com  Thu Mar 14 21:21:16 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 01:21:16 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
Message-ID: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>

Hi

I'm using dist::zilla and found the BioPerl plugin. I noticed that the
bug tracker information is set to

  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
  bugtracker.mailto = bug-${dist}@rt.cpan.org

shouldn't they set for https://redmine.open-bio.org/projects/bioperl?

Carn?


From cjfields at illinois.edu  Thu Mar 14 21:59:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 01:59:53 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1CF@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 6:55 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>>> Could this be done and a separate distribution created for it? None of
>>>>> the empty repositories seems fitting for it.
>>>>> 
>>>> 
>>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>> 
>>> Could you (or some other admin) prepare a separate Bio-biblio
>>> repository? I'm splitting them now and need a repo to push into.
>>> 
>> 
>> Done:
>> 
>> https://github.com/bioperl/Bio-Biblio
> 
> Thanks, I'm trying to prepare a release of the Bio-biblio distribution
> soon. I'd like to do a 1.7 release first. One with minimal changes
> compared to the current bioperl-live. Could someone give me
> co-maintenance of the Bio::Biblio namespace? Or should I just prepare
> everything for the release and wait for someone else to just accept
> it? Also, the Bio-biblio distribution also has modules on the
> Bio::DB::biblio namespace.
> 
> Carn?

That's fine; you can actually do a point release (say, 1.7) and list the proper Bio::* dependencies you need.  I wouldn't list Bio::Root::Root specifically.  

Does anyone here have a problem with Carn? taking co-maintenance of these modules on CPAN?  Please speak up over the next few days, otherwise I'll go ahead and grant it.  Would be nice to have someone looking after these.

chris

From cjfields at illinois.edu  Thu Mar 14 22:00:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:00:43 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>

Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?

chris

On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
> bug tracker information is set to
> 
>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>  bugtracker.mailto = bug-${dist}@rt.cpan.org
> 
> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Thu Mar 14 22:04:23 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 02:04:23 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>

On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>> bug tracker information is set to
>>
>>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>  bugtracker.mailto = bug-${dist}@rt.cpan.org
>>
>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>
>> Carn?
>>
>
> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>
> chris

Yes it is. But only the version 0.01.


From cjfields at illinois.edu  Thu Mar 14 22:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:41:28 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>> bug tracker information is set to
>>> 
>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>> 
>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>> 
>>> Carn?
>>> 
>> 
>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>> 
>> chris
> 
> Yes it is. But only the version 0.01.

Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

chris

From carandraug+dev at gmail.com  Thu Mar 14 23:15:11 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 03:15:11 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>

On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>> bug tracker information is set to
>>>>
>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>
>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>
>>>> Carn?
>>>>
>>>
>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>
>>> chris
>>
>> Yes it is. But only the version 0.01.
>
> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

I think I got it working with the BioPerl bundle. It passes all tests.
Now I was trying to set Pod::Weaver to write the feedback section
automatically but might be better to set it up as pasrt of the BioPerl
bundle.

Carn?


From fossandonc at hotmail.com  Fri Mar 15 10:26:44 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 11:26:44 -0300
Subject: [Bioperl-l] Bug #2936
Message-ID: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>

Hello,

Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven?t
received any feedback yet.

https://redmine.open-bio.org/issues/2936

 

Probably everybody is busy, so I would like to ask only if the proposed fix
is acceptable. If the fix were fine, I could prepare changes in my forked
repo, add tests (in ?t/Seq/PrimarySeq.t????) and make a pull request. What
do you think?

 

Cheers,

 

--

Francisco J. Ossandon

Bioinformatician.

Ph.D. Candidate, University Andres Bello.

Center for Bioinformatics and Genome Biology,

Fundacion Ciencia para la Vida.

Santiago, Chile.

 <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm

 



From cjfields at illinois.edu  Fri Mar 15 10:46:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 14:46:11 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9FAFE@CHIMBX5.ad.uillinois.edu>

Sure, a pull request would be good.  I suggest making sure you are in sync with the 'master' branch first, but I don't think you'll run into conflicts with that.  

My guess is we'll need to pull this into a branch and test rigorously first if it is to go into a bioperl 1.6.  One of the (many?) problems with Bio::Location is that it assumes all features are on linear chromosomes, so there is quite a bit of logic/magic built-in with that assumption that tends to be wrong (e.g. sort order of sublocations and so on, which breaks split locations).  

Frankly, I think we could really simplify this logic so that it is less magic, less fuzzy, and it would bite us in the ass a lot less, but of course this breaks backcompat.  So, my feeling is such fixes would be handled better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com> wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven't
> received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the proposed fix
> is acceptable. If the fix were fine, I could prepare changes in my forked
> repo, add tests (in "t/Seq/PrimarySeq.t"???) and make a pull request. What
> do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From mastarr9 at gmail.com  Fri Mar 15 00:54:49 2013
From: mastarr9 at gmail.com (Matt)
Date: Thu, 14 Mar 2013 23:54:49 -0500
Subject: [Bioperl-l] using a bioperl module after installing.
Message-ID: <5142A999.7090308@gmail.com>

I used "fink" to install bioperl. I see that the installation had no 
problems and that the Bio/SeqIO module exists in hard 
drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually 
make any use of bioperl in a script.

On the bioperl wiki I see that this common error message comes from the 
module sometimes not being installed but, in my case, I think that it is 
installed but "lost".  How can I reinstall or move or change the path to 
make bioperl actually work?
Thanks!

Information:

  * perl v5.10.0
  * Bioperl-pm5.10.0
  * OSX 10.6.8
  * Goal: To simply use a bioperl module
  * The code that gives the error (Using komodo edit):
      o #!/usr/bin/perl -w
        use strict;
        require Bio::SeqiO;
  * The error message:
      o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
        /Library/Perl/Updates/5.10.0
        /System/Library/Perl/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/5.10.0
        /Library/Perl/5.10.0/darwin-thread-multi-2level
        /Library/Perl/5.10.0
        /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
        /Network/Library/Perl/5.10.0 /Network/Library/Perl
        /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
        test.pl line 3.


From mhague at mail.sfsu.edu  Fri Mar 15 15:21:45 2013
From: mhague at mail.sfsu.edu (Michael Hague)
Date: Fri, 15 Mar 2013 12:21:45 -0700
Subject: [Bioperl-l] PopGen Question
Message-ID: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>

Hello,
I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:


use Bio::AlignIO;
use Bio::PopGen::Utilities;
use Bio::PopGen::Statistics;
use Bio::PopGen::Population;

my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
                           				 -format => 'fasta');
my $aln1 = $io1->next_aln;


my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
													-include_monomorphic => 1);

my $stats1 = Bio::PopGen::Statistics->new();
my $D1 = $stats1->tajima_D($pop1);
my $theta1  = $stats1->theta($pop1);
my $segsites1 = $stats1->segregating_sites_count($pop1);

print "\nPopulation #1:\n";
print "Number of segregating sites = $segsites1\n";
print "Tajima\'s D = $D1\n";
print "Watterson\'s theta = $theta1\n\n";

However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?

Thanks so much for the help,
Mike


From cjfields at illinois.edu  Fri Mar 15 16:04:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 20:04:37 +0000
Subject: [Bioperl-l] using a bioperl module after installing.
In-Reply-To: <5142A999.7090308@gmail.com>
References: <5142A999.7090308@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA020F@CHIMBX5.ad.uillinois.edu>

Even if you use fink, you may still need to set the PERL5LIB path to point to that location.  Have you done that?

chris
 
On Mar 14, 2013, at 11:54 PM, Matt <mastarr9 at gmail.com> wrote:

> I used "fink" to install bioperl. I see that the installation had no problems and that the Bio/SeqIO module exists in hard drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually make any use of bioperl in a script.
> 
> On the bioperl wiki I see that this common error message comes from the module sometimes not being installed but, in my case, I think that it is installed but "lost".  How can I reinstall or move or change the path to make bioperl actually work?
> Thanks!
> 
> Information:
> 
> * perl v5.10.0
> * Bioperl-pm5.10.0
> * OSX 10.6.8
> * Goal: To simply use a bioperl module
> * The code that gives the error (Using komodo edit):
>     o #!/usr/bin/perl -w
>       use strict;
>       require Bio::SeqiO;
> * The error message:
>     o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
>       /Library/Perl/Updates/5.10.0
>       /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/5.10.0
>       /Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Library/Perl/5.10.0
>       /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Network/Library/Perl/5.10.0 /Network/Library/Perl
>       /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
>       test.pl line 3.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From fossandonc at hotmail.com  Fri Mar 15 17:36:53 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 18:36:53 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <001d01ce2191$60406310$20c12930$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
Message-ID: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>

Ok,  I did the changes and added a pull request in the repository. All the
tests in "t/Seq/PrimarySeq.t" keeps passing (except the TODOs), including
the ones I added. Everything seems fine on my end.

About the Location/Split module, the lines that I don?t agree at all are the
ones that reverse the segment order in to_FTstring:
	# If the split type is join, the order is important;
	# otherwise must be 5'->3' regardless
	my @locs = ($stype eq 'join' && (!$guide && $strand == -1)) ?
	           reverse $self->sub_Location() : $self->sub_Location() ;

It don?t make sense to me to do that, because doing that you get coordinates
that will NOT give you the expected nucleotide sequence. Another thing that
is weird to me is that the sublocations are free to have different strands
values (like the first being positive strand and the second being negative
strand), since I can't think of one example where that can happen in real
genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
have sublocations in opposite strands at the same time and then extract the
sequence, so I wonder if I'm wrong and there are real cases like that...

As you say, those things would have to wait until later, but at least this
particular bug should be closed. =)

Regards,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: viernes, 15 de marzo de 2013 11:46
Para: Francisco J. Ossand?n
CC: bioperl mailing list
Asunto: Re: [Bioperl-l] Bug #2936

Sure, a pull request would be good.  I suggest making sure you are in sync
with the 'master' branch first, but I don't think you'll run into conflicts
with that.  

My guess is we'll need to pull this into a branch and test rigorously first
if it is to go into a bioperl 1.6.  One of the (many?) problems with
Bio::Location is that it assumes all features are on linear chromosomes, so
there is quite a bit of logic/magic built-in with that assumption that tends
to be wrong (e.g. sort order of sublocations and so on, which breaks split
locations).  

Frankly, I think we could really simplify this logic so that it is less
magic, less fuzzy, and it would bite us in the ass a lot less, but of course
this breaks backcompat.  So, my feeling is such fixes would be handled
better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com>
wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but 
> haven't received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the 
> proposed fix is acceptable. If the fix were fine, I could prepare 
> changes in my forked repo, add tests (in "t/Seq/PrimarySeq.t"???) and 
> make a pull request. What do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From p.j.a.cock at googlemail.com  Sat Mar 16 08:46:22 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sat, 16 Mar 2013 12:46:22 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
Message-ID: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>

On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>
> ... Another thing that
> is weird to me is that the sublocations are free to have different strands
> values (like the first being positive strand and the second being negative
> strand), since I can't think of one example where that can happen in real
> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
> have sublocations in opposite strands at the same time and then extract the
> sequence, so I wonder if I'm wrong and there are real cases like that...
>

This is a real biological phenomena - trans-splicing, often in tRNA genes,
for example:
http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced

As a result the BioPerl / BioSQL / Biopython etc location models do have
to cope with this corner case.  Worse, there are examples where pieces
from different chromosomes are spliced together - which is even harder
to deal with - like my favourite pathological example, nad1 in NC_016406
(and NC_016402), which has the following GenBank location string:

join(complement(149815..150200),
complement(295492..295573),complement(293787..293978),
NC_016402.1:6618..6676,181647..181905)

See also:
http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html

Peter


From cjfields at illinois.edu  Sat Mar 16 10:02:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 16 Mar 2013 14:02:12 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA0D59@CHIMBX5.ad.uillinois.edu>

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different strands
>> values (like the first being positive strand and the second being negative
>> strand), since I can't think of one example where that can happen in real
>> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
>> have sublocations in opposite strands at the same time and then extract the
>> sequence, so I wonder if I'm wrong and there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA genes,
> for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do have
> to cope with this corner case.  Worse, there are examples where pieces
> from different chromosomes are spliced together - which is even harder
> to deal with - like my favourite pathological example, nad1 in NC_016406
> (and NC_016402), which has the following GenBank location string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used for Bio::Location deals with cases like this, but there is an assumption made to deal with some cases like this that is wrong for others (say, circular chromosomes where a feature wraps the origin, where sorting messes things up).  It really needs a top to bottom overhaul to be explicit about the join, but such an overhaul will break some expected behavior, hence my suggestion of putting this in a bioperl v2.

chris

From carandraug+dev at gmail.com  Sat Mar 16 18:27:31 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 16 Mar 2013 22:27:31 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
Message-ID: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>

On 15 March 2013 03:15, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>>> bug tracker information is set to
>>>>>
>>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>>
>>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>>
>>>>> Carn?
>>>>>
>>>>
>>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>>
>>>> chris
>>>
>>> Yes it is. But only the version 0.01.
>>
>> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)
>
> I think I got it working with the BioPerl bundle. It passes all tests.
> Now I was trying to set Pod::Weaver to write the feedback section
> automatically but might be better to set it up as pasrt of the BioPerl
> bundle.

I made a bunch of changes to the BioPerl bundle. I didn't touched the
podweaver part, I just wanted to get a feel of it first, as this was
new stuff to me. I replaced some of the code on the bundle with
plugins that have since been written, and renamed the options so that
they match the option names of the plugins being used.

I do believe that these options are an improvement but since it's a
lot of changes and behaves differently from the previous version, I
created a fork and a branch on my own repo. If no one opposes I will
push them to the main repo.

https://github.com/carandraug/dist-zilla-pluginbundle-bioperl/blob/purging/lib/Dist/Zilla/PluginBundle/BioPerl.pm

Carn?


From fossandonc at hotmail.com  Sun Mar 17 23:09:17 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 18 Mar 2013 00:09:17 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>	<001d01ce2191$60406310$20c12930$@illinois.edu>	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
	<000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
Message-ID: <SNT133-ds9166254353FA597757A40CFE80@phx.gbl>

Wow, trans-splicing is a phenomena I was not aware about, thanks for telling
me. Then, the Guide Strand of the Split-location object must always check if
all the sublocations are present in the same strand; so if all sublocations
are positive the Guide have to be positive, if all are negative the Guide
have to be negative as well, and if there is a mix of strands in
sublocations the Guide have to be undef... The changes I made in flip_strand
didn?t check for the strand consistency in the sublocations when setting the
Guide Strand, so I have to add that.

Ok, how about this, in the following lines I will analyze all possibilities
for location coordinates, step by step, from simpler to complex. Please
follow my reasoning in every step and tell me if there is something you
don?t agree, so I can work on the code and use these cases as tests, and
then make another pull request. Let?s see when there is a reversal of the
sublocations order needed and when is not. For this time, I will only check
cases where the DNA comes from the same chromosome/plasmid/contig


One thing to keep in mind is that the flipped coordinates should reconstruct
the reverse-complement (revcom) of the original sequence.

Example sequence used below (fictional 20bp circular plasmid):
AAAAACCCCCGGGGGTTTTT


### Reasoning: For the following cases, where ALL segments are in the same
strand, NO ORDER REVERSAL is needed because for the complement-strand
sequences the code can join all the positive sequences first and then
complement it complete at the final step. Also, since all segments are in
the same strand, Guide Strand have to be set with the same value than the
sublocations.

# Single location
Coordinates: 1..5 => AAAAA
Revcom: complement(1..5) => TTTTT

# Basic split, both locations in same strand
Coords: join(6..10,16..20) => CCCCCTTTTT
Revcom: complement(join(6..10,16..20)) => AAAAAGGGGG

# Cut by origin-split, same strand, single sequence that pass through origin
Coords: join(16..20,1..2) => TTTTTAA
Revcom: complement(join(16..20,1..2)) => TTAAAAA

# Cut by origin-combo split, same strand, 2 sequences with 1st passing
through origin
Coords: join(19..20,1..2,11..13) => TTAAGGG
Revcom: complement(join(19..20,1..2,11..13)) => CCCTTAA 

# Cut by origin-combo split, same strand, 2 sequences with 2nd passing
through origin
Coords: join(6..10,19..20,1..4) => CCCCCTTAAAA
Revcom: complement(join(6..10,19..20,1..4)) => TTTTAAGGGGG


### Reasoning: For the following cases, where segments are in MIXED strands,
ORDER REVERSAL is needed because the code have to complement some segments
and others not, so it have to complement those segments first and then join
them at the last step. Also, since there is no strand consistency in all
segments, Guide Strand have to be set with undef value.

# Trans-splicing, 2 sequences in different strands, 2nd in complement
Coords: join(6..10,complement(16..20)) => CCCCCAAAAA
Revcom: join(16..20,complement(6..10)) => TTTTTGGGGG

# Trans-splicing, 2 sequences in different strands, 1st in complement
Coords: join(complement(16..20),6..10) => AAAAACCCCC
Revcom: join(complement(6..10),16..20) => GGGGGTTTTT

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 2nd in complement
Coords: join(19..20,1..3,complement(11..13)) => TTAAACCC
Revcom: join(11..13,complement(1..3),complement(19..20)) => GGGTTTAA

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 1st in complement
Coords: join(complement(1..3),complement(19..20), 11..13) => TTTAAGGG
Revcom: join(complement(11..13), 19..20,1..3) => CCCTTAAA

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 2nd in complement
Coords: join(6..10,complement(1..2),complement(18..20),) => CCCCCTTAAA
Revcom: join(18..20,1..2, complement(6..10)) => TTTAAGGGGG

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 1st in complement
Coords: join(complement(6..10),18..20,1..2) => GGGGGTTTAA
Revcom: join(complement(1..2),complement(18..20), 6..10) => TTAAACCCCC

####

As summary, Guide Strand must ensure that all the sublocations have the same
strand value set before using that value, and be undef if there is no
consistency (like in trans-splicing); so any new "add_sub_Location" should
check the other sublocations strands and set Guide Strand according to the
consistency. Establishing Guide Strand value from the beginning and updating
it accordingly with any change in the Split location object, should
correctly signal when to reverse the sublocations order and when not.

Thoughts??

Francisco J.  Ossandon


-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: s?bado, 16 de marzo de 2013 11:02
Para: Peter Cock
CC: bioperl mailing list; Francisco J. Ossand?n
Asunto: Re: [Bioperl-l] Bug #2936

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different 
>> strands values (like the first being positive strand and the second 
>> being negative strand), since I can't think of one example where that 
>> can happen in real genomes. In fact one of the tests in PrimarySeq.t 
>> is designed exactly to have sublocations in opposite strands at the 
>> same time and then extract the sequence, so I wonder if I'm wrong and
there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA 
> genes, for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transplice
> d
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do 
> have to cope with this corner case.  Worse, there are examples where 
> pieces from different chromosomes are spliced together - which is even 
> harder to deal with - like my favourite pathological example, nad1 in 
> NC_016406 (and NC_016402), which has the following GenBank location
string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-gen
> bank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used
for Bio::Location deals with cases like this, but there is an assumption
made to deal with some cases like this that is wrong for others (say,
circular chromosomes where a feature wraps the origin, where sorting messes
things up).  It really needs a top to bottom overhaul to be explicit about
the join, but such an overhaul will break some expected behavior, hence my
suggestion of putting this in a bioperl v2.

chris
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From antony.vincent.1 at ulaval.ca  Mon Mar 18 07:43:30 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 04:43:30 -0700 (PDT)
Subject: [Bioperl-l]  Generate a hsp from emboss format?
Message-ID: <35187436.post@talk.nabble.com>


Hi,
I have a script who uses emboss (water) for a dynamic programming alignment.
Is this possible to generate (convert) my result in emboss format in a hsp
(blast) like.

I need (I think) an hsp format because it's much easier for parse only one
of the two strand in the alignment (and this is what I need).

Thanks!
-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35187436.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From p.j.a.cock at googlemail.com  Mon Mar 18 08:00:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 18 Mar 2013 12:00:21 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <35187436.post@talk.nabble.com>
References: <35187436.post@talk.nabble.com>
Message-ID: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>

On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>
> Hi,
> I have a script who uses emboss (water) for a dynamic programming alignment.
> Is this possible to generate (convert) my result in emboss format in a hsp
> (blast) like.
>
> I need (I think) an hsp format because it's much easier for parse only one
> of the two strand in the alignment (and this is what I need).
>
> Thanks!

EMBOSS water (and related tools like needle) support a range of output
formats - have you looked at those yet?

Peter

From cjfields at illinois.edu  Mon Mar 18 13:19:02 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 17:19:02 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>

On Mar 18, 2013, at 7:00 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>> 
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>> 
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>> 
>> Thanks!
> 
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?
> 
> Peter


Antony,

Bio::AlignIO::emboss is supposed to support water/needle output; have you tried that?  Also, I'm not sure what advantage having this in a BLAST-like output would have over other human-readable formats; any reasons you would need this specific output?

chris



From cjfields at illinois.edu  Mon Mar 18 17:26:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 21:26:22 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA3EA4@CHIMBX5.ad.uillinois.edu>

Just a heads-up, if there are any students interested in the Google Summer of Code, the Open Bioinformatics Foundation is planning on participating again this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are looking for prospective projects.  

We're open for any project ideas this year, so let us know what you would like to do!

chris

From antony.vincent.1 at ulaval.ca  Mon Mar 18 17:35:13 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 14:35:13 -0700 (PDT)
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
Message-ID: <35190011.post@talk.nabble.com>


Hi!
For example, with this code I can easily modify only one string:

 #! /usr/bin/perl -w
 
# use strict;
 use Bio::SeqIO;
 use Bio::Tools::Run::StandAloneBlast;
 use Bio::Seq;
 use warnings;
 
###########################################################################################################
# Usage information
die "Usage: $0 <sequence 1> <sequence 2> <BLAST algorithme> <minimum % of
identity>\n", if (@ARGV != 4);
 my ($infile1,$infile2,$algo,$identity) = @ARGV;
##########################################################################################################


 my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if


	print $hsp->algorithm, ": Identity ", 100*$hsp->frac_identical, "\%, Rank
", $hsp->rank, " (evalue:", $hsp->evalue, ")\n";
	print "\t", $hsp->query_string;
	print "\n";
	print "\t", $hsp->homology_string;
	print "\n";
	print "\t", $hsp->hit_string;
	print "\n\n";
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

This is why I want to have this format. Is this possible?
Thanks!


-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35190011.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From p.rice at imperial.ac.uk  Tue Mar 19 06:51:52 2013
From: p.rice at imperial.ac.uk (Peter Rice)
Date: Tue, 19 Mar 2013 10:51:52 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <51484348.5070603@imperial.ac.uk>

On 18/03/2013 12:00, Peter Cock wrote:
> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>>
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>>
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>>
>> Thanks!
>
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?

The full list for the latest EMBOSS release alignment formats is below. 
They are selected by the -aformat qualifier for any application with an 
"align" output.

It would also be relatively simple to add new formats for the next 
release if they would be useful.

Multiple sequence formats:

"fasta",     "Fasta format sequence",
"msf",       "MSF format sequence",
"clustal",   "clustalw format sequence",
"mega",       "Mega format sequence",
"meganon",       "Mega non-interleaved format sequence",
"nexus",   "nexus/paup format sequence",
"nexusnon",   "nexus/paup non-interleaved format sequence",
"phylip",   "phylip format sequence",
"phylipnon", "phylip non-interleaved format sequence",
"selex",       "SELEX format sequence",
"treecon",       "Treecon format sequence",

Multiple alignment formats:

"markx0",    "Pearson MARKX0 format",
"markx1",    "Pearson MARKX1 format",
"markx2",    "Pearson MARKX2 format",
"markx3",    "Pearson MARKX3 format",
"markx10",   "Pearson MARKX10 format",
"match","Start and end of matches between sequence pairs",
"multiple",  "Simple multiple alignment",
"pair",      "Simple pairwise alignment",
"simple",    "Simple multiple alignment",
"sam",       "Sequence alignent/map (SAM) format",
"score",     "Score values for pairs of sequences",
"srs",       "Simple multiple sequence format for SRS",
"srspair",   "Simple pairwise sequence format for SRS",
"tcoffee",   "TCOFFEE program format",

regards,

Peter Rice
EMBOSS Team


From carandraug+dev at gmail.com  Tue Mar 19 19:02:59 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 19 Mar 2013 23:02:59 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
Message-ID: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>

On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
> I do believe that these options are an improvement but since it's a
> lot of changes and behaves differently from the previous version, I
> created a fork and a branch on my own repo. If no one opposes I will
> push them to the main repo.

Pushed.

Carn?


From cjfields at illinois.edu  Tue Mar 19 22:06:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 20 Mar 2013 02:06:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>

On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> I do believe that these options are an improvement but since it's a
>> lot of changes and behaves differently from the previous version, I
>> created a fork and a branch on my own repo. If no one opposes I will
>> push them to the main repo.
> 
> Pushed.
> 
> Carn?

Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

chris

From carandraug+dev at gmail.com  Tue Mar 19 23:09:52 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 20 Mar 2013 03:09:52 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>

On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> I do believe that these options are an improvement but since it's a
>>> lot of changes and behaves differently from the previous version, I
>>> created a fork and a branch on my own repo. If no one opposes I will
>>> push them to the main repo.
>>
>> Pushed.
>>
>> Carn?
>
> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

I was hoping that it would get more use. jhannah/deafferret tells me
that the people who volunteer to do the CPAN work get burned out. With
this properly set up, it should be as simple as running "dzil
release".

I'm also writing a pod weaver plugin bundle for bioperl but would like
some thought on what others think this should be doing.

Carn?


From fs5 at sanger.ac.uk  Wed Mar 20 18:09:40 2013
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Wed, 20 Mar 2013 22:09:40 +0000
Subject: [Bioperl-l] Bio::DB::Sam - finding clipped regions
Message-ID: <514A33A4.3050107@sanger.ac.uk>

Hi,

I need to report all the positions on a reference sequence where aligned 
reads in a bam file have been hard-clipped.
I am using Bio::DB::Sam and I know that I can use callbacks to traverse 
each individual read and get information about its alignment to each 
position on the reference as in

my $sam = Bio::DB::Sam->new(

   -bam  =>$bam,

   -fasta=>$fasta,

);

my $callback = sub {

   my ( $id, $pos, $p ) = @_;

   for my $pileup (@$p) {

     my $aln  = $pileup->alignment;

     my $cigar = $aln->cigar_str;

     # other stuff here

     # ...

  };

$sam->fast_pileup( $sequence_id, $callback );



But I don't see a straight-forward way (accepting that there may not be 
one of course) to ask "is the next base of the read hardclipped".
It's not that difficult to unravel the cigar string and I have the start 
of the alignment for the read, so I can follow the cigar string along to 
the current base on the reference to see what the alignment is there and 
what happens next.
I've just got that feeling that I'm missing something and there is 
probably a better and more efficient way of doing this, maybe with 
another tool? Using samtools mpileup I can get positions of SNPs and 
INDELS but I can't see a way of collecting the hard-clipped positions 
that I need or is that possible somehow (ok, not BioPerl, I know)

Thanks for your help guys!

Frank



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From scott at scottcain.net  Wed Mar 20 22:28:09 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 20 Mar 2013 22:28:09 -0400
Subject: [Bioperl-l] Last day for early registration for GMOD 2013
Message-ID: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>

Hi,

With several guest speakers, including Jane Lomax from GO, Joseph
Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
Centre, this GMOD meeting is shaping up to be a very intersting
meeting indeed.  Today (March 21) is the last day to register with the
early registration pricing.  To register, go to

  http://gmod2013.eventbrite.com/

I look forward to seeing you next month (April 5-6) in Cambridge,
England.  For more information about GMOD 2013, go to

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

From sofia at neuro.utah.edu  Thu Mar 21 10:51:43 2013
From: sofia at neuro.utah.edu (Sofia M Robb)
Date: Thu, 21 Mar 2013 14:51:43 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
Message-ID: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>

Hello All,

The following link http://bioperl.org/cgi-bin/deob_interface.cgi results in an internal server error. I hope that someone can point the link in the right direction.

Thanks,
Sofia


From p.j.a.cock at googlemail.com  Thu Mar 21 11:28:03 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 21 Mar 2013 15:28:03 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
In-Reply-To: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
References: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
Message-ID: <CAKVJ-_46=1zbFjLL+ovow4449hZ7qWa+woPz8VkbLLy_LnYNGw@mail.gmail.com>

On Thu, Mar 21, 2013 at 2:51 PM, Sofia M Robb <sofia at neuro.utah.edu> wrote:
> Hello All,
>
> The following link http://bioperl.org/cgi-bin/deob_interface.cgi results
> in an internal server error. I hope that someone can point the link in
> the right direction.
>
> Thanks,
> Sofia

That might be related to the server move at the end of last year.
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Whomever looks after the deobfuscator - please drop the Sys Admin
team an email on the root-l mailing list if you need assistance.

Regards,

Peter

From carandraug+dev at gmail.com  Thu Mar 21 22:11:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 22 Mar 2013 02:11:18 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
Message-ID: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>

On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>> I do believe that these options are an improvement but since it's a
>>>> lot of changes and behaves differently from the previous version, I
>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>> push them to the main repo.
>>>
>>> Pushed.
>>>
>>
>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>
> I'm also writing a pod weaver plugin bundle for bioperl but would like
> some thought on what others think this should be doing.

So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
give some feedback if it's adequate for the rest of the project.

https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

To minimize the number of files added to each distro, I also wrote
another plugin which the PluginBundle uses. I wrote it today so you're
likely to not have it installed yet.

https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Carn?


From jason.stajich at gmail.com  Fri Mar 22 02:19:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 21 Mar 2013 20:19:23 -1000
Subject: [Bioperl-l] PopGen Question
In-Reply-To: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
References: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
Message-ID: <F6333CA1-8FAD-4022-BC5B-19FB51CE95AC@gmail.com>

Once you convert it into the population object ($pop1) you can iterate through the markers and request the allele frequency from each of these.

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/Population.html
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/MarkerI.html

 for my $name ( $population->get_marker_names ) {
   my $marker = $population->get_Marker($name);
   print "marker $marker\n";
   my %af = $marker->get_Allele_Frequencies;
   foreach my $allele ( keys %af ) {
      print "$allele $af{$allele}\n";
   }
  }


unfortunately the wiki code seems to be messed up for autolinking out to the pdoc documentation so some of the links on the bioperl website don't get properly made.  something to be fixed I hope.

Jason
On Mar 15, 2013, at 9:21 AM, Michael Hague <mhague at mail.sfsu.edu> wrote:

> Hello,
> I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:
> 
> 
> use Bio::AlignIO;
> use Bio::PopGen::Utilities;
> use Bio::PopGen::Statistics;
> use Bio::PopGen::Population;
> 
> my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
>                           				 -format => 'fasta');
> my $aln1 = $io1->next_aln;
> 
> 
> my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
> 													-include_monomorphic => 1);
> 
> my $stats1 = Bio::PopGen::Statistics->new();
> my $D1 = $stats1->tajima_D($pop1);
> my $theta1  = $stats1->theta($pop1);
> my $segsites1 = $stats1->segregating_sites_count($pop1);
> 
> print "\nPopulation #1:\n";
> print "Number of segregating sites = $segsites1\n";
> print "Tajima\'s D = $D1\n";
> print "Watterson\'s theta = $theta1\n\n";
> 
> However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?
> 
> Thanks so much for the help,
> Mike
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org



From briano at bioteam.net  Sat Mar 23 11:21:58 2013
From: briano at bioteam.net (Brian Osborne)
Date: Sat, 23 Mar 2013 11:21:58 -0400
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
Message-ID: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>

Hanny,

I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.

> 
> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> 
> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> 
> Hanny

Brian O.



From cjfields at illinois.edu  Sat Mar 23 13:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 23 Mar 2013 17:41:28 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
	<7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DBFE3F@CHIMBX5.ad.uillinois.edu>

On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:

> Hanny,
> 
> I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> 
>> 
>> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
>> 
>> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
>> 
>> Hanny
> 
> Brian O.


My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.

chris

From carandraug+dev at gmail.com  Sat Mar 23 21:20:04 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 01:20:04 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
Message-ID: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>

Hi everyone

just announcing that Bio-Biblio version 1.70 just got released.

This release has minimum changes, mainly the split from bioperl-live.
As part of the release with Dist::Zilla, a few changes were made to
the documentation and all source use the utf8 pragma.

Carn?


From hlapp at drycafe.net  Sat Mar 23 21:21:49 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 23 Mar 2013 21:21:49 -0400
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
Message-ID: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>

Congrats, great job! -hilmar

On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:

> Hi everyone
> 
> just announcing that Bio-Biblio version 1.70 just got released.
> 
> This release has minimum changes, mainly the split from bioperl-live.
> As part of the release with Dist::Zilla, a few changes were made to
> the documentation and all source use the utf8 pragma.
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Sat Mar 23 21:59:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 01:59:31 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
	<7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC01CB@CHIMBX5.ad.uillinois.edu>

Agreed, great job!

I may go ahead and pull these from the v1 branch, just to make sure they don't clobber your release.  

chris

On Mar 23, 2013, at 8:21 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Congrats, great job! -hilmar
> 
> On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:
> 
>> Hi everyone
>> 
>> just announcing that Bio-Biblio version 1.70 just got released.
>> 
>> This release has minimum changes, mainly the split from bioperl-live.
>> As part of the release with Dist::Zilla, a few changes were made to
>> the documentation and all source use the utf8 pragma.
>> 
>> Carn?
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Sat Mar 23 23:54:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 03:54:48 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <CAPOrs_0OkB+FgrraMSsMztweCxoyZ7GbHyGEKbO18GA1a2wiow@mail.gmail.com>

On 22 March 2013 02:11, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>> I do believe that these options are an improvement but since it's a
>>>>> lot of changes and behaves differently from the previous version, I
>>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>>> push them to the main repo.
>>>>
>>>> Pushed.
>>>>
>>>
>>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>>
>> I'm also writing a pod weaver plugin bundle for bioperl but would like
>> some thought on what others think this should be doing.
>
> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
> give some feedback if it's adequate for the rest of the project.
>
> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>
> To minimize the number of files added to each distro, I also wrote
> another plugin which the PluginBundle uses. I wrote it today so you're
> likely to not have it installed yet.
>
> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Could a new release of this pluginbundle be made? I have made a lot of
changes to it but I believe it's ready for "production". I used it to
release Bio-biblio and seems to have worked fine. I tried to set it up
so that all it's needed to do is:

1 - change version number on the dist.ini file (there's no need to
commit this change, the PluginBundle will take care of that)
2 - run dzil release

Carn?


From elanorbust2 at yahoo.com  Sun Mar 24 06:14:32 2013
From: elanorbust2 at yahoo.com (sally roberts)
Date: Sun, 24 Mar 2013 03:14:32 -0700 (PDT)
Subject: [Bioperl-l] http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
Message-ID: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>

http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html

From cjfields at illinois.edu  Sun Mar 24 10:32:38 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 14:32:38 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_75F1512441D48A74101FEE2D@qq.com>
References: <tencent_75F1512441D48A74101FEE2D@qq.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC07D0@CHIMBX5.ad.uillinois.edu>

ActivePerl as of a few years or so ago could install modules directly from CPAN.  Have you tried that?  Also, any reason you are using ActivePerl on Linux?  Lots of very nice options out there for linux, including  perlbrew:

http://perlbrew.pl/

The problem we historically have with Windows support is that very few of our developers use it (let alone have access to a Windows machine).  If anyone wants to take this on I would be more than supportive.

chris

On Mar 24, 2013, at 5:44 AM, ciel <58363553 at qq.com> wrote:

> 
> Thanks!
> 
> So, since their web site migrration , I guess I couldn't install bioperl temporary whether in windows or linux. 
> 
> Hanny  
> 
> ------------------ Original ------------------
> From:  "Fields, Christopher J"<cjfields at illinois.edu>;
> Date:  Sun, Mar 24, 2013 01:41 AM
> To:  "Brian Osborne"<briano at bioteam.net>;
> Cc:  "ciel"<58363553 at qq.com>; "Bioperl-L"<bioperl-l at bioperl.org>;
> Subject:  Re: [Bioperl-l] bioperl installation problem
> 
> On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:
> 
> > Hanny,
> > 
> > I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> > 
> >> 
> >> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> >> 
> >> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> >> 
> >> Hanny
> > 
> > Brian O.
> 
> 
> My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.
> 
> chris.



From alexeymorozov1991 at gmail.com  Sun Mar 24 21:00:51 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Mon, 25 Mar 2013 10:00:51 +0900
Subject: [Bioperl-l]
	http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
In-Reply-To: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
References: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
Message-ID: <CAK=7cMMsxCvP+jVYyqDAbaS4_9rycmSVmKUwo-HYTx3nOFA5AQ@mail.gmail.com>

Someone ban the spammer, please.


2013/3/24 sally roberts <elanorbust2 at yahoo.com>

> http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

From 58363553 at qq.com  Fri Mar 22 12:21:00 2013
From: 58363553 at qq.com (=?ISO-8859-1?B?Y2llbA==?=)
Date: Sat, 23 Mar 2013 00:21:00 +0800
Subject: [Bioperl-l] bioperl installation problem
Message-ID: <tencent_4DDD95B145899AF5173CBF5A@qq.com>

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx


Hanny


From lzwright at gmail.com  Thu Mar 21 17:08:41 2013
From: lzwright at gmail.com (liz wright)
Date: Thu, 21 Mar 2013 17:08:41 -0400
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
Message-ID: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>

Hi, I just force installed bioperl on ubuntu linux as this approach was
proposed as a viable alternative when certain tests fail, but I would like
to check that the fail errors listed below will not significantly impair
bioperl usage as I am new to all this and don't really know how to
interpret the error messages.  Thanks, Liz Wright


* WARNING: Configuration was initially created with Module::Build
  version '0.38' but we are now using version '0.4003'.
  If errors occur, you must re-run the Build.PL or Makefile.PL script.
Will try to install symlinks to /usr/local/bin
  CJFIELDS/BioPerl-1.6.1.tar.gz
  sudo ./Build install  -- OK
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
failure ignored because 'force' in effect
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
failure ignored because 'force' in effect
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
failure ignored because 'force' in effect
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
failure ignored because 'force' in effect

From lzwright at gmail.com  Fri Mar 22 08:44:10 2013
From: lzwright at gmail.com (liz wright)
Date: Fri, 22 Mar 2013 08:44:10 -0400
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>

As a follow up to my previous message, this gives a bit more information as
to why the make tests failed:

  make test had returned bad status, won't install without force
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test NO
 RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
'/usr/bin/perl Build.PL --installdirs site' returned status 512
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness failed
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
not OK (XML::DOM); additionally test harness failed
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
not OK (XML::SAX::Expat)
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
missing
(Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)

On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:

> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect
>
>
>

From carandraug+dev at gmail.com  Mon Mar 25 02:40:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 25 Mar 2013 06:40:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
Message-ID: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>

Hi

I need something to keep a bunch of genes belonging to the same family
organized. It is more than a plain hash since the family can be
divided into multiple ways (subfamilies, types and classes) that
overlap each other, but using a database seems overkill to me. I
couldn't find a module on CPAN that does it so I might write one if no
one suggests an alternative. Basically, with it I wanna be able to do
something like this

  my $histones = Bio::Family->new(
      -classes      => ['canonical', 'variant'],
      -types        => ['H2A', 'H2B', 'H3', 'H4'],
      -subfamilies => [ ... ],
  );

  $histones->add_member ($seqob,
      -class => 'canonical',
      -type  => 'H3',
  );

  @all_members = $histones->members;
  @canonicals  = $histones->class('canonical');

I already wrote a bit of POD for it
http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
on its design before start coding, as I fear it might be too focused
for the problem I have at hand. Could someone give me some advice
about it?

I'm also thinking that maybe I should write some sort of general perl
module, outside the Bio::* namespace.

Thanks,
Carn?


From longbow0 at gmail.com  Mon Mar 25 04:42:38 2013
From: longbow0 at gmail.com (longbow leo)
Date: Mon, 25 Mar 2013 16:42:38 +0800
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
Message-ID: <CAKPXXke637b18wS3DPPrunw1+n-q3NciSvsP=bxEeLDC5n7yVw@mail.gmail.com>

Hi Liz,

There are already "bioperl' and "bioperl-run" packages for ubuntu. It is
not necessary to install bioperl from source code.

Haizhou

On Fri, Mar 22, 2013 at 8:44 PM, liz wright <lzwright at gmail.com> wrote:

> As a follow up to my previous message, this gives a bit more information as
> to why the make tests failed:
>
>   make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test NO
>  RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
> '/usr/bin/perl Build.PL --installdirs site' returned status 512
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
> missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness
> failed
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
> not OK (XML::DOM); additionally test harness failed
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
> not OK (XML::SAX::Expat)
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
> missing
>
> (Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)
>
> On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:
>
> > Hi, I just force installed bioperl on ubuntu linux as this approach was
> > proposed as a viable alternative when certain tests fail, but I would
> like
> > to check that the fail errors listed below will not significantly impair
> > bioperl usage as I am new to all this and don't really know how to
> > interpret the error messages.  Thanks, Liz Wright
> >
> >
> >
> > * WARNING: Configuration was initially created with Module::Build
> >   version '0.38' but we are now using version '0.4003'.
> >   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> > Will try to install symlinks to /usr/local/bin
> >   CJFIELDS/BioPerl-1.6.1.tar.gz
> >   sudo ./Build install  -- OK
> > Failed during this command:
> >  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> > failure ignored because 'force' in effect
> >  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> > failure ignored because 'force' in effect
> >  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TODDR/XML-Parser-2.41.tar.gz                 : make NO
> >  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> > failure ignored because 'force' in effect
> >  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> > failure ignored because 'force' in effect
> >
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From l.m.timmermans at students.uu.nl  Mon Mar 25 07:19:36 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Mon, 25 Mar 2013 12:19:36 +0100
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>

On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect

Most of those are XML modules that need an external XML library. Force
installing won't solve that problem. Installing expat (on my ubuntu
that'd be libexpat1) should be the solution. Odds are the other
failures are dependent failures that will also disappear.

Leon

From cjfields at illinois.edu  Mon Mar 25 08:54:21 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:54:21 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>

IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:

https://metacpan.org/module/Bio::Cluster::FamilyI

My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

chris

On Mar 25, 2013, at 1:40 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I need something to keep a bunch of genes belonging to the same family
> organized. It is more than a plain hash since the family can be
> divided into multiple ways (subfamilies, types and classes) that
> overlap each other, but using a database seems overkill to me. I
> couldn't find a module on CPAN that does it so I might write one if no
> one suggests an alternative. Basically, with it I wanna be able to do
> something like this
> 
>  my $histones = Bio::Family->new(
>      -classes      => ['canonical', 'variant'],
>      -types        => ['H2A', 'H2B', 'H3', 'H4'],
>      -subfamilies => [ ... ],
>  );
> 
>  $histones->add_member ($seqob,
>      -class => 'canonical',
>      -type  => 'H3',
>  );
> 
>  @all_members = $histones->members;
>  @canonicals  = $histones->class('canonical');
> 
> I already wrote a bit of POD for it
> http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
> on its design before start coding, as I fear it might be too focused
> for the problem I have at hand. Could someone give me some advice
> about it?
> 
> I'm also thinking that maybe I should write some sort of general perl
> module, outside the Bio::* namespace.
> 
> Thanks,
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Mon Mar 25 08:56:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:56:37 +0000
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1733@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 6:19 AM, Leon Timmermans <l.m.timmermans at students.uu.nl> wrote:

> On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
>> Hi, I just force installed bioperl on ubuntu linux as this approach was
>> proposed as a viable alternative when certain tests fail, but I would like
>> to check that the fail errors listed below will not significantly impair
>> bioperl usage as I am new to all this and don't really know how to
>> interpret the error messages.  Thanks, Liz Wright
>> 
>> 
>> * WARNING: Configuration was initially created with Module::Build
>>  version '0.38' but we are now using version '0.4003'.
>>  If errors occur, you must re-run the Build.PL or Makefile.PL script.
>> Will try to install symlinks to /usr/local/bin
>>  CJFIELDS/BioPerl-1.6.1.tar.gz
>>  sudo ./Build install  -- OK
>> Failed during this command:
>> LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
>> failure ignored because 'force' in effect
>> KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
>> failure ignored because 'force' in effect
>> BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TODDR/XML-Parser-2.41.tar.gz                 : make NO
>> MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
>> failure ignored because 'force' in effect
>> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
>> failure ignored because 'force' in effect
> 
> Most of those are XML modules that need an external XML library. Force
> installing won't solve that problem. Installing expat (on my ubuntu
> that'd be libexpat1) should be the solution. Odds are the other
> failures are dependent failures that will also disappear.
> 
> Leon

Also, the version on CPAN has been updated to handle 'optional' dependencies; AcePerl for instance is pretty much in maintenance mode (maybe deprecated) and hasn't been updated in years.

chris



From fossandonc at hotmail.com  Mon Mar 25 09:29:48 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 25 Mar 2013 10:29:48 -0300
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <000201ce2959$17ed7830$47c86890$@qq.com>
References: <000201ce2959$17ed7830$47c86890$@qq.com>
Message-ID: <SNT133-ds57FF786B3A8DB70E8F9FACFD70@phx.gbl>

Hi,
I use Windows but I dropped ActivePerl some time ago in preference of
Strawberry Perl (http://strawberryperl.com/), which have better support for
installation directly from CPAN via command line.

I'm not sure if I understood correctly but you installed new Perl 5.16 over
the old 5.10?? In that case I would recommend to completely uninstall the
previous Perl version and then install the new clean Perl version.

On the other hand, the error message points to a problem connecting to the
Uwinnipeg server, so maybe they are down (in fact I just tried on my browser
and received the same error so they have problems with their servers), maybe
use Bribes instead; you don?t need to add ALL the repos anyway, just be sure
to add the http://bioperl.org/DIST, which contains the
"BioPerl-1.6.1-ppm.tar.gz", the last ActivePerl release that can be install
using the Perl Package Manager.

If you want to install the latest version, you will have to ditch the PPM,
type CPAN in command line and use that interface to get the
"BioPerl-1.6.901"
(http://www.bioperl.org/wiki/Installing_BioPerl_on_Windows#Installation_usin
g_CPAN_or_manual_installation). Beware that BioPerl will always give some
tests errors when installing that way, so you have to add "force" when
installing and everything will be fine.

Hope that helps,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de ciel
Enviado el: viernes, 22 de marzo de 2013 13:21
Para: bioperl-l
Asunto: [Bioperl-l] bioperl installation problem

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl
version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version
ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as
:"failed 503 Service temporarily Unavailable", how can I deal with this
problem? thx


Hanny

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hartzell at alerce.com  Mon Mar 25 12:23:32 2013
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 25 Mar 2013 09:23:32 -0700
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <20816.31236.737983.55186@gargle.gargle.HOWL>

Carn? Draug writes:
 > [...]
 > So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
 > Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
 > give some feedback if it's adequate for the rest of the project.
 > 
 > https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

Looks wonderful!

I use a "private" section that I think corresponds to what you call
"internal".  Is there a BioPerl tradition one way or the other?

You might make the SYNOPSIS just a tad less confusing if you point
some meaningful text into the text sections of the GenerateSection
parts, something like "text = Info about mailing lists goes here".  I
scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
lists" had an empty attribute and the other two had nonsense text.  It
looks like FEEDBACK is just an empty level 1 header, but
otherwise....

 > To minimize the number of files added to each distro, I also wrote
 > another plugin which the PluginBundle uses. I wrote it today so you're
 > likely to not have it installed yet.
 > 
 > https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

I can see that being useful. In the name, did you mean "interpolated"
(which you use further down) where you say "interpreted"?

This is a useful contribution!

g.


From cjfields at illinois.edu  Mon Mar 25 12:46:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 16:46:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <20816.31236.737983.55186@gargle.gargle.HOWL>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:

> Carn? Draug writes:
>> [...]
>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>> give some feedback if it's adequate for the rest of the project.
>> 
>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
> 
> Looks wonderful!
> 
> I use a "private" section that I think corresponds to what you call
> "internal".  Is there a BioPerl tradition one way or the other?

Not really, but there probably should be a more standard way of doing this.

> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".  I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....
> 
>> To minimize the number of files added to each distro, I also wrote
>> another plugin which the PluginBundle uses. I wrote it today so you're
>> likely to not have it installed yet.
>> 
>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
> 
> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?
> 
> This is a useful contribution!
> 
> g.

Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

chris



From carandraug+dev at gmail.com  Mon Mar 25 21:13:36 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 01:13:36 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
	<118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2F4yaXPR7ySHQ2jy0UjA5-FhfrWgNvkoF=0DKq5nzHeg@mail.gmail.com>

On 25 March 2013 16:23, George Hartzell <hartzell at alerce.com> wrote:
> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".

I don't understand your suggestion. Could you explain it again please?

> I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....

It's not empty. Feedback is level 1, which contains three level 2
headings for mailing list, support and reporting bugs. The code being
generated should match exactly the feedback section of all current
BioPerl modules. See the feedback section of the Bio::DB::BiblioI that
I recently released with this set up:

https://metacpan.org/module/Bio::DB::BiblioI#FEEDBACK

and compare with the old release of Bio::SeqIO

https://metacpan.org/module/Bio::SeqIO#FEEDBACK

> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?

Yes, that's what I meant. I have just pushed the fix, thank you.

On 25 March 2013 16:46, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:
>
>> Carn? Draug writes:
>>> [...]
>>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>>> give some feedback if it's adequate for the rest of the project.
>>>
>>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>>
>> Looks wonderful!
>>
>> I use a "private" section that I think corresponds to what you call
>> "internal".  Is there a BioPerl tradition one way or the other?
>
> Not really, but there probably should be a more standard way of doing this.

I think the large majority of the modules have a head1 APPENDIX that
says "Internal methods are usually preceded with a _" which contained
each method and attribute by the same order they appear on the code
inside a head2. I just followed the name that was already there
"internal", but it's very easy to change. At the moment, what I set up
recognizes the following:

=attr (for attributes)
=method
=func (for functions)
=internal (internal methods)

It doesn't matter the order they appear on the source, PodWeaver will
group and reorder them. It is easy to change the keywords, and add or
remove the groups. Just let me know what the bundle should be doing.
Take a look at

https://github.com/bioperl/Bio-Biblio/blob/master/lib/Bio/DB/BiblioI.pm

which generates

https://metacpan.org/module/Bio::DB::BiblioI

>>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
>>
>> [...]
>>
>> This is a useful contribution!
>>
>
> Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

I wrote another plugin the day after to generate the legal section
which is mainly aimed at BioPerl and distributions with many modules,
where the authors and copyright owners are not always the same. It
takes the copyright information from a block of comments in each
source file.

https://metacpan.org/module/Pod::Weaver::Section::Legal::Complicated

And yesterday the contributors plugin was released again after also
implementing the option to find the names of contributors in the
source of individual files

https://metacpan.org/module/Pod::Weaver::Section::Contributors

I can easily make the changes on our pluginbundles, or write new ones.
And authors from other packages are usually happy to receive patches
so it's also easy to expand on the ones that already exist. The only
problem left is defining what a BioPerl POD should look like. The pod
weaver pluginbundle as it is now, is just what looked appropriate to
me. But would be great if someone could comment on it so adjustments
to it can be made.

Carn?


From amelia.ireland at gmod.org  Mon Mar 25 19:55:23 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Mon, 25 Mar 2013 16:55:23 -0700
Subject: [Bioperl-l] [Gmod-gbrowse] Last day for early registration for
	GMOD 2013
In-Reply-To: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
References: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
Message-ID: <CAALsq01L4pRuOTsHh-wxmHuKBs24g3Q=DW2ngqaYq4386FAmHQ@mail.gmail.com>

GMOD is very pleased to announce the keynote speaker for the 2013 GMOD
community meeting is Dr. Kentaro Yoshida from the Sainsbury Lab (
http://tsl.ac.uk), talking about the Open Ash Dieback effort. This
pioneering bioinformatics project is employing two increasingly important
paradigms--open access to data and crowdsourcing--to gather genetic
analyses of ash and a fungal pathogen that is threatening tree populations
in the UK. Expect an interesting and inspiring talk!

Online registration: http://gmod2013.eventbrite.com

If you are interested in attending remotely, we will be using Go To Meeting
(http://gotomeeting.com) to allow people to attend virtually. Please email
me if you would like to join in.

Look forward to seeing you all in Cambridge!


On Wed, Mar 20, 2013 at 7:28 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi,
>
> With several guest speakers, including Jane Lomax from GO, Joseph
> Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
> Centre, this GMOD meeting is shaping up to be a very intersting
> meeting indeed.  Today (March 21) is the last day to register with the
> early registration pricing.  To register, go to
>
>   http://gmod2013.eventbrite.com/
>
> I look forward to seeing you next month (April 5-6) in Cambridge,
> England.  For more information about GMOD 2013, go to
>
>   http://www.gmod.org/wiki/April_2013_GMOD_Meeting
>
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject

From carandraug+dev at gmail.com  Mon Mar 25 23:48:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 03:48:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2VDEt5OeKsZdNegygdTv_ZPJXcVXO6JS65sFjVCVKKZg@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI

This module mentions Bio::Cluster::Family but I can't seem to find it anywhere.

> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I think I was overcomplicating, this class might do what I want
thought in a different way. My idea of a family of genes doesn't
really match it, but I should be able to work with it by mixing it
with Set::Object.

Thank you,
Carn?


From briano at bioteam.net  Tue Mar 26 13:51:07 2013
From: briano at bioteam.net (Brian Osborne)
Date: Tue, 26 Mar 2013 13:51:07 -0400
Subject: [Bioperl-l] Wiki details
Message-ID: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>

All,

I'm looking at various module pages in the Wiki and it seems that all links are broken. For example, the "<biblio>" parser tag does not work, parser functions like #setvar aren't working and because of this the link to CPAN is broken, and so on. I'm guessing that some upgrade did not restore custom code or install extensions used in the earlier version, and Special:Version confirms this, this code is not installed.

If someone would like to contact me privately and give me credentials I can take a look at the MediaWiki directory, see if I can fix this.

Brian O.



From p.j.a.cock at googlemail.com  Tue Mar 26 14:10:10 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 26 Mar 2013 18:10:10 +0000
Subject: [Bioperl-l] Wiki details
In-Reply-To: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
References: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
Message-ID: <CAKVJ-_5nOp8sXBhLRJ2Kvrzyf0rUGjTfs=PMd7pX_CqYAQ6djg@mail.gmail.com>

On Tue, Mar 26, 2013 at 5:51 PM, Brian Osborne <briano at bioteam.net> wrote:
> All,
>
> I'm looking at various module pages in the Wiki and it seems that all
> links are broken. For example, the "<biblio>" parser tag does not work,
> parser functions like #setvar aren't working and because of this the link to
> CPAN is broken, and so on. I'm guessing that some upgrade did not restore
> custom code or install extensions used in the earlier version, and
> Special:Version confirms this, this code is not installed.
>
> If someone would like to contact me privately and give me credentials I
> can take a look at the MediaWiki directory, see if I can fix this.
>
> Brian O.

Hi Brian,

I was aware of issues with the  "<biblio>" plugin, but not all of this.
Most likely this is from the server move at the end of 2012,
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Assuming someone senior from BioPerl (or Chris Dag?) will vouch
for you, we'd ask you to join the root-l mailing list where OBF server
admin stuff happens. We'll need a preferred username (e.g. briano
or bosborne) and your SSH public key (the new server does not
accept simple username/password logins).

Regards,

Peter
(With his OBF hat on)

From antony.vincent.1 at ulaval.ca  Tue Mar 26 19:24:20 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 16:24:20 -0700 (PDT)
Subject: [Bioperl-l]  One letter protein sequence to three letters
Message-ID: <35222270.post@talk.nabble.com>


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I
try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From Russell.Smithies at agresearch.co.nz  Tue Mar 26 19:44:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 12:44:35 +1300
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAA77@exchsth.agresearch.co.nz>

You're passing an ordinary String to Bio::SeqUtils->seq3 (that's what $hsp->query_string returns) but  I think it needs to be a Bio::PrimarySeqI compliant object.

try this:

$seqobj = Bio::PrimarySeq->new ( -seq => $hsp->query_string);
$polypeptide_3char = Bio::SeqUtils->seq3($seqobj);


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Wednesday, 27 March 2013 12:24 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] One letter protein sequence to three letters


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");  my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
--
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From antony.vincent.1 at ulaval.ca  Tue Mar 26 21:32:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 18:32:09 -0700 (PDT)
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <35222552.post@talk.nabble.com>


Yes! That works and I understand now, thanks for you precious help!
:handshake:

Antony03 wrote:
> 
> Hi!
> 
> I wan't to parse a blastp output for have an hsp with three letters code.
> I try with this:
> 
> my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
>   				    -format => 'fasta' );
>  my $query1 = <$query1_in>; 
>  my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
>   				      -format => 'fasta' );
>  my $query2 = <$query2_in>; 
>  
>  my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>
> "$algo");
>  my $report = $factory->bl2seq($query1, $query2);
> 
> ############################################################################################################
>  while (my $result = $report->next_result) {  # while 1
>     print "Query: ".$result->query_name."\n\n";
>     while (my $hit = $result->next_hit) {     # while 2
>  	while (my $hsp = $hit->next_hsp) {    # while 3
>  
> if ( $hsp->percent_identity >= "$identity" ) 
> 
> 	{ # start of if
> 	
> 	$qseq = $hsp->query_string;
> 	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);
> 
> 	print $polypeptide_3char;
> 
> 	
> 		
> }
>  	} # end of while 3
>     print "\n";
>     }	# end of while 2
>  }	# end of while 3
> 
> And I got this error:
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Not a Bio::PrimarySeqI object but [$self]
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
> STACK: blast_parsing.pl:36
> -----------------------------------------------------------
> I don't understand why my code generate this error!
> 
> Thanks :)
> 

-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222552.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From alexeymorozov1991 at gmail.com  Tue Mar 26 22:34:01 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Wed, 27 Mar 2013 11:34:01 +0900
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <35222552.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
	<35222552.post@talk.nabble.com>
Message-ID: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?

From Russell.Smithies at agresearch.co.nz  Tue Mar 26 22:50:24 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 15:50:24 +1300
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>

Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
Or is there a chance that $identity is going to contain a string rather than a float?

I could be completely wrong of course  ...

--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
Sent: Wednesday, 27 March 2013 3:34 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From cjfields at illinois.edu  Tue Mar 26 23:13:19 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 27 Mar 2013 03:13:19 +0000
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC4070@CHIMBX5.ad.uillinois.edu>

You are correct.   Quotes should be unnecessary in this case, percent identities are calculated I believe from the midline.

chris

On Mar 26, 2013, at 9:50 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
> Or is there a chance that $identity is going to contain a string rather than a float?
> 
> I could be completely wrong of course  ...
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
> Sent: Wednesday, 27 March 2013 3:34 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters
> 
> Well, there is one little thing I don't get. Why is
> 
> if ( $hsp->percent_identity >= "$identity" )
> 
> any better than
> 
> if ( $hsp->percent_identity >= $identity)
> 
> Ie what do quotes do?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From adsj at novozymes.com  Wed Mar 27 08:19:01 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:19:01 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
Message-ID: <87li99593e.fsf@topper.koldfront.dk>

We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
with drawing panels that have tracks with split locations - an exception
is thrown in 2.24.

Here are the outputs of the test-script I've made:

  Bio::Graphics::VERSION: 1.995
  Simple location  ... ok
  Join location  ... ok

and

  Bio::Graphics::VERSION: 2.24
  Simple location  ... ok
  Join location  ... Can't locate object method "has_tag" via package "Bio::Location::Simple" at /usr/share/perl5/Bio/Graphics/Glyph.pm line 706, <DATA> line 192.

The test script looks like this:

== =
#!/usr/bin/perl

use strict;
use warnings;

use Bio::Graphics;

use Bio::SeqFeature::Generic;
use Bio::Factory::FTLocationFactory;

print "Bio::Graphics::VERSION: $Bio::Graphics::VERSION\n";

test_panel_with_location('1..12',              'Simple location');
test_panel_with_location('join(1..10,15..20)', 'Join location');

sub test_panel_with_location {
    my ($location_string, $msg)=@_;

    print "$msg  ... ";
    my $location=Bio::Factory::FTLocationFactory->from_string($location_string);
    my $seq=Bio::SeqFeature::Generic->new;
    $seq->location($location);

    my $panel=Bio::Graphics::Panel->new(-length=>500, -width=>500);
    $panel->add_track($seq);
    eval { $panel->png };
    print $@ || "ok\n";
}
== =

Am I doing something wrong in the script, or is this a regression in
Bio::Graphics somewhere?


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com


From adsj at novozymes.com  Wed Mar 27 08:33:53 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:33:53 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
In-Reply-To: <87li99593e.fsf@topper.koldfront.dk> ("Adam =?iso-8859-1?Q?Sj?=
	=?iso-8859-1?Q?=F8gren=22's?= message of
	"Wed, 27 Mar 2013 13:19:01 +0100")
References: <87li99593e.fsf@topper.koldfront.dk>
Message-ID: <87hajx58em.fsf@topper.koldfront.dk>

adsj at novozymes.com (Adam Sj?gren) writes:

> We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
> with drawing panels that have tracks with split locations - an exception
> is thrown in 2.24.

[...]

Ahh, this has been fixed between 2.24 and 2.32 - (we upgraded to 2.24
because that is the version in the latest Ubuntu LTS).

2.32 works fine:

  Bio::Graphics::VERSION: 2.32
  Simple location  ... ok
  Join location  ... ok

Sorry for the noise.


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com


From carandraug+dev at gmail.com  Thu Mar 28 10:55:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 14:55:48 +0000
Subject: [Bioperl-l]  Google Summer of Code - BioPerl proposals
Message-ID: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>

On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
> Just a heads-up, if there are any students interested in the Google Summer of
> Code, the Open Bioinformatics Foundation is planning on participating again
> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
> looking for prospective projects.
>
> We're open for any project ideas this year, so let us know what you would like
> to do!

Hi

I had already mentioned that I would like to finish the split of the
project into smaller distributions. Is it acceptable to finish
projects from previous years? I noticed that the wiki page for BioPerl
projects is still empty for this year. Should I fill it? Would someone
be able to mentor that?

Carn?


From carandraug+dev at gmail.com  Thu Mar 28 12:23:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 16:23:18 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_32AU=Vc1yZofWyLM+CVQj0Xa6et+7rKHrXSHVU-TY2sA@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI
>
> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I'm looking at these now and thinking of making the split from live
into a separate distribution now. But I'm unsure about two of the
files

Bio/ClusterIO/dbsnp.pm
Bio/Cluster/SequenceFamily.pm

Would you agree that these would fit better into a Bio-Variations and
Bio-Seq distribution?

Carn?


From hlapp at drycafe.net  Sat Mar 30 13:24:26 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 30 Mar 2013 12:24:26 -0500
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
Message-ID: <723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>

Hi Carn?,

Not sure I've missed a response to this. If indeed there hasn't been one, let me just chime in non-authoritatively that in principle there's nothing wrong with picking up past pieces. I would argue you'd have to make a convincing argument as to why and how you'd surmount the hurdles that brought the previous project to a premature end (or why it ran out of time and you won't), and as to how it's desirability has not diminished since then even though nobody else picked it up.

If you want to apply as a student, you don't strictly have to put it up on the wiki, but it'd be prudent to discuss your ideas on this list prior to submission. Presumably you were planning that anyway, though.

-hilmar

Sent with a tap.

On Mar 28, 2013, at 9:55 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
>> Just a heads-up, if there are any students interested in the Google Summer of
>> Code, the Open Bioinformatics Foundation is planning on participating again
>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>> looking for prospective projects.
>> 
>> We're open for any project ideas this year, so let us know what you would like
>> to do!
> 
> Hi
> 
> I had already mentioned that I would like to finish the split of the
> project into smaller distributions. Is it acceptable to finish
> projects from previous years? I noticed that the wiki page for BioPerl
> projects is still empty for this year. Should I fill it? Would someone
> be able to mentor that?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From briano at bioteam.net  Sun Mar 31 10:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>

From briano at bioteam.net  Sun Mar 31 10:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>

From briano at bioteam.net  Sun Mar 31 11:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>

From briano at bioteam.net  Sun Mar 31 11:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>

From cjfields at illinois.edu  Sun Mar 31 20:34:16 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Apr 2013 00:34:16 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>

I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.  

chris

On Mar 30, 2013, at 12:24 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Hi Carn?,
> 
> Not sure I've missed a response to this. If indeed there hasn't been one, let me just chime in non-authoritatively that in principle there's nothing wrong with picking up past pieces. I would argue you'd have to make a convincing argument as to why and how you'd surmount the hurdles that brought the previous project to a premature end (or why it ran out of time and you won't), and as to how it's desirability has not diminished since then even though nobody else picked it up.
> 
> If you want to apply as a student, you don't strictly have to put it up on the wiki, but it'd be prudent to discuss your ideas on this list prior to submission. Presumably you were planning that anyway, though.
> 
> -hilmar
> 
> Sent with a tap.
> 
> On Mar 28, 2013, at 9:55 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
> 
>> On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
>>> Just a heads-up, if there are any students interested in the Google Summer of
>>> Code, the Open Bioinformatics Foundation is planning on participating again
>>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>>> looking for prospective projects.
>>> 
>>> We're open for any project ideas this year, so let us know what you would like
>>> to do!
>> 
>> Hi
>> 
>> I had already mentioned that I would like to finish the split of the
>> project into smaller distributions. Is it acceptable to finish
>> projects from previous years? I noticed that the wiki page for BioPerl
>> projects is still empty for this year. Should I fill it? Would someone
>> be able to mentor that?
>> 
>> Carn?
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Sun Mar 31 22:05:19 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 1 Apr 2013 03:05:19 +0100
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>

On 1 April 2013 01:34, Fields, Christopher J <cjfields at illinois.edu> wrote:
> I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.

Why did the project ran out of time 2 years ago? The blog posts about
it are very few and don't sound too bad. It mentions having prepared a
couple of them, but none was actually ever released. Instead, the
source was also kept in bioperl-live and seems to have already
branched. Is there any reason for this? It was my understanding that
splitting the project is still desirable, from a discussion back in
February

http://article.gmane.org/gmane.comp.lang.perl.bio.general/26395

it just happens that no one has picked it up yet.

I think splitting bioperl-live into subdistributions and make a new
1.70 release of each of them is perfectly doable over a summer. And I
say this after having split and release Bio-Biblio. This is one of my
itches with BioPerl. I have been using it for almost 3 years, but have
never seen a release. I would like to make new releases of everything,
no changes at the start, but take them to the point that "dzil
release" does everything. Make it really easy for anyone to come in
and contribute and even easier for a maintainer to make a new release
after receiving a contribution. Is this desirable for the project?

Carn?


From cjfields at illinois.edu  Sun Mar 31 23:28:55 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Apr 2013 03:28:55 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC8BD8@CHIMBX5.ad.uillinois.edu>

On Mar 31, 2013, at 9:05 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 1 April 2013 01:34, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.
> 
> Why did the project ran out of time 2 years ago? The blog posts about
> it are very few and don't sound too bad. It mentions having prepared a
> couple of them, but none was actually ever released. Instead, the
> source was also kept in bioperl-live and seems to have already
> branched. Is there any reason for this? It was my understanding that
> splitting the project is still desirable, from a discussion back in
> February
> 
> http://article.gmane.org/gmane.comp.lang.perl.bio.general/26395
> 
> it just happens that no one has picked it up yet.

The project actually made a lot of headway; the particular pieces moved out (Bio::Root, Bio::Factory, etc) worked fine, but we never followed up on exactly what to do next on master branch.  It's perfectly feasible for someone to go ahead and finish the initial part of that (in fact, I believe there were some branches that started along this path but never merged back in).

FWIW, Sheena also started the Dist::Zilla bundle you have been working on as well, with the same intent you have.  So the fundamental groundwork is there.

> I think splitting bioperl-live into subdistributions and make a new
> 1.70 release of each of them is perfectly doable over a summer. And I
> say this after having split and release Bio-Biblio. This is one of my
> itches with BioPerl. I have been using it for almost 3 years, but have
> never seen a release. I would like to make new releases of everything,
> no changes at the start, but take them to the point that "dzil
> release" does everything. Make it really easy for anyone to come in
> and contribute and even easier for a maintainer to make a new release
> after receiving a contribution. Is this desirable for the project?
> 
> Carn?


The last Bioperl release was in 2011 IIRC, so we're long overdue, but it's not quite 3 yrs :)  

Hilmar's point is pretty valid, namely that a case would have to be made as to why the initial run at it wasn't completed, or why it would work better this time.  We're not suggesting that this can't be done, but the above point would have to be answered.  Frankly, the project has been pretty reliant on me for releases, so it's perfectly valid to point out the modules haven't made it out yet b/c I haven't made a release since then.  From that point of view, this would be a continuation of that work, maybe with the intent/focus on making code releases much easier.

Regarding updating Bioperl to use Dist::Zilla amongst other modern perl tools (Moose included), yes, it is very much our wish/intent to have this, in any way possible.  But I don't think we can call it BioPerl v1.7, simply based on past release cycles; we're somewhat bound by deprecations, etc.  We really need a clean break.  

So, my general feeling is that while we are cleaving out code and releasing the independent dist and core, we should re-christen core as 1.9 (e.g. pre-v2).  We move to v2 when we feel we're at the right point.  Each of the individual distributions would have to start with their own versions, anything greater than the point where they left the core/live distribution should work.  I agree with you in that I don't think it would take a long time, but we also have bioperl-run in the mix (and in many cases it would make sense to combine wrappers with the proper parsers), so simply cleaving out from one repo may not be the best approach.

With that in mind, my point was meant to indicate we can also start afresh with a section of the code that you would like to focus on, using some of the same ideas (pulling out the relevant modules you want to work on).  This might be an attainable goal in the minds of GSoC reviewers and might suit your particular needs (for instance, if you had a research project reliant on such code).  I'm supportive either way, and I don't think you'll have a problem finding a mentor if you need one.

chris





From l.m.timmermans at students.uu.nl  Fri Mar  1 16:49:58 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Fri, 1 Mar 2013 22:49:58 +0100
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
Message-ID: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>

On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
> Greetings,
>
> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>
> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>
> Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetw!
>  ork::RandomFactory -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA::ESEfinder -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameSubs -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::interpro -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::berkeleydb -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::entrezgene -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tinyseq -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::chadoxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (opt!
>  ional_features -> Bio::SeqIO::game::gameWriter -> requires) [Validatio
> n: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::FileCache -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::bsml_sax -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Primer3 -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::HtSNP -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Compatible -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Taxonomy::entrez -> requires) [Validation: 1.2], Expected a ma!
>  p structure from string or file. (optional_features -> Bio::SeqIO::agave -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::TagHaplotype -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::SeqFeature::Store::FeatureFileLoader -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::Protein* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::blastxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::EUtilities -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Draw::Cladogram -> requires) [Validation: 1!
>  .2], Expected a map structure from string or file. (optional_features
> -> Bio::Tools::SeqPattern -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tigrxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Collection -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Draw::Pictogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::Writer::BSMLResultWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::HIVQuery -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::TreeIO::svggraph -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::eutils -> requires) [Validation: 1.2], Expected a map structure from string or file. (opti!
>  onal_features -> Bio::PhyloNetwork -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern::BackTranslate -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::GenBank -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Variation::IO::xml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::GraphViz -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Annotated -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::NCBIHelper -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::HIV -> requires) [Validation: 1.2], Expected a map structure from string or file. (!
>  optional_features -> Bio::Tools::Analysis::DNA* -> requires) [Validati
> on: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Run::RemoteBlast -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::excel -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::ClusterIO::dbsnp -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Microarray::Tools::ReseqChip -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::soap -> requires) [Validation: 1.2]
> at /usr/local/lib/perl5/5.10.1/Module/Build/Base.pm line 4559
>
> Could not create MYMETA files
> Creating new 'Build' script for 'BioPerl' version '1.006001'

What versions of Module::Build and CPAN::Meta are you using?

> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.

Yeah, 1.6.1 equals 1.006001. See also
http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
Do note that it is no longer the lastest release, latest is 1.6.901
and a new release is expected on a short notice.

Leon



From cjfields at illinois.edu  Fri Mar  1 18:11:39 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 1 Mar 2013 23:11:39 +0000
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
	<CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6E70B5F7@CHIMBX5.ad.uillinois.edu>

On Mar 1, 2013, at 3:49 PM, Leon Timmermans <l.m.timmermans at students.uu.nl>
 wrote:

> On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
>> Greetings,
>> 
>> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>> 
>> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>> ?.
> 
>> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.
> 
> Yeah, 1.6.1 equals 1.006001. See also
> http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
> Do note that it is no longer the lastest release, latest is 1.6.901
> and a new release is expected on a short notice.
> 
> Leon

Yup, hoping to work on it tonight and tomorrow.  Travis-CI indicates all normal tests are passing, I'll run through a few remaining ones.  Some we can't address directly; there are a number of warnings popping up I can't do anything about (they originate from Graph).

chris


From pcantalupo at gmail.com  Sat Mar  2 12:28:15 2013
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Sat, 2 Mar 2013 12:28:15 -0500
Subject: [Bioperl-l] Fix for Bug #3376 broke somewhere else
In-Reply-To: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
References: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
Message-ID: <CAJqbkv5-cXLh_cMa3rWoOVv7PijY2Orq=Smvqd3Xij887iVhMg@mail.gmail.com>

Hi Francisco,

Nice catch. Please submit a new bug report for this and reference bug
3376. Please provide a minimal hmmer output file, a script and the
expected output. Then, I'll look into it and fix the bug.

Thank you,

Paul

Paul Cantalupo
University of Pittsburgh


On Thu, Feb 28, 2013 at 10:36 AM, Francisco J. Ossand?n
<fossandonc at hotmail.com> wrote:
> Hi,
> I was re-checking Bug #3302 using the Bio::SearchIO modules of the
> repository and found that now it can't parse a Hmmer2 file that was
> previously fine. After tracking the problem, I discovered that a change in a
> regular expression to fix another bug broke the parse.
>
> The fix for the Bug #3376 consisted in adding an extra condition to omit
> lines where end of domain indicator is split across lines
> (https://redmine.open-bio.org/issues/3376):
> TEST: domain 1 of 1, from 8 to 97: score 184.7, E = 2.5e-56
>                    *->svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDn
>                       sv+qqqq+  +    +vtAiAiAigYRYRYRAv Wn GsLs G nDn
>         Test     8    SVYQQQQGGSA----MVTAIAIAIGYRYRYRAVVWNKGSLSTGTNDN 50
>
>                    DnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr<-
>                    DnDq +d LYtiYYsvtv +ss+p q+v+HHHaH+asstkiiiki P
>         Test    51 DNDQAAD-LYTIYYSVTVSASSWPGQSVTHHHAHPASSTKIIIKIAPS   97
>
>                    *
>
>         Test     -   -
> This case is characterized by the 2 dashes in the line...
>
> So the expression added in hmmer2.pm - ?next_result?
> (https://github.com/bioperl/bioperl-live/commit/142e5d79e3a6593db32bf0af9904
> 8f47d01bd3f2):
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\-\s+\-\s*$/ ) ### <--- This regex was
> designed for bug 3376
>                         {
>                             next;
>                         }
>
> But the expression used is too broad because it uses the "^.+" just before
> the 2 dashes, and it broke these lines parsing, where is full of dashes:
>                    KyACrqCdtiVQAPaPakpIErGiptaGLLArvlVSKyaEHlPLYRQsEI
>
>   lcl|gi|340     - -------------------------------------------------- -
>
>                    yaRqGVeiaRstLadWVgrtgarLaPLvdALaeyVLkeGklHADeTPVqV
>                          +i  s L   V++ + r
>   lcl|gi|340 60938 ------AIMISGLIHGVSARCLRF-------------------------- 60955
>
> I think a reasonable fix that still fixes the original bug and restore the
> function for this case is to add an extra \s+ in the regex just before the
> first dash, so the expression makes sure that the first dash is the one that
> comes AFTER the description (and is replacing the usual coordinate number)
> and is not the last of an alignment or a series of dashes like the one
> above:
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\s+\-\s+\-\s*$/ ) ### <--- Tweaked regex
>                         {
>                             next;
>                         }
> I tested it and it works fine, hope you find the fix acceptable.
>
> Cheers,
>
> --
> Francisco J. Ossandon
> Bioinformatician.
> Ph.D. Candidate, University Andres Bello.
> Center for Bioinformatics and Genome Biology,
> Fundacion Ciencia para la Vida.
> Santiago, Chile.
> www.cienciavida.cl/CBGB.htm
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hlapp at drycafe.net  Sun Mar  3 12:53:34 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sun, 3 Mar 2013 12:53:34 -0500
Subject: [Bioperl-l] GSoC 2013 is ON
Message-ID: <F68E8168-80A5-4681-9912-8655998A9F40@drycafe.net>

Forwarding on behalf of Pjotr Prins, who just volunteered to serve as OBF's GSoC admin for this year.

~~~

Game on! GSoC 2013 is ON. I am running with the OBF project
administration this year for the Google Summer of code (GSoC). 
First and foremost I want to thank Robert Buels and others for making
OBF/GSoC a success in the previous three years! This year, Robert, Chris
Fields and Hilmar Lapp will act as backup administrators.

The deadline for the OBF application for GSoC2013 as a mentoring
organisation is Friday March 29! See

 http://www.google-melange.com/gsoc/events/google/gsoc2013

Similar to previous years, each Bio* project needs to update and add project
ideas on the project's individual OBF wiki page and create links from the main
OBF page at

 http://www.open-bio.org/wiki/Google_Summer_of_Code

(we will update the main information on that page soon).

So, for each of the OBF projects that wants to do GSoC again this
year:

1. Update the list of project ideas on your project's GSoC page (BioPython,
  BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done
  or no longer relevant, etc. For an example see

    http://bioruby.open-bio.org/wiki/Google_Summer_of_Code

2. Update the final list of project ideas on the main OBF GSoC page
  to match.

    http://www.open-bio.org/wiki/Google_Summer_of_Code

3. Register with gsoc at lists.open-bio.org

4. Announce it on that list when you are ready :)

Anyone can submit a project idea! Former GSoC students are especially
encouraged to contribute ideas to the mailing lists.

Please have the updates done by Friday March 22nd. The number and quality of
the project ideas are part of the evaluation process for whether OBF is
accepted as a Summer of Code organisation again this year, so let's come up
with some good ones!

Pj. (Pjotr Prins)

Important dates: 

 * March 22nd: Finalise project ideas
 * March 29th: Deadline OBF mentoring organisation submission to Google

http://www.open-bio.org/wiki/Google_Summer_of_Code



From carandraug+dev at gmail.com  Sun Mar  3 20:58:41 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 01:58:41 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <512B3DCB.7050008@uni-wuerzburg.de>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
Message-ID: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>

On 25 February 2013 10:32, Andreas Leimbach
<andreas.leimbach at uni-wuerzburg.de> wrote:
> On 25.2.13 11:08, Carn? Draug wrote:
>>
>> I'm writing a perl module to write a description of the variance
>> between 2 sequences as described on
>> http://www.hgvs.org/mutnomen/recs-prot.html
>>
>> Basically, given 2 sequences, would returns something like "p.Lys2del
>> p.His25_Met26insGln" if those are the differences. It also accounts
>> for the existence of - characters on the sequences that may come from
>> their alignment.
>>
>> My question is, where on the project tree should I place the module?
>>
>> Also, is there something already written that would convert from 1 to
>> 3 letter code?
>>
> for your last question:
> You can convert aa strings from one to three letter code with
> 'Bio::SeqUtils'.

Thank you. I have never used Bio::SeqUtils. Not only does solve my
problem, but also seems to be the right place to insert my code.

If no one objects, I'll add a new method to Bio::SeqUtils named
"describe_mutation".

Carn?



From cjfields at illinois.edu  Sun Mar  3 22:45:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 03:45:45 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 7:58 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 25 February 2013 10:32, Andreas Leimbach
> <andreas.leimbach at uni-wuerzburg.de> wrote:
>> On 25.2.13 11:08, Carn? Draug wrote:
>>> 
>>> I'm writing a perl module to write a description of the variance
>>> between 2 sequences as described on
>>> http://www.hgvs.org/mutnomen/recs-prot.html
>>> 
>>> Basically, given 2 sequences, would returns something like "p.Lys2del
>>> p.His25_Met26insGln" if those are the differences. It also accounts
>>> for the existence of - characters on the sequences that may come from
>>> their alignment.
>>> 
>>> My question is, where on the project tree should I place the module?
>>> 
>>> Also, is there something already written that would convert from 1 to
>>> 3 letter code?
>>> 
>> for your last question:
>> You can convert aa strings from one to three letter code with
>> 'Bio::SeqUtils'.
> 
> Thank you. I have never used Bio::SeqUtils. Not only does solve my
> problem, but also seems to be the right place to insert my code.
> 
> If no one objects, I'll add a new method to Bio::SeqUtils named
> "describe_mutation".
> 
> Carn?

I'm fine with that; at some point it might be worth thinking about whether we need to organize the various *Utils modules a bit better.  As most of these export methods, they would be good targets for reorganization at some point (maybe into a general Bio::Utils namespace).

chris



From carandraug+dev at gmail.com  Sun Mar  3 23:15:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 04:15:51 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>

On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
> [...] at some point it might be worth thinking about whether we need to
> organize the various *Utils modules a bit better.  As most of these export
> methods, they would be good targets for reorganization at some point
> (maybe into a general Bio::Utils namespace).

Do you mean placing all of them into a separate Util distribution? I
think it makes more sense to keep them close to what they deal with.

If it's just moving them all into Bio::Utils:: may be a good idea. At
the moment there's not much of a model for their naming. I found these
ones (am I missing anything that does not have Utils on the name?)

Bio/Coordinate/Utils.pm
Bio/SeqUtils.pm
Bio/Search/SearchUtils.pm
Bio/Search/BlastUtils.pm
Bio/Search/Tiling/MapTileUtils.pm

Also, only the last one seems to export anything.

Carn?



From cjfields at illinois.edu  Sun Mar  3 23:50:15 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 04:50:15 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> [...] at some point it might be worth thinking about whether we need to
>> organize the various *Utils modules a bit better.  As most of these export
>> methods, they would be good targets for reorganization at some point
>> (maybe into a general Bio::Utils namespace).
> 
> Do you mean placing all of them into a separate Util distribution? I
> think it makes more sense to keep them close to what they deal with.

No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

> If it's just moving them all into Bio::Utils:: may be a good idea. At
> the moment there's not much of a model for their naming. I found these
> ones (am I missing anything that does not have Utils on the name?)
> 
> Bio/Coordinate/Utils.pm
> Bio/SeqUtils.pm
> Bio/Search/SearchUtils.pm
> Bio/Search/BlastUtils.pm
> Bio/Search/Tiling/MapTileUtils.pm
> 
> Also, only the last one seems to export anything.
> 
> Carn?


A few mentioned above.  I don't think they have to be object classes, their entire purpose is to add functionality, so a full-blown class is probably a bit overkill (no one is likely to override their behavior).  

I could also see subdividing these up: DNA, RNA, and protein specific methods as well (for instance the 1->3 letter amino acid conversions, which would never be used on DNA).  It just depends how fine-grained we want to get.  

chris


From cjfields at illinois.edu  Tue Mar  5 09:46:34 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 5 Mar 2013 14:46:34 +0000
Subject: [Bioperl-l] Quick update on BioPerl release
In-Reply-To: <511C14AA.9030107@gmail.com>
References: <118F034CF4C3EF48A96F86CE585B94BF6CE24CF5@CHIMBX5.ad.uillinois.edu>
	<511C14AA.9030107@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F79C09@CHIMBX5.ad.uillinois.edu>

Just a note to keep everyone updated: the upcoming BioPerl release hasn't dropped off my (our) radar, but it will slip probably to the beginning of next week, likely Sunday-Monday CST.  There are a couple of changes/fixes that I would like to see going in (namely the recent HMMER fixes on master among others), and not insignificantly I've been tied up with a few $job-related tasks that have eaten up my time.

chris

On Feb 13, 2013, at 4:33 PM, Florent Angly <florent.angly at gmail.com> wrote:

> On 14/02/13 01:18, Fields, Christopher J wrote:
>> I*highly*  recommend using X.Y versioning for simplicity (e.g. no more 3-point versions)
> Yes, I support the X.Y versioning as well.
> Florent
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From clarsen at vecna.com  Tue Mar  5 15:55:05 2013
From: clarsen at vecna.com (Chris Larsen)
Date: Tue, 5 Mar 2013 15:55:05 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
	->1.6.1) ?
Message-ID: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>

Hello BioPerl-l,

Issue with partial codon translation. 

At our bioinformatics resource center we are using BioPerl to translate partial sequences to amino acids. This is necessary in the case of certain virus GenBank files, which are typically untranslated from polyprotein into their final mature peptide format, and no amino acid sequence is given in the source file. We need to make one from our mat_peptide generator. However our developers are finding that in their migration from BioPerl 1.6.0 to 1.6.1, the final amino acid generated from a partial nucleotide sequence is now being dropped, and this is resulting in several hundred files being altered relative to legacy. Here is an example:

In the hepC virus genome : AB014488

The nucleotide sequence (only) is given:

caagctgtca tggacatggt ggcgggggcc cactggggag tcctagcggg ccttgcctac
tattccatgg tggggaactg ggctaaggtt ttgattgtga tgctactctt cgccggcgtt
gacgggcata cccgcgtgac ggggggggtg caaggccacg tcacctctac actcacgtcc
ctctttagac ctggggcgtc ccagaaaatt cagcttgtaa acaccaatgg cagttggcac
atcaacagga ctgccctgaa ctgcaatgac tccctccaaa ctgggttcct tgccgcgctg
ttctacacac acaagttcaa cgcgtccgga tgcccggagc gcatggccag ctgccgctcc
attgacaagt tcgaccaggg atggggtccc atcacttatg cccaacctga caactcggac
cagaggccgt attgctggca ctatgcacct cgacagtgtg gtatcgtacc cgcgtcgcag
gtgtgcggtc cagtgtattg cttcacccca agccctgttg tggtggggac gaccgatcgt
tccggtgccc ctacgtataa ctgggg

where this ends in the partial codon of 'gg'. (Dont bother, this is 188 and 2/3 aa). A biologist might know that this terminus is always going to be a Glycine, G, since the third position is irrelevant, and so we would like to extend the partial codon into another amino acid in the last 'E2' protein encoded by this genome fragment. It's not sequenced but we can infer. The viral proteins are so short, it really matters! We want that G (and SPTAVRL). However the newer BioPerl version is not giving us the last amino acid. The functionality appears to be turned off, or a default argument was changed?  Issue with -complete ?

Sorry, not good quite enough in (bio)perl to find the solution myself. Only know it is not working now, and am trying to prevent the DBA from stabbing me in the neck with a spork because 4% of the records are now diff in the new pipeline. (Partial seqs, exactly 2 of 3 bp,  non-stop terminus in the available CDS). They are not telling me that errors don't occur within a string, only at the terminus, in viral polyproteins, and only when is not a stop codon. Ergo, color me confused.

I believe this is being handled by:

Bio::Tools::CodonTable and $obj->translate().

where the docs state the method:

"Returns a string of one letter amino acid codes from 
           nucleotide sequence input. The imput (sic) can be of any length. 
(...)
if the codon is two nucleotides long and if by adding
               an a third character 'N', it codes for a single amino
               acid (with exceptions above), return that, otherwise
               return empty string."

But I defer to the much larger bioperl-l wisdom. Sorry for the complexity. The options for them seem to be to continue using the 1.6.0 version to generate the longer better string, and 1.6.1 for everything else; but I'd rather the DBA team just uses one version of BioPerl. They could also update their version to 1.6.9. But, migrating a whole industrial pipeline to a new version for a production system also isnt trivial, so rather than hoping blindly for the fix in v1.6.9, I am asking here if the functionality works for others, and for which versions, and if its truly a bug, or has been fixed or changed, and as of what version. It would be great if one tiny piece could be replaced and the whole problem vanishes...But we may find it is our problem too. 

Hoping we just have to turn on this changed functionality, but we also want to see the issue documented. Cannot find the solution in BIO's docs. Sorry Brian!

I just want all the extra [SPTAVRLG] we can get. Any guidance I will graciously convey back to the team and try to work it out.

Thanks,

Chris

PS: Chris F and Amir discuss : highly related issue: http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html

"why should CodonTable::translate() automatically 'complete' the translation for incomplete codons by default?  I would consider this a bug."
 
-- 

Christopher Larsen, Ph.D.
Sr. Scientist / Grants Manager
Vecna Medical
Phone: (240) 965-4525
Fax: (240) 547-6133

clarsen at vecna dot com
http://vecna.com

Better Technology, Better World (TM)

The contents of this message may be privileged and confidential. Therefore, if this message has been received in error, please delete it. Your receipt of this message is not intended to waive any applicable privilege. Please do not disseminate this message without the permission of the author.









From Amir_Karger at hms.harvard.edu  Wed Mar  6 13:18:13 2013
From: Amir_Karger at hms.harvard.edu (Karger, Amir)
Date: Wed, 6 Mar 2013 13:18:13 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>
Message-ID: <CD5CF244.51003%amir_karger@hms.harvard.edu>

On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:

>Hello BioPerl-l,
>
>A biologist might know that this terminus is always going to be a
>Glycine, G, since the third position is irrelevant, and so we would like
>to extend the partial codon into another amino acid in the last 'E2'
>protein encoded by this genome fragment. It's not sequenced but we can
>infer. The viral proteins are so short, it really matters! We want that G
>(and SPTAVRL). However the newer BioPerl version is not giving us the
>last amino acid. The functionality appears to be turned off, or a default
>argument was changed?  Issue with -complete ?
>
>
>
>PS: Chris F and Amir discuss : highly related issue:
>http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>
>"why should CodonTable::translate() automatically 'complete' the
>translation for incomplete codons by default?  I would consider this a
>bug."

I guess one man's bug is another man's feature.

Sorry to have ruined your pipeline.

-Amir




From cjfields at illinois.edu  Wed Mar  6 14:19:23 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 6 Mar 2013 19:19:23 +0000
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <CD5CF244.51003%amir_karger@hms.harvard.edu>
References: <CD5CF244.51003%amir_karger@hms.harvard.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D8FF30@CHIMBX5.ad.uillinois.edu>

On Mar 6, 2013, at 12:18 PM, "Karger, Amir" <Amir_Karger at hms.harvard.edu> wrote:

> On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:
> 
>> Hello BioPerl-l,
>> 
>> A biologist might know that this terminus is always going to be a
>> Glycine, G, since the third position is irrelevant, and so we would like
>> to extend the partial codon into another amino acid in the last 'E2'
>> protein encoded by this genome fragment. It's not sequenced but we can
>> infer. The viral proteins are so short, it really matters! We want that G
>> (and SPTAVRL). However the newer BioPerl version is not giving us the
>> last amino acid. The functionality appears to be turned off, or a default
>> argument was changed?  Issue with -complete ?
>> 
>> 
>> 
>> PS: Chris F and Amir discuss : highly related issue:
>> http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>> 
>> "why should CodonTable::translate() automatically 'complete' the
>> translation for incomplete codons by default?  I would consider this a
>> bug."
> 
> I guess one man's bug is another man's feature.
> 
> Sorry to have ruined your pipeline.
> 
> -Amir

Chris, Amir,

Just a note: BioPerl is now at 1.6.901 on CPAN (released in 2011) and will be at 1.6.902 sometime next week.  

IIRC (and from back-reading in that thread), the problem was one of consistency, namely that translate() from PrimarySeqI and CodonTable act differently, and that to intuit what is the 'correct' thing to do in this case was possibly wrong from the PrimarySeqI end.  We went the route of least magic and least surprise, namely to return just the translated sequence w/o guessing whether the sequence in question is complete.  

So in my opinion, the old behavior was a bug, and the new behavior is more consistent.  The magic way is still there, though; pass in '-complete => 1'.  I can check that, just in case, to make sure it works.

chris




From a0071251 at nus.edu.sg  Thu Mar  7 00:24:06 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 13:24:06 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
Message-ID: <BBEBCF29-53C3-4BCD-AE6C-33B42D8F5933@nus.edu.sg>



Dear BioPerl,


I have encountered failed tests while installing Bioperl-1.6.901 from CPAN.
i downloaded BioPerl-1.6.901.tar and ran 'tar xvfz BioPerl-1.6.901.tar'
It gave me a message saying 'tar: Error exit delayed from previous errors.' but i moved on to install using 'perl Build.PL'
it gave me a message saying that some files are missing. I just moved on again and eventually when i ran './Build test', it told me that 32//55 test programs failed and 1/2436 subtests failed.
you will find a detailed report of the errors in the attached file.

Please take a look and let me know where i have gone wrong.
I am suspecting that the problem started when i extracted .tar file, but i have no idea how to correct that.

Your help will be much appreciated.
Thank you for your time and help.


Sincerely,
Ah Jung


-------------- next part --------------
A non-text attachment was scrubbed...
Name: error_from_Bioperl_installation
Type: application/octet-stream
Size: 126548 bytes
Desc: error_from_Bioperl_installation
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0002.obj>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ATT00001.txt
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0002.txt>

From a0071251 at nus.edu.sg  Thu Mar  7 01:15:58 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 14:15:58 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
	(continued)
Message-ID: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>



Dear BioPerl,

I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
Hope this helps to clarify the problem further.

Thank you,
Ah Jung

-------------- next part --------------
A non-text attachment was scrubbed...
Name: error2
Type: application/octet-stream
Size: 71030 bytes
Desc: error2
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/363ab81b/attachment-0002.obj>

From scott at scottcain.net  Thu Mar  7 11:01:37 2013
From: scott at scottcain.net (Scott Cain)
Date: Thu, 7 Mar 2013 11:01:37 -0500
Subject: [Bioperl-l] Failed ./Build test while installing
	Bioperl-1.6.901 (continued)
In-Reply-To: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
References: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
Message-ID: <CA+JTaoxRxE5RtZuYwaW1OAG=G+TxkCQO3WC+OpCx7kzKKYoxCA@mail.gmail.com>

Hi Ah Jung,

The first problem you reported was because you didn't download the
whole tar file (the were a warning message that it was truncated, and
then messages that there were files missing); you just needed to
download it again.

For this message, you have this the first time cpan tries to install a module:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/Library/Perl/5.12/darwin-thread-multi-2level'
Do not have write permissions on '/Library/Perl/5.12/darwin-thread-multi-2level'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

When running cpan, you need to either run it as root (ie, "sudo cpan")
or configure it to use a local directory where you do have write
permission.  The former is probably easier, whereas the latter is
probably better.

Scott


On Thu, Mar 7, 2013 at 1:15 AM, Jeon Ah Jung <a0071251 at nus.edu.sg> wrote:
>
>
> Dear BioPerl,
>
> I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
> Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
> Hope this helps to clarify the problem further.
>
> Thank you,
> Ah Jung
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From liyc1989 at gmail.com  Thu Mar  7 17:52:18 2013
From: liyc1989 at gmail.com (yichao li)
Date: Thu, 7 Mar 2013 17:52:18 -0500
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
Message-ID: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>

Hi,

            In the SYSNOPSIS, it says:

my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
  for my $feat ($in->next_feature) {
    # do something with $feat (a Bio::SeqFeature::Annotated object)
  }

  my $out = Bio::FeatureIO(-format=>'bed');
  for my $feat ($seq->get_seqFeatures) {
    $out->write_feature($feat);
  }

Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
'file.bed');*

If not, an error will occur.


------------------------------------
Best wishes,
Yichao
Ohio University Bioinformatics Lab
Phone: (740)-591-1289


From ragowthaman at gmail.com  Fri Mar  8 14:41:38 2013
From: ragowthaman at gmail.com (gowtham)
Date: Fri, 8 Mar 2013 11:41:38 -0800
Subject: [Bioperl-l] Writing alignment objects read via Bio::DB::Sam
Message-ID: <CAMvwBZnuEYHCFqOwyGuTPs9CZRxWhsGhJfpSzQ_Mrm4CO5mMJA@mail.gmail.com>

Hi Every One,
I'm using Bio::DB::Sam->new(-bam='') method to read a bam file. And I am
able to query individual values of each alignment record. For example
'XM','AS', and 'AS' tags, or alignment start end positions etc. After
filtering these records for some values (eg, mismatches), i would like to
write them back into a "SAM" (preferable BAM) format.

I am not able to find a method that writes the record. Can someone help me
with this?

Though, I am able to open a new bam file for  writing using
Bio::DB::Bam->open(my.bam, 'w'), I dont know how to convert the SAM
alignment i read from (Bio::DB::SAM) to be written using this.

write1() does not accept alignment object read by Bio::DB::SAM, it accepts
objects read only by Bio::DB::BAM.


Thanks very much in advance,
Gowthaman
-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).


From witch.of.agnessi at gmail.com  Fri Mar  8 20:24:01 2013
From: witch.of.agnessi at gmail.com (witch.of.agnessi at gmail.com)
Date: Fri, 8 Mar 2013 17:24:01 -0800 (PST)
Subject: [Bioperl-l] How to find 'is_a'/'part_of' relationship using
	GO::Termfinder
Message-ID: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>

Hello All,

I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
 node. I wonder How I can extract the type of relationship,
like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
any better way to do this in Bioperl?

Thanks in advance


 


From antony.vincent.1 at ulaval.ca  Fri Mar  8 22:56:59 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Fri, 8 Mar 2013 19:56:59 -0800 (PST)
Subject: [Bioperl-l]  sh: 1: Syntax error: "(" unexpected
Message-ID: <35154292.post@talk.nabble.com>


Hi!

I'm trying to use emboss program (water or needle) with a bioperl script. I
got this error when I try the script: sh: 1: Syntax error: "(" unexpected

Here is the script:

#!/usr/bin/perl 

 # get an EMBOSS factory
  use Bio::Factory::EMBOSS;
  use Bio::AlignIO;
  use Bio::SeqIO;
  $f = Bio::Factory::EMBOSS -> new();
  # get an EMBOSS application  object from the factory
  $water = $f->program('water');
    $inputfilename = "krt1.fasta";
    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
                             '-format' => 'fasta');

    $inputfilename2 = "krt2.fasta";
    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
                             '-format' => 'fasta');
  # here is an example of running the application -
  # water can compare 1 sequence against 1 or more sequences
  # in a database using Smith-Waterman
  #this would be a list of seqs to compare 
                       # (could be just 1)
  my $wateroutfile = 'out.water';
  $water->run({-sequences => $seq_to_test,
               -seqall    => \@seqs_to_check,
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => $wateroutfile});
  # now you might want to get the alignment
  
  my $alnin = Bio::AlignIO->new(-format => 'emboss',
                                       -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }

Have you an idea of what can do this error?

Thanks!
-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From l.m.timmermans at students.uu.nl  Sat Mar  9 08:43:54 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Sat, 9 Mar 2013 14:43:54 +0100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>

On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected

The error suggests the script is interpreted by the shell instead of
perl. Are you sure the hashbang (#!) is the absolute first thing in
the file. No whitespace or BOM character in the front?

Leon


From carandraug+dev at gmail.com  Sat Mar  9 09:03:50 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:03:50 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>

On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>  wrote:
>
>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> [...] at some point it might be worth thinking about whether we need to
>>> organize the various *Utils modules a bit better.  As most of these export
>>> methods, they would be good targets for reorganization at some point
>>> (maybe into a general Bio::Utils namespace).
>>
>> Do you mean placing all of them into a separate Util distribution? I
>> think it makes more sense to keep them close to what they deal with.
>
> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

How would you define exportable? I usually don't like the idea of
having functions exported by default. Specially since it's so easy for
the user to load them themselves.

Carn?



From carandraug+dev at gmail.com  Sat Mar  9 09:47:08 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:47:08 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
	Bio::DB::EUtilities ?
Message-ID: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>

Hi

I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
module, part of bioperl-live, seems to be re-implementing pieces of
Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

According to Bio::DB::Biblio::eutils documentation, it should not be
used directly, instead should be used through Bio::DB::Biblio. This
means that it could be replaced by Bio::DB::EUtilities without any
disturbance (other than adding a dependency and as long as users have
been respecting the recommendations).

Carn?



From cjfields at illinois.edu  Sat Mar  9 10:07:20 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:07:20 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate
	of	Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
> module, part of bioperl-live, seems to be re-implementing pieces of
> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.

> According to Bio::DB::Biblio::eutils documentation, it should not be
> used directly, instead should be used through Bio::DB::Biblio. This
> means that it could be replaced by Bio::DB::EUtilities without any
> disturbance (other than adding a dependency and as long as users have
> been respecting the recommendations).
> 
> Carn?

Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

chris


From cjfields at illinois.edu  Sat Mar  9 10:05:33 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:05:33 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94D74@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:03 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>> wrote:
>> 
>>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> [...] at some point it might be worth thinking about whether we need to
>>>> organize the various *Utils modules a bit better.  As most of these export
>>>> methods, they would be good targets for reorganization at some point
>>>> (maybe into a general Bio::Utils namespace).
>>> 
>>> Do you mean placing all of them into a separate Util distribution? I
>>> think it makes more sense to keep them close to what they deal with.
>> 
>> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?
> 
> How would you define exportable? I usually don't like the idea of
> having functions exported by default. Specially since it's so easy for
> the user to load them themselves.
> 
> Carn?

Yes, I agree (no export by default).

chris


From carandraug+dev at gmail.com  Sat Mar  9 16:20:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 21:20:51 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>

On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>> module, part of bioperl-live, seems to be re-implementing pieces of
>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>
> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>
>> According to Bio::DB::Biblio::eutils documentation, it should not be
>> used directly, instead should be used through Bio::DB::Biblio. This
>> means that it could be replaced by Bio::DB::EUtilities without any
>> disturbance (other than adding a dependency and as long as users have
>> been respecting the recommendations).
>>
>> Carn?
>
> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

So I was looking at this but seems that would cause an issue with
circular dependency. Not at module level, but at distribution level
(Bio-Eutilities is dependent on bioperl-live and bioperl-live
dependent on Bio-EUtilities because of Bio::DB::Biblio).

This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
Could this be done and a separate distribution created for it? None of
the empty repositories seems fitting for it.

Carn?



From cjfields at illinois.edu  Sat Mar  9 17:06:41 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 22:06:41 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>


On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>>> module, part of bioperl-live, seems to be re-implementing pieces of
>>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>> 
>> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>> 
>>> According to Bio::DB::Biblio::eutils documentation, it should not be
>>> used directly, instead should be used through Bio::DB::Biblio. This
>>> means that it could be replaced by Bio::DB::EUtilities without any
>>> disturbance (other than adding a dependency and as long as users have
>>> been respecting the recommendations).
>>> 
>>> Carn?
>> 
>> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).
> 
> So I was looking at this but seems that would cause an issue with
> circular dependency. Not at module level, but at distribution level
> (Bio-Eutilities is dependent on bioperl-live and bioperl-live
> dependent on Bio-EUtilities because of Bio::DB::Biblio).
> 
> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
> Could this be done and a separate distribution created for it? None of
> the empty repositories seems fitting for it.
> 
> Carn?

Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

chris





From carandraug+dev at gmail.com  Sat Mar  9 22:06:02 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 10 Mar 2013 03:06:02 +0000
Subject: [Bioperl-l] graphics of gene distribution through a genome interval
Message-ID: <CAPOrs_1BwNeGLse000t6rmNEhneP_svosM2KYhMO+8OO6JrZ-w@mail.gmail.com>

Hi everyone

I was wondering if anyone knows any tools to produce this type of
diagram? http://picpaste.com/1fqB4e8h.png It a piece of genome with
some gene positions marked. And it has nice "zoom-in boxes" around
some more cluttered regions. I've seen these more than once but do not
know how to generate one. Could someone give me a pointer?

Thanks,
Carn?



From antony.vincent.1 at ulaval.ca  Sun Mar 10 09:17:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 06:17:09 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From Russell.Smithies at agresearch.co.nz  Sun Mar 10 16:30:36 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 11 Mar 2013 09:30:36 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>

I'll get in first and say it's best to 'use strict', and 'use warnings'  ;-)

Perhaps some of the params to water have changed? It looks like it wants filenames, not objects.
I get the same errors with your code - which I think is coming from water.

If I do this it seems to work OK:
---------------------------------------
#!/usr/bin/perl

# get an EMBOSS factory
use Bio::Factory::EMBOSS;
use Bio::AlignIO;
use Bio::SeqIO;

use strict;
use warnings;

my $f = Bio::Factory::EMBOSS -> new();
# get an EMBOSS application  object from the factory
my $water = $f->program('water');
my $wateroutfile = 'out.water';
$water->run({  -verbose => 1,
               -asequence => 'krt1.fasta',
               -bsequence => 'krt2.fasta',
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => 'out.water'});
------------------------------------------------


illustrious$ cat out.water
########################################
# Program: water
# Rundate: Mon 11 Mar 2013 09:29:36
# Commandline: water
#    -gapopen 10.0
#    -gapextend 0.5
#    -outfile out.water
#    -asequence krt1.fasta
#    -verbose 1
#    -bsequence krt2.fasta
#    -auto
# Align_format: srspair
# Report_file: out.water
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: K2C1_HUMAN
# 2: K22E_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     436/667 (65.4%)
# Similarity:   499/667 (74.8%)
# Gaps:          78/667 (11.7%)
# Score: 2023.5
#
#
#=======================================

K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR     45
                     ||.|.|.:|..|.||     |||||||.:....||:|||
K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------     39

K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG     91
                      .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA     86

K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG    130
                     ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG    136

K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR    179
                     | ||||.|||         ||||.||::||||||||||::|||||.||::
K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ    177

K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP    229
                     ||||||:|||:|||||||||||||||||||||||||||::..||..||||
K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP    227

K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN    279
                     .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA    277

K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ    329
                     |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS    327

K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE    379
                     :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE    377

K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA    429
                     ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA    427

K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI    479
                     |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI    477

K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG    521
                     ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG    525

K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS    568
                        ||||.||.|||||||...||.||.||| ||.        |||| |||
K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS    565

K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR    616
                     |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG    610

K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
                     |..|||    |||||||
K22E_HUMAN       611 GYGSGG----GGSSSVK    623


#---------------------------------------
#---------------------------------------



--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Monday, 11 March 2013 2:17 a.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From antony.vincent.1 at ulaval.ca  Sun Mar 10 17:59:51 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 14:59:51 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
	<35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
Message-ID: <35158468.post@talk.nabble.com>


That's works! Thanks a lot!

Smithies, Russell wrote:
> 
> I'll get in first and say it's best to 'use strict', and 'use warnings' 
> ;-)
> 
> Perhaps some of the params to water have changed? It looks like it wants
> filenames, not objects.
> I get the same errors with your code - which I think is coming from water.
> 
> If I do this it seems to work OK:
> ---------------------------------------
> #!/usr/bin/perl
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> 
> use strict;
> use warnings;
> 
> my $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> my $water = $f->program('water');
> my $wateroutfile = 'out.water';
> $water->run({  -verbose => 1,
>                -asequence => 'krt1.fasta',
>                -bsequence => 'krt2.fasta',
>                -gapopen   => '10.0',
>                -gapextend => '0.5',
>                -outfile   => 'out.water'});
> ------------------------------------------------
> 
> 
> illustrious$ cat out.water
> ########################################
> # Program: water
> # Rundate: Mon 11 Mar 2013 09:29:36
> # Commandline: water
> #    -gapopen 10.0
> #    -gapextend 0.5
> #    -outfile out.water
> #    -asequence krt1.fasta
> #    -verbose 1
> #    -bsequence krt2.fasta
> #    -auto
> # Align_format: srspair
> # Report_file: out.water
> ########################################
> 
> #=======================================
> #
> # Aligned_sequences: 2
> # 1: K2C1_HUMAN
> # 2: K22E_HUMAN
> # Matrix: EBLOSUM62
> # Gap_penalty: 10.0
> # Extend_penalty: 0.5
> #
> # Length: 667
> # Identity:     436/667 (65.4%)
> # Similarity:   499/667 (74.8%)
> # Gaps:          78/667 (11.7%)
> # Score: 2023.5
> #
> #
> #=======================================
> 
> K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR    
> 45
>                      ||.|.|.:|..|.||     |||||||.:....||:|||
> K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------    
> 39
> 
> K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG    
> 91
>                       .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
> K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA    
> 86
> 
> K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG   
> 130
>                      ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
> K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG   
> 136
> 
> K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR   
> 179
>                      | ||||.|||         ||||.||::||||||||||::|||||.||::
> K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ   
> 177
> 
> K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP   
> 229
>                      ||||||:|||:|||||||||||||||||||||||||||::..||..||||
> K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP   
> 227
> 
> K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN   
> 279
>                      .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
> K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA   
> 277
> 
> K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ   
> 329
>                      |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
> K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS   
> 327
> 
> K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE   
> 379
>                      :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
> K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE   
> 377
> 
> K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA   
> 429
>                      ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
> K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA   
> 427
> 
> K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI   
> 479
>                      |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
> K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI   
> 477
> 
> K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG   
> 521
>                      ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
> K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG   
> 525
> 
> K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS   
> 568
>                         ||||.||.|||||||...||.||.||| ||.        |||| |||
> K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS   
> 565
> 
> K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR   
> 616
>                      |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
> K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG   
> 610
> 
> K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
>                      |..|||    |||||||
> K22E_HUMAN       611 GYGSGG----GGSSSVK    623
> 
> 
> #---------------------------------------
> #---------------------------------------
> 
> 
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Monday, 11 March 2013 2:17 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it
> like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this
> why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl
>>> script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context:
> http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35158468.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From liamelbourne at me.com  Sat Mar  9 04:18:34 2013
From: liamelbourne at me.com (Liam Elbourne)
Date: Sat, 09 Mar 2013 20:18:34 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <7A059EB2-147A-4B26-B321-DEB40D1693EC@me.com>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
>  use Bio::Factory::EMBOSS;
>  use Bio::AlignIO;
>  use Bio::SeqIO;
>  $f = Bio::Factory::EMBOSS -> new();
>  # get an EMBOSS application  object from the factory
>  $water = $f->program('water');
>    $inputfilename = "krt1.fasta";
>    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                             '-format' => 'fasta');
> 
>    $inputfilename2 = "krt2.fasta";
>    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                             '-format' => 'fasta');
>  # here is an example of running the application -
>  # water can compare 1 sequence against 1 or more sequences
>  # in a database using Smith-Waterman
>  #this would be a list of seqs to compare 
>                       # (could be just 1)
>  my $wateroutfile = 'out.water';
>  $water->run({-sequences => $seq_to_test,
>               -seqall    => \@seqs_to_check,
>               -gapopen   => '10.0',
>               -gapextend => '0.5',
>               -outfile   => $wateroutfile});
>  # now you might want to get the alignment
> 
>  my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                       -file   => $wateroutfile);
> 
>  while ( my $aln = $alnin->next_aln ) {
>      # process the alignment -- these will be Bio::SimpleAlign objects
>  }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From antony.vincent.1 at ulaval.ca  Sat Mar  9 13:24:43 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 10:24:43 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From liam.elbourne at mq.edu.au  Sat Mar  9 06:39:44 2013
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Sat, 9 Mar 2013 22:39:44 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <0C3E5EF2-9A20-4C33-94B7-93F242E69704@mq.edu.au>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> $water = $f->program('water');
>   $inputfilename = "krt1.fasta";
>   $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                            '-format' => 'fasta');
> 
>   $inputfilename2 = "krt2.fasta";
>   @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                            '-format' => 'fasta');
> # here is an example of running the application -
> # water can compare 1 sequence against 1 or more sequences
> # in a database using Smith-Waterman
> #this would be a list of seqs to compare 
>                      # (could be just 1)
> my $wateroutfile = 'out.water';
> $water->run({-sequences => $seq_to_test,
>              -seqall    => \@seqs_to_check,
>              -gapopen   => '10.0',
>              -gapextend => '0.5',
>              -outfile   => $wateroutfile});
> # now you might want to get the alignment
> 
> my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                      -file   => $wateroutfile);
> 
> while ( my $aln = $alnin->next_aln ) {
>     # process the alignment -- these will be Bio::SimpleAlign objects
> }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 235 bytes
Desc: Message signed with OpenPGP using GPGMail
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130309/0fd852ec/attachment-0002.bin>

From antony.vincent.1 at ulaval.ca  Sat Mar  9 21:59:26 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 18:59:26 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From sidd.basu at gmail.com  Mon Mar 11 13:16:45 2013
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Mon, 11 Mar 2013 12:16:45 -0500
Subject: [Bioperl-l] Re: How to find 'is_a'/'part_of' relationship
	using	GO::Termfinder
In-Reply-To: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
References: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
Message-ID: <513e1181.aade320a.5bee.ffff87da@mx.google.com>

Hi, 

On Fri, 08 Mar 2013, witch.of.agnessi at gmail.com wrote:

> Hello All,
> 
> I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
>  node. I wonder How I can extract the type of relationship,
> like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
> any better way to do this in Bioperl?

You could use the Bioperl's ontology module in this case. For example,  here is how
you could start with ...

1. Parse gene_ontology obo file with Bio::OntologyIO
https://metacpan.org/module/Bio::OntologyIO

2. Once you get the ontology object(Bio::Ontology::Ontology), you could
use the *find_terms*
https://metacpan.org/module/Bio::Ontology::Ontology#find_terms
to get your term objects.

3. Then use the graph lookup methods
   such as *get_relationships*, get_child_terms, get_parent_terms,
   get_ancestor_terms that takes a term and relationship objects to extract
   whatever connection you are looking for. 

Hope this helps, 
-siddhartha


   


> 
> Thanks in advance
> 
> 
>  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From Russell.Smithies at agresearch.co.nz  Mon Mar 11 14:09:56 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 12 Mar 2013 07:09:56 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>

I suspect that there's several versions of water and the parameters have changed.
This is the version I'm using and I can reproduce the errors:

intrepid$ water -h
Smith-Waterman local alignment of sequences
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -gapopen            float      [10.0 for any sequence] The gap open penalty
                                  is the score taken away when a gap is
                                  created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value assumes you are using the EBLOSUM62
                                  matrix for protein sequences, and the
                                  EDNAFULL matrix for nucleotide sequences.
                                  (Number from 0.000 to 100.000)
   -gapextend          float      [0.5 for any sequence] The gap extension
                                  penalty is added to the standard gap penalty
                                  for each base or residue in the gap. This
                                  is how long gaps are penalized. Usually you
                                  will expect a few long gaps rather than many
                                  short gaps, so the gap extension penalty
                                  should be lower than the gap penalty. An
                                  exception is where one or both sequences are
                                  single reads with possible sequencing
                                  errors in which case you would expect many
                                  single base gaps. You can get this result by
                                  setting the gap open penalty to zero (or
                                  very low) and using the gap extension
                                  penalty to control gap scoring. (Number from
                                  0.000 to 10.000)
  [-outfile]           align      [*.water] Output alignment file name
                                  (default -aformat srspair)

   Additional (Optional) qualifiers:
   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.

   Advanced (Unprompted) qualifiers:
   -[no]brief          boolean    [Y] Brief identity and similarity

   General qualifiers:
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Sunday, 10 March 2013 3:59 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From cjfields at illinois.edu  Mon Mar 11 16:57:59 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 11 Mar 2013 20:57:59 +0000
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
References: <35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D96D47@CHIMBX5.ad.uillinois.edu>

I think the EMBOSS code checks the ACD file for whatever version of EMBOSS is installed, parses the parameters out of that, and uses those for input.  I don't remember if it accepts a Bio::Seq as input (I don't recall it doing so), but if it does then we should file that as a bug.

chris

On Mar 11, 2013, at 1:09 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> I suspect that there's several versions of water and the parameters have changed.
> This is the version I'm using and I can reproduce the errors:
> 
> intrepid$ water -h
> Smith-Waterman local alignment of sequences
> Version: EMBOSS:6.5.0.0
> 
>   Standard (Mandatory) qualifiers:
>  [-asequence]         sequence   Sequence filename and optional format, or
>                                  reference (input USA)
>  [-bsequence]         seqall     Sequence(s) filename and optional format, or
>                                  reference (input USA)
>   -gapopen            float      [10.0 for any sequence] The gap open penalty
>                                  is the score taken away when a gap is
>                                  created. The best value depends on the
>                                  choice of comparison matrix. The default
>                                  value assumes you are using the EBLOSUM62
>                                  matrix for protein sequences, and the
>                                  EDNAFULL matrix for nucleotide sequences.
>                                  (Number from 0.000 to 100.000)
>   -gapextend          float      [0.5 for any sequence] The gap extension
>                                  penalty is added to the standard gap penalty
>                                  for each base or residue in the gap. This
>                                  is how long gaps are penalized. Usually you
>                                  will expect a few long gaps rather than many
>                                  short gaps, so the gap extension penalty
>                                  should be lower than the gap penalty. An
>                                  exception is where one or both sequences are
>                                  single reads with possible sequencing
>                                  errors in which case you would expect many
>                                  single base gaps. You can get this result by
>                                  setting the gap open penalty to zero (or
>                                  very low) and using the gap extension
>                                  penalty to control gap scoring. (Number from
>                                  0.000 to 10.000)
>  [-outfile]           align      [*.water] Output alignment file name
>                                  (default -aformat srspair)
> 
>   Additional (Optional) qualifiers:
>   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
>                                  This is the scoring matrix file used when
>                                  comparing sequences. By default it is the
>                                  file 'EBLOSUM62' (for proteins) or the file
>                                  'EDNAFULL' (for nucleic sequences). These
>                                  files are found in the 'data' directory of
>                                  the EMBOSS installation.
> 
>   Advanced (Unprompted) qualifiers:
>   -[no]brief          boolean    [Y] Brief identity and similarity
> 
>   General qualifiers:
>   -help               boolean    Report command line options and exit. More
>                                  information on associated and general
>                                  qualifiers can be found with -help -verbose
> 
> 
> --Russell
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Sunday, 10 March 2013 3:59 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From bosborne11 at verizon.net  Tue Mar 12 11:04:36 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 12 Mar 2013 11:04:36 -0400
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
In-Reply-To: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
References: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
Message-ID: <C262A6D6-3967-4290-90FF-738A1A8CCC3F@verizon.net>

Yichao,

Fixed. Thank you for pointing that out.

Brian O.


On Mar 7, 2013, at 5:52 PM, yichao li <liyc1989 at gmail.com> wrote:

> Hi,
> 
>            In the SYSNOPSIS, it says:
> 
> my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
>  for my $feat ($in->next_feature) {
>    # do something with $feat (a Bio::SeqFeature::Annotated object)
>  }
> 
>  my $out = Bio::FeatureIO(-format=>'bed');
>  for my $feat ($seq->get_seqFeatures) {
>    $out->write_feature($feat);
>  }
> 
> Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
> 'file.bed');*
> 
> If not, an error will occur.
> 
> 
> ------------------------------------
> Best wishes,
> Yichao
> Ohio University Bioinformatics Lab
> Phone: (740)-591-1289
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Tue Mar 12 18:43:05 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 12 Mar 2013 22:43:05 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>

On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>> Could this be done and a separate distribution created for it? None of
>> the empty repositories seems fitting for it.
>>
>
> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

Could you (or some other admin) prepare a separate Bio-biblio
repository? I'm splitting them now and need a repo to push into.

Thanks,
Carn?



From cjfields at illinois.edu  Tue Mar 12 19:42:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 12 Mar 2013 23:42:11 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>

Done:

https://github.com/bioperl/Bio-Biblio

chris

On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>> Could this be done and a separate distribution created for it? None of
>>> the empty repositories seems fitting for it.
>>> 
>> 
>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
> 
> Could you (or some other admin) prepare a separate Bio-biblio
> repository? I'm splitting them now and need a repo to push into.
> 
> Thanks,
> Carn?




From therealsisterdot at gmail.com  Mon Mar 11 06:31:42 2013
From: therealsisterdot at gmail.com (sisterdot)
Date: Mon, 11 Mar 2013 03:31:42 -0700 (PDT)
Subject: [Bioperl-l] parsing psiblast + ?
Message-ID: <97a3d346-c5dd-41f4-b71d-042cc92f7ee9@googlegroups.com>

hey hey, 

i am using perl v5.10.0 and Bio::SearchIO 1.006901

i would like to use psiblast 2.2.27 + (instead of blastpgp), but parsing 
via  
new Bio::SearchIO(-format => "blast",-file => "$file")
doesn't seem to work well- individual iterations are interpreted as 
separate results.

Bio::SearchIO doesn't seem to really understand "psiblast +" default 
pairwise output, or am i mistaken?
if i am not mistaken, are there alternatives in Bioperl for parsing 
"psiblast +" with the default "-outfmt 0"?

thanks a lot
sis


From scott at scottcain.net  Wed Mar 13 22:51:55 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 13 Mar 2013 22:51:55 -0400
Subject: [Bioperl-l] Early registration for GMOD meeting closes in one week
Message-ID: <CA+JTaozZFOWKcsZ0bDqUS1mD_E2kWLUGi_1bA+bGj6GKb9eJdg@mail.gmail.com>

Hello,

The GMOD meeting is in Cambridge, England on April 5-6 (right before
the Biocurator meeting) and early registration closes March 21 (in one
week).  It is shaping up to be a good meeting with several interesting
talks scheduled.  Please try to make it!  For more information on the
meeting, see the meeting page:

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

and to save some money on your registration, go to

  http://gmod2013.eventbrite.com/

before March 21 to register.

If you'd like to give a talk at the meeting please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From carandraug+dev at gmail.com  Thu Mar 14 19:55:27 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 14 Mar 2013 23:55:27 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>

On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>> Could this be done and a separate distribution created for it? None of
>>>> the empty repositories seems fitting for it.
>>>>
>>>
>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>
>> Could you (or some other admin) prepare a separate Bio-biblio
>> repository? I'm splitting them now and need a repo to push into.
>>
>
> Done:
>
> https://github.com/bioperl/Bio-Biblio

Thanks, I'm trying to prepare a release of the Bio-biblio distribution
soon. I'd like to do a 1.7 release first. One with minimal changes
compared to the current bioperl-live. Could someone give me
co-maintenance of the Bio::Biblio namespace? Or should I just prepare
everything for the release and wait for someone else to just accept
it? Also, the Bio-biblio distribution also has modules on the
Bio::DB::biblio namespace.

Carn?



From carandraug+dev at gmail.com  Thu Mar 14 21:21:16 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 01:21:16 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
Message-ID: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>

Hi

I'm using dist::zilla and found the BioPerl plugin. I noticed that the
bug tracker information is set to

  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
  bugtracker.mailto = bug-${dist}@rt.cpan.org

shouldn't they set for https://redmine.open-bio.org/projects/bioperl?

Carn?



From cjfields at illinois.edu  Thu Mar 14 21:59:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 01:59:53 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1CF@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 6:55 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>>> Could this be done and a separate distribution created for it? None of
>>>>> the empty repositories seems fitting for it.
>>>>> 
>>>> 
>>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>> 
>>> Could you (or some other admin) prepare a separate Bio-biblio
>>> repository? I'm splitting them now and need a repo to push into.
>>> 
>> 
>> Done:
>> 
>> https://github.com/bioperl/Bio-Biblio
> 
> Thanks, I'm trying to prepare a release of the Bio-biblio distribution
> soon. I'd like to do a 1.7 release first. One with minimal changes
> compared to the current bioperl-live. Could someone give me
> co-maintenance of the Bio::Biblio namespace? Or should I just prepare
> everything for the release and wait for someone else to just accept
> it? Also, the Bio-biblio distribution also has modules on the
> Bio::DB::biblio namespace.
> 
> Carn?

That's fine; you can actually do a point release (say, 1.7) and list the proper Bio::* dependencies you need.  I wouldn't list Bio::Root::Root specifically.  

Does anyone here have a problem with Carn? taking co-maintenance of these modules on CPAN?  Please speak up over the next few days, otherwise I'll go ahead and grant it.  Would be nice to have someone looking after these.

chris


From cjfields at illinois.edu  Thu Mar 14 22:00:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:00:43 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>

Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?

chris

On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
> bug tracker information is set to
> 
>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>  bugtracker.mailto = bug-${dist}@rt.cpan.org
> 
> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Thu Mar 14 22:04:23 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 02:04:23 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>

On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>> bug tracker information is set to
>>
>>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>  bugtracker.mailto = bug-${dist}@rt.cpan.org
>>
>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>
>> Carn?
>>
>
> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>
> chris

Yes it is. But only the version 0.01.



From cjfields at illinois.edu  Thu Mar 14 22:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:41:28 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>> bug tracker information is set to
>>> 
>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>> 
>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>> 
>>> Carn?
>>> 
>> 
>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>> 
>> chris
> 
> Yes it is. But only the version 0.01.

Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

chris


From carandraug+dev at gmail.com  Thu Mar 14 23:15:11 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 03:15:11 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>

On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>> bug tracker information is set to
>>>>
>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>
>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>
>>>> Carn?
>>>>
>>>
>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>
>>> chris
>>
>> Yes it is. But only the version 0.01.
>
> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

I think I got it working with the BioPerl bundle. It passes all tests.
Now I was trying to set Pod::Weaver to write the feedback section
automatically but might be better to set it up as pasrt of the BioPerl
bundle.

Carn?



From fossandonc at hotmail.com  Fri Mar 15 10:26:44 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 11:26:44 -0300
Subject: [Bioperl-l] Bug #2936
Message-ID: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>

Hello,

Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven?t
received any feedback yet.

https://redmine.open-bio.org/issues/2936

 

Probably everybody is busy, so I would like to ask only if the proposed fix
is acceptable. If the fix were fine, I could prepare changes in my forked
repo, add tests (in ?t/Seq/PrimarySeq.t????) and make a pull request. What
do you think?

 

Cheers,

 

--

Francisco J. Ossandon

Bioinformatician.

Ph.D. Candidate, University Andres Bello.

Center for Bioinformatics and Genome Biology,

Fundacion Ciencia para la Vida.

Santiago, Chile.

 <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm

 




From cjfields at illinois.edu  Fri Mar 15 10:46:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 14:46:11 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9FAFE@CHIMBX5.ad.uillinois.edu>

Sure, a pull request would be good.  I suggest making sure you are in sync with the 'master' branch first, but I don't think you'll run into conflicts with that.  

My guess is we'll need to pull this into a branch and test rigorously first if it is to go into a bioperl 1.6.  One of the (many?) problems with Bio::Location is that it assumes all features are on linear chromosomes, so there is quite a bit of logic/magic built-in with that assumption that tends to be wrong (e.g. sort order of sublocations and so on, which breaks split locations).  

Frankly, I think we could really simplify this logic so that it is less magic, less fuzzy, and it would bite us in the ass a lot less, but of course this breaks backcompat.  So, my feeling is such fixes would be handled better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com> wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven't
> received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the proposed fix
> is acceptable. If the fix were fine, I could prepare changes in my forked
> repo, add tests (in "t/Seq/PrimarySeq.t"???) and make a pull request. What
> do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From mastarr9 at gmail.com  Fri Mar 15 00:54:49 2013
From: mastarr9 at gmail.com (Matt)
Date: Thu, 14 Mar 2013 23:54:49 -0500
Subject: [Bioperl-l] using a bioperl module after installing.
Message-ID: <5142A999.7090308@gmail.com>

I used "fink" to install bioperl. I see that the installation had no 
problems and that the Bio/SeqIO module exists in hard 
drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually 
make any use of bioperl in a script.

On the bioperl wiki I see that this common error message comes from the 
module sometimes not being installed but, in my case, I think that it is 
installed but "lost".  How can I reinstall or move or change the path to 
make bioperl actually work?
Thanks!

Information:

  * perl v5.10.0
  * Bioperl-pm5.10.0
  * OSX 10.6.8
  * Goal: To simply use a bioperl module
  * The code that gives the error (Using komodo edit):
      o #!/usr/bin/perl -w
        use strict;
        require Bio::SeqiO;
  * The error message:
      o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
        /Library/Perl/Updates/5.10.0
        /System/Library/Perl/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/5.10.0
        /Library/Perl/5.10.0/darwin-thread-multi-2level
        /Library/Perl/5.10.0
        /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
        /Network/Library/Perl/5.10.0 /Network/Library/Perl
        /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
        test.pl line 3.



From mhague at mail.sfsu.edu  Fri Mar 15 15:21:45 2013
From: mhague at mail.sfsu.edu (Michael Hague)
Date: Fri, 15 Mar 2013 12:21:45 -0700
Subject: [Bioperl-l] PopGen Question
Message-ID: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>

Hello,
I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:


use Bio::AlignIO;
use Bio::PopGen::Utilities;
use Bio::PopGen::Statistics;
use Bio::PopGen::Population;

my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
                           				 -format => 'fasta');
my $aln1 = $io1->next_aln;


my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
													-include_monomorphic => 1);

my $stats1 = Bio::PopGen::Statistics->new();
my $D1 = $stats1->tajima_D($pop1);
my $theta1  = $stats1->theta($pop1);
my $segsites1 = $stats1->segregating_sites_count($pop1);

print "\nPopulation #1:\n";
print "Number of segregating sites = $segsites1\n";
print "Tajima\'s D = $D1\n";
print "Watterson\'s theta = $theta1\n\n";

However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?

Thanks so much for the help,
Mike



From cjfields at illinois.edu  Fri Mar 15 16:04:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 20:04:37 +0000
Subject: [Bioperl-l] using a bioperl module after installing.
In-Reply-To: <5142A999.7090308@gmail.com>
References: <5142A999.7090308@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA020F@CHIMBX5.ad.uillinois.edu>

Even if you use fink, you may still need to set the PERL5LIB path to point to that location.  Have you done that?

chris
 
On Mar 14, 2013, at 11:54 PM, Matt <mastarr9 at gmail.com> wrote:

> I used "fink" to install bioperl. I see that the installation had no problems and that the Bio/SeqIO module exists in hard drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually make any use of bioperl in a script.
> 
> On the bioperl wiki I see that this common error message comes from the module sometimes not being installed but, in my case, I think that it is installed but "lost".  How can I reinstall or move or change the path to make bioperl actually work?
> Thanks!
> 
> Information:
> 
> * perl v5.10.0
> * Bioperl-pm5.10.0
> * OSX 10.6.8
> * Goal: To simply use a bioperl module
> * The code that gives the error (Using komodo edit):
>     o #!/usr/bin/perl -w
>       use strict;
>       require Bio::SeqiO;
> * The error message:
>     o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
>       /Library/Perl/Updates/5.10.0
>       /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/5.10.0
>       /Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Library/Perl/5.10.0
>       /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Network/Library/Perl/5.10.0 /Network/Library/Perl
>       /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
>       test.pl line 3.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From fossandonc at hotmail.com  Fri Mar 15 17:36:53 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 18:36:53 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <001d01ce2191$60406310$20c12930$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
Message-ID: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>

Ok,  I did the changes and added a pull request in the repository. All the
tests in "t/Seq/PrimarySeq.t" keeps passing (except the TODOs), including
the ones I added. Everything seems fine on my end.

About the Location/Split module, the lines that I don?t agree at all are the
ones that reverse the segment order in to_FTstring:
	# If the split type is join, the order is important;
	# otherwise must be 5'->3' regardless
	my @locs = ($stype eq 'join' && (!$guide && $strand == -1)) ?
	           reverse $self->sub_Location() : $self->sub_Location() ;

It don?t make sense to me to do that, because doing that you get coordinates
that will NOT give you the expected nucleotide sequence. Another thing that
is weird to me is that the sublocations are free to have different strands
values (like the first being positive strand and the second being negative
strand), since I can't think of one example where that can happen in real
genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
have sublocations in opposite strands at the same time and then extract the
sequence, so I wonder if I'm wrong and there are real cases like that...

As you say, those things would have to wait until later, but at least this
particular bug should be closed. =)

Regards,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: viernes, 15 de marzo de 2013 11:46
Para: Francisco J. Ossand?n
CC: bioperl mailing list
Asunto: Re: [Bioperl-l] Bug #2936

Sure, a pull request would be good.  I suggest making sure you are in sync
with the 'master' branch first, but I don't think you'll run into conflicts
with that.  

My guess is we'll need to pull this into a branch and test rigorously first
if it is to go into a bioperl 1.6.  One of the (many?) problems with
Bio::Location is that it assumes all features are on linear chromosomes, so
there is quite a bit of logic/magic built-in with that assumption that tends
to be wrong (e.g. sort order of sublocations and so on, which breaks split
locations).  

Frankly, I think we could really simplify this logic so that it is less
magic, less fuzzy, and it would bite us in the ass a lot less, but of course
this breaks backcompat.  So, my feeling is such fixes would be handled
better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com>
wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but 
> haven't received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the 
> proposed fix is acceptable. If the fix were fine, I could prepare 
> changes in my forked repo, add tests (in "t/Seq/PrimarySeq.t"???) and 
> make a pull request. What do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From p.j.a.cock at googlemail.com  Sat Mar 16 08:46:22 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sat, 16 Mar 2013 12:46:22 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
Message-ID: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>

On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>
> ... Another thing that
> is weird to me is that the sublocations are free to have different strands
> values (like the first being positive strand and the second being negative
> strand), since I can't think of one example where that can happen in real
> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
> have sublocations in opposite strands at the same time and then extract the
> sequence, so I wonder if I'm wrong and there are real cases like that...
>

This is a real biological phenomena - trans-splicing, often in tRNA genes,
for example:
http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced

As a result the BioPerl / BioSQL / Biopython etc location models do have
to cope with this corner case.  Worse, there are examples where pieces
from different chromosomes are spliced together - which is even harder
to deal with - like my favourite pathological example, nad1 in NC_016406
(and NC_016402), which has the following GenBank location string:

join(complement(149815..150200),
complement(295492..295573),complement(293787..293978),
NC_016402.1:6618..6676,181647..181905)

See also:
http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html

Peter



From cjfields at illinois.edu  Sat Mar 16 10:02:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 16 Mar 2013 14:02:12 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA0D59@CHIMBX5.ad.uillinois.edu>

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different strands
>> values (like the first being positive strand and the second being negative
>> strand), since I can't think of one example where that can happen in real
>> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
>> have sublocations in opposite strands at the same time and then extract the
>> sequence, so I wonder if I'm wrong and there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA genes,
> for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do have
> to cope with this corner case.  Worse, there are examples where pieces
> from different chromosomes are spliced together - which is even harder
> to deal with - like my favourite pathological example, nad1 in NC_016406
> (and NC_016402), which has the following GenBank location string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used for Bio::Location deals with cases like this, but there is an assumption made to deal with some cases like this that is wrong for others (say, circular chromosomes where a feature wraps the origin, where sorting messes things up).  It really needs a top to bottom overhaul to be explicit about the join, but such an overhaul will break some expected behavior, hence my suggestion of putting this in a bioperl v2.

chris


From carandraug+dev at gmail.com  Sat Mar 16 18:27:31 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 16 Mar 2013 22:27:31 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
Message-ID: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>

On 15 March 2013 03:15, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>>> bug tracker information is set to
>>>>>
>>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>>
>>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>>
>>>>> Carn?
>>>>>
>>>>
>>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>>
>>>> chris
>>>
>>> Yes it is. But only the version 0.01.
>>
>> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)
>
> I think I got it working with the BioPerl bundle. It passes all tests.
> Now I was trying to set Pod::Weaver to write the feedback section
> automatically but might be better to set it up as pasrt of the BioPerl
> bundle.

I made a bunch of changes to the BioPerl bundle. I didn't touched the
podweaver part, I just wanted to get a feel of it first, as this was
new stuff to me. I replaced some of the code on the bundle with
plugins that have since been written, and renamed the options so that
they match the option names of the plugins being used.

I do believe that these options are an improvement but since it's a
lot of changes and behaves differently from the previous version, I
created a fork and a branch on my own repo. If no one opposes I will
push them to the main repo.

https://github.com/carandraug/dist-zilla-pluginbundle-bioperl/blob/purging/lib/Dist/Zilla/PluginBundle/BioPerl.pm

Carn?



From fossandonc at hotmail.com  Sun Mar 17 23:09:17 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 18 Mar 2013 00:09:17 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>	<001d01ce2191$60406310$20c12930$@illinois.edu>	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
	<000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
Message-ID: <SNT133-ds9166254353FA597757A40CFE80@phx.gbl>

Wow, trans-splicing is a phenomena I was not aware about, thanks for telling
me. Then, the Guide Strand of the Split-location object must always check if
all the sublocations are present in the same strand; so if all sublocations
are positive the Guide have to be positive, if all are negative the Guide
have to be negative as well, and if there is a mix of strands in
sublocations the Guide have to be undef... The changes I made in flip_strand
didn?t check for the strand consistency in the sublocations when setting the
Guide Strand, so I have to add that.

Ok, how about this, in the following lines I will analyze all possibilities
for location coordinates, step by step, from simpler to complex. Please
follow my reasoning in every step and tell me if there is something you
don?t agree, so I can work on the code and use these cases as tests, and
then make another pull request. Let?s see when there is a reversal of the
sublocations order needed and when is not. For this time, I will only check
cases where the DNA comes from the same chromosome/plasmid/contig


One thing to keep in mind is that the flipped coordinates should reconstruct
the reverse-complement (revcom) of the original sequence.

Example sequence used below (fictional 20bp circular plasmid):
AAAAACCCCCGGGGGTTTTT


### Reasoning: For the following cases, where ALL segments are in the same
strand, NO ORDER REVERSAL is needed because for the complement-strand
sequences the code can join all the positive sequences first and then
complement it complete at the final step. Also, since all segments are in
the same strand, Guide Strand have to be set with the same value than the
sublocations.

# Single location
Coordinates: 1..5 => AAAAA
Revcom: complement(1..5) => TTTTT

# Basic split, both locations in same strand
Coords: join(6..10,16..20) => CCCCCTTTTT
Revcom: complement(join(6..10,16..20)) => AAAAAGGGGG

# Cut by origin-split, same strand, single sequence that pass through origin
Coords: join(16..20,1..2) => TTTTTAA
Revcom: complement(join(16..20,1..2)) => TTAAAAA

# Cut by origin-combo split, same strand, 2 sequences with 1st passing
through origin
Coords: join(19..20,1..2,11..13) => TTAAGGG
Revcom: complement(join(19..20,1..2,11..13)) => CCCTTAA 

# Cut by origin-combo split, same strand, 2 sequences with 2nd passing
through origin
Coords: join(6..10,19..20,1..4) => CCCCCTTAAAA
Revcom: complement(join(6..10,19..20,1..4)) => TTTTAAGGGGG


### Reasoning: For the following cases, where segments are in MIXED strands,
ORDER REVERSAL is needed because the code have to complement some segments
and others not, so it have to complement those segments first and then join
them at the last step. Also, since there is no strand consistency in all
segments, Guide Strand have to be set with undef value.

# Trans-splicing, 2 sequences in different strands, 2nd in complement
Coords: join(6..10,complement(16..20)) => CCCCCAAAAA
Revcom: join(16..20,complement(6..10)) => TTTTTGGGGG

# Trans-splicing, 2 sequences in different strands, 1st in complement
Coords: join(complement(16..20),6..10) => AAAAACCCCC
Revcom: join(complement(6..10),16..20) => GGGGGTTTTT

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 2nd in complement
Coords: join(19..20,1..3,complement(11..13)) => TTAAACCC
Revcom: join(11..13,complement(1..3),complement(19..20)) => GGGTTTAA

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 1st in complement
Coords: join(complement(1..3),complement(19..20), 11..13) => TTTAAGGG
Revcom: join(complement(11..13), 19..20,1..3) => CCCTTAAA

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 2nd in complement
Coords: join(6..10,complement(1..2),complement(18..20),) => CCCCCTTAAA
Revcom: join(18..20,1..2, complement(6..10)) => TTTAAGGGGG

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 1st in complement
Coords: join(complement(6..10),18..20,1..2) => GGGGGTTTAA
Revcom: join(complement(1..2),complement(18..20), 6..10) => TTAAACCCCC

####

As summary, Guide Strand must ensure that all the sublocations have the same
strand value set before using that value, and be undef if there is no
consistency (like in trans-splicing); so any new "add_sub_Location" should
check the other sublocations strands and set Guide Strand according to the
consistency. Establishing Guide Strand value from the beginning and updating
it accordingly with any change in the Split location object, should
correctly signal when to reverse the sublocations order and when not.

Thoughts??

Francisco J.  Ossandon


-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: s?bado, 16 de marzo de 2013 11:02
Para: Peter Cock
CC: bioperl mailing list; Francisco J. Ossand?n
Asunto: Re: [Bioperl-l] Bug #2936

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different 
>> strands values (like the first being positive strand and the second 
>> being negative strand), since I can't think of one example where that 
>> can happen in real genomes. In fact one of the tests in PrimarySeq.t 
>> is designed exactly to have sublocations in opposite strands at the 
>> same time and then extract the sequence, so I wonder if I'm wrong and
there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA 
> genes, for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transplice
> d
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do 
> have to cope with this corner case.  Worse, there are examples where 
> pieces from different chromosomes are spliced together - which is even 
> harder to deal with - like my favourite pathological example, nad1 in 
> NC_016406 (and NC_016402), which has the following GenBank location
string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-gen
> bank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used
for Bio::Location deals with cases like this, but there is an assumption
made to deal with some cases like this that is wrong for others (say,
circular chromosomes where a feature wraps the origin, where sorting messes
things up).  It really needs a top to bottom overhaul to be explicit about
the join, but such an overhaul will break some expected behavior, hence my
suggestion of putting this in a bioperl v2.

chris
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From antony.vincent.1 at ulaval.ca  Mon Mar 18 07:43:30 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 04:43:30 -0700 (PDT)
Subject: [Bioperl-l]  Generate a hsp from emboss format?
Message-ID: <35187436.post@talk.nabble.com>


Hi,
I have a script who uses emboss (water) for a dynamic programming alignment.
Is this possible to generate (convert) my result in emboss format in a hsp
(blast) like.

I need (I think) an hsp format because it's much easier for parse only one
of the two strand in the alignment (and this is what I need).

Thanks!
-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35187436.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From p.j.a.cock at googlemail.com  Mon Mar 18 08:00:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 18 Mar 2013 12:00:21 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <35187436.post@talk.nabble.com>
References: <35187436.post@talk.nabble.com>
Message-ID: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>

On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>
> Hi,
> I have a script who uses emboss (water) for a dynamic programming alignment.
> Is this possible to generate (convert) my result in emboss format in a hsp
> (blast) like.
>
> I need (I think) an hsp format because it's much easier for parse only one
> of the two strand in the alignment (and this is what I need).
>
> Thanks!

EMBOSS water (and related tools like needle) support a range of output
formats - have you looked at those yet?

Peter


From cjfields at illinois.edu  Mon Mar 18 13:19:02 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 17:19:02 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>

On Mar 18, 2013, at 7:00 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>> 
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>> 
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>> 
>> Thanks!
> 
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?
> 
> Peter


Antony,

Bio::AlignIO::emboss is supposed to support water/needle output; have you tried that?  Also, I'm not sure what advantage having this in a BLAST-like output would have over other human-readable formats; any reasons you would need this specific output?

chris




From cjfields at illinois.edu  Mon Mar 18 17:26:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 21:26:22 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA3EA4@CHIMBX5.ad.uillinois.edu>

Just a heads-up, if there are any students interested in the Google Summer of Code, the Open Bioinformatics Foundation is planning on participating again this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are looking for prospective projects.  

We're open for any project ideas this year, so let us know what you would like to do!

chris


From antony.vincent.1 at ulaval.ca  Mon Mar 18 17:35:13 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 14:35:13 -0700 (PDT)
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
Message-ID: <35190011.post@talk.nabble.com>


Hi!
For example, with this code I can easily modify only one string:

 #! /usr/bin/perl -w
 
# use strict;
 use Bio::SeqIO;
 use Bio::Tools::Run::StandAloneBlast;
 use Bio::Seq;
 use warnings;
 
###########################################################################################################
# Usage information
die "Usage: $0 <sequence 1> <sequence 2> <BLAST algorithme> <minimum % of
identity>\n", if (@ARGV != 4);
 my ($infile1,$infile2,$algo,$identity) = @ARGV;
##########################################################################################################


 my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if


	print $hsp->algorithm, ": Identity ", 100*$hsp->frac_identical, "\%, Rank
", $hsp->rank, " (evalue:", $hsp->evalue, ")\n";
	print "\t", $hsp->query_string;
	print "\n";
	print "\t", $hsp->homology_string;
	print "\n";
	print "\t", $hsp->hit_string;
	print "\n\n";
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

This is why I want to have this format. Is this possible?
Thanks!


-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35190011.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From p.rice at imperial.ac.uk  Tue Mar 19 06:51:52 2013
From: p.rice at imperial.ac.uk (Peter Rice)
Date: Tue, 19 Mar 2013 10:51:52 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <51484348.5070603@imperial.ac.uk>

On 18/03/2013 12:00, Peter Cock wrote:
> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>>
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>>
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>>
>> Thanks!
>
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?

The full list for the latest EMBOSS release alignment formats is below. 
They are selected by the -aformat qualifier for any application with an 
"align" output.

It would also be relatively simple to add new formats for the next 
release if they would be useful.

Multiple sequence formats:

"fasta",     "Fasta format sequence",
"msf",       "MSF format sequence",
"clustal",   "clustalw format sequence",
"mega",       "Mega format sequence",
"meganon",       "Mega non-interleaved format sequence",
"nexus",   "nexus/paup format sequence",
"nexusnon",   "nexus/paup non-interleaved format sequence",
"phylip",   "phylip format sequence",
"phylipnon", "phylip non-interleaved format sequence",
"selex",       "SELEX format sequence",
"treecon",       "Treecon format sequence",

Multiple alignment formats:

"markx0",    "Pearson MARKX0 format",
"markx1",    "Pearson MARKX1 format",
"markx2",    "Pearson MARKX2 format",
"markx3",    "Pearson MARKX3 format",
"markx10",   "Pearson MARKX10 format",
"match","Start and end of matches between sequence pairs",
"multiple",  "Simple multiple alignment",
"pair",      "Simple pairwise alignment",
"simple",    "Simple multiple alignment",
"sam",       "Sequence alignent/map (SAM) format",
"score",     "Score values for pairs of sequences",
"srs",       "Simple multiple sequence format for SRS",
"srspair",   "Simple pairwise sequence format for SRS",
"tcoffee",   "TCOFFEE program format",

regards,

Peter Rice
EMBOSS Team



From carandraug+dev at gmail.com  Tue Mar 19 19:02:59 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 19 Mar 2013 23:02:59 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
Message-ID: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>

On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
> I do believe that these options are an improvement but since it's a
> lot of changes and behaves differently from the previous version, I
> created a fork and a branch on my own repo. If no one opposes I will
> push them to the main repo.

Pushed.

Carn?



From cjfields at illinois.edu  Tue Mar 19 22:06:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 20 Mar 2013 02:06:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>

On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> I do believe that these options are an improvement but since it's a
>> lot of changes and behaves differently from the previous version, I
>> created a fork and a branch on my own repo. If no one opposes I will
>> push them to the main repo.
> 
> Pushed.
> 
> Carn?

Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

chris


From carandraug+dev at gmail.com  Tue Mar 19 23:09:52 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 20 Mar 2013 03:09:52 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>

On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> I do believe that these options are an improvement but since it's a
>>> lot of changes and behaves differently from the previous version, I
>>> created a fork and a branch on my own repo. If no one opposes I will
>>> push them to the main repo.
>>
>> Pushed.
>>
>> Carn?
>
> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

I was hoping that it would get more use. jhannah/deafferret tells me
that the people who volunteer to do the CPAN work get burned out. With
this properly set up, it should be as simple as running "dzil
release".

I'm also writing a pod weaver plugin bundle for bioperl but would like
some thought on what others think this should be doing.

Carn?



From fs5 at sanger.ac.uk  Wed Mar 20 18:09:40 2013
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Wed, 20 Mar 2013 22:09:40 +0000
Subject: [Bioperl-l] Bio::DB::Sam - finding clipped regions
Message-ID: <514A33A4.3050107@sanger.ac.uk>

Hi,

I need to report all the positions on a reference sequence where aligned 
reads in a bam file have been hard-clipped.
I am using Bio::DB::Sam and I know that I can use callbacks to traverse 
each individual read and get information about its alignment to each 
position on the reference as in

my $sam = Bio::DB::Sam->new(

   -bam  =>$bam,

   -fasta=>$fasta,

);

my $callback = sub {

   my ( $id, $pos, $p ) = @_;

   for my $pileup (@$p) {

     my $aln  = $pileup->alignment;

     my $cigar = $aln->cigar_str;

     # other stuff here

     # ...

  };

$sam->fast_pileup( $sequence_id, $callback );



But I don't see a straight-forward way (accepting that there may not be 
one of course) to ask "is the next base of the read hardclipped".
It's not that difficult to unravel the cigar string and I have the start 
of the alignment for the read, so I can follow the cigar string along to 
the current base on the reference to see what the alignment is there and 
what happens next.
I've just got that feeling that I'm missing something and there is 
probably a better and more efficient way of doing this, maybe with 
another tool? Using samtools mpileup I can get positions of SNPs and 
INDELS but I can't see a way of collecting the hard-clipped positions 
that I need or is that possible somehow (ok, not BioPerl, I know)

Thanks for your help guys!

Frank



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From scott at scottcain.net  Wed Mar 20 22:28:09 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 20 Mar 2013 22:28:09 -0400
Subject: [Bioperl-l] Last day for early registration for GMOD 2013
Message-ID: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>

Hi,

With several guest speakers, including Jane Lomax from GO, Joseph
Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
Centre, this GMOD meeting is shaping up to be a very intersting
meeting indeed.  Today (March 21) is the last day to register with the
early registration pricing.  To register, go to

  http://gmod2013.eventbrite.com/

I look forward to seeing you next month (April 5-6) in Cambridge,
England.  For more information about GMOD 2013, go to

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From sofia at neuro.utah.edu  Thu Mar 21 10:51:43 2013
From: sofia at neuro.utah.edu (Sofia M Robb)
Date: Thu, 21 Mar 2013 14:51:43 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
Message-ID: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>

Hello All,

The following link http://bioperl.org/cgi-bin/deob_interface.cgi results in an internal server error. I hope that someone can point the link in the right direction.

Thanks,
Sofia



From p.j.a.cock at googlemail.com  Thu Mar 21 11:28:03 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 21 Mar 2013 15:28:03 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
In-Reply-To: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
References: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
Message-ID: <CAKVJ-_46=1zbFjLL+ovow4449hZ7qWa+woPz8VkbLLy_LnYNGw@mail.gmail.com>

On Thu, Mar 21, 2013 at 2:51 PM, Sofia M Robb <sofia at neuro.utah.edu> wrote:
> Hello All,
>
> The following link http://bioperl.org/cgi-bin/deob_interface.cgi results
> in an internal server error. I hope that someone can point the link in
> the right direction.
>
> Thanks,
> Sofia

That might be related to the server move at the end of last year.
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Whomever looks after the deobfuscator - please drop the Sys Admin
team an email on the root-l mailing list if you need assistance.

Regards,

Peter


From carandraug+dev at gmail.com  Thu Mar 21 22:11:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 22 Mar 2013 02:11:18 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
Message-ID: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>

On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>> I do believe that these options are an improvement but since it's a
>>>> lot of changes and behaves differently from the previous version, I
>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>> push them to the main repo.
>>>
>>> Pushed.
>>>
>>
>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>
> I'm also writing a pod weaver plugin bundle for bioperl but would like
> some thought on what others think this should be doing.

So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
give some feedback if it's adequate for the rest of the project.

https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

To minimize the number of files added to each distro, I also wrote
another plugin which the PluginBundle uses. I wrote it today so you're
likely to not have it installed yet.

https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Carn?



From jason.stajich at gmail.com  Fri Mar 22 02:19:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 21 Mar 2013 20:19:23 -1000
Subject: [Bioperl-l] PopGen Question
In-Reply-To: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
References: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
Message-ID: <F6333CA1-8FAD-4022-BC5B-19FB51CE95AC@gmail.com>

Once you convert it into the population object ($pop1) you can iterate through the markers and request the allele frequency from each of these.

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/Population.html
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/MarkerI.html

 for my $name ( $population->get_marker_names ) {
   my $marker = $population->get_Marker($name);
   print "marker $marker\n";
   my %af = $marker->get_Allele_Frequencies;
   foreach my $allele ( keys %af ) {
      print "$allele $af{$allele}\n";
   }
  }


unfortunately the wiki code seems to be messed up for autolinking out to the pdoc documentation so some of the links on the bioperl website don't get properly made.  something to be fixed I hope.

Jason
On Mar 15, 2013, at 9:21 AM, Michael Hague <mhague at mail.sfsu.edu> wrote:

> Hello,
> I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:
> 
> 
> use Bio::AlignIO;
> use Bio::PopGen::Utilities;
> use Bio::PopGen::Statistics;
> use Bio::PopGen::Population;
> 
> my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
>                           				 -format => 'fasta');
> my $aln1 = $io1->next_aln;
> 
> 
> my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
> 													-include_monomorphic => 1);
> 
> my $stats1 = Bio::PopGen::Statistics->new();
> my $D1 = $stats1->tajima_D($pop1);
> my $theta1  = $stats1->theta($pop1);
> my $segsites1 = $stats1->segregating_sites_count($pop1);
> 
> print "\nPopulation #1:\n";
> print "Number of segregating sites = $segsites1\n";
> print "Tajima\'s D = $D1\n";
> print "Watterson\'s theta = $theta1\n\n";
> 
> However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?
> 
> Thanks so much for the help,
> Mike
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From briano at bioteam.net  Sat Mar 23 11:21:58 2013
From: briano at bioteam.net (Brian Osborne)
Date: Sat, 23 Mar 2013 11:21:58 -0400
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
Message-ID: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>

Hanny,

I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.

> 
> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> 
> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> 
> Hanny

Brian O.




From cjfields at illinois.edu  Sat Mar 23 13:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 23 Mar 2013 17:41:28 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
	<7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DBFE3F@CHIMBX5.ad.uillinois.edu>

On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:

> Hanny,
> 
> I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> 
>> 
>> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
>> 
>> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
>> 
>> Hanny
> 
> Brian O.


My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.

chris


From carandraug+dev at gmail.com  Sat Mar 23 21:20:04 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 01:20:04 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
Message-ID: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>

Hi everyone

just announcing that Bio-Biblio version 1.70 just got released.

This release has minimum changes, mainly the split from bioperl-live.
As part of the release with Dist::Zilla, a few changes were made to
the documentation and all source use the utf8 pragma.

Carn?



From hlapp at drycafe.net  Sat Mar 23 21:21:49 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 23 Mar 2013 21:21:49 -0400
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
Message-ID: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>

Congrats, great job! -hilmar

On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:

> Hi everyone
> 
> just announcing that Bio-Biblio version 1.70 just got released.
> 
> This release has minimum changes, mainly the split from bioperl-live.
> As part of the release with Dist::Zilla, a few changes were made to
> the documentation and all source use the utf8 pragma.
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From cjfields at illinois.edu  Sat Mar 23 21:59:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 01:59:31 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
	<7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC01CB@CHIMBX5.ad.uillinois.edu>

Agreed, great job!

I may go ahead and pull these from the v1 branch, just to make sure they don't clobber your release.  

chris

On Mar 23, 2013, at 8:21 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Congrats, great job! -hilmar
> 
> On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:
> 
>> Hi everyone
>> 
>> just announcing that Bio-Biblio version 1.70 just got released.
>> 
>> This release has minimum changes, mainly the split from bioperl-live.
>> As part of the release with Dist::Zilla, a few changes were made to
>> the documentation and all source use the utf8 pragma.
>> 
>> Carn?
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Sat Mar 23 23:54:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 03:54:48 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <CAPOrs_0OkB+FgrraMSsMztweCxoyZ7GbHyGEKbO18GA1a2wiow@mail.gmail.com>

On 22 March 2013 02:11, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>> I do believe that these options are an improvement but since it's a
>>>>> lot of changes and behaves differently from the previous version, I
>>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>>> push them to the main repo.
>>>>
>>>> Pushed.
>>>>
>>>
>>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>>
>> I'm also writing a pod weaver plugin bundle for bioperl but would like
>> some thought on what others think this should be doing.
>
> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
> give some feedback if it's adequate for the rest of the project.
>
> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>
> To minimize the number of files added to each distro, I also wrote
> another plugin which the PluginBundle uses. I wrote it today so you're
> likely to not have it installed yet.
>
> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Could a new release of this pluginbundle be made? I have made a lot of
changes to it but I believe it's ready for "production". I used it to
release Bio-biblio and seems to have worked fine. I tried to set it up
so that all it's needed to do is:

1 - change version number on the dist.ini file (there's no need to
commit this change, the PluginBundle will take care of that)
2 - run dzil release

Carn?



From elanorbust2 at yahoo.com  Sun Mar 24 06:14:32 2013
From: elanorbust2 at yahoo.com (sally roberts)
Date: Sun, 24 Mar 2013 03:14:32 -0700 (PDT)
Subject: [Bioperl-l] http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
Message-ID: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>

http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html


From cjfields at illinois.edu  Sun Mar 24 10:32:38 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 14:32:38 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_75F1512441D48A74101FEE2D@qq.com>
References: <tencent_75F1512441D48A74101FEE2D@qq.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC07D0@CHIMBX5.ad.uillinois.edu>

ActivePerl as of a few years or so ago could install modules directly from CPAN.  Have you tried that?  Also, any reason you are using ActivePerl on Linux?  Lots of very nice options out there for linux, including  perlbrew:

http://perlbrew.pl/

The problem we historically have with Windows support is that very few of our developers use it (let alone have access to a Windows machine).  If anyone wants to take this on I would be more than supportive.

chris

On Mar 24, 2013, at 5:44 AM, ciel <58363553 at qq.com> wrote:

> 
> Thanks!
> 
> So, since their web site migrration , I guess I couldn't install bioperl temporary whether in windows or linux. 
> 
> Hanny  
> 
> ------------------ Original ------------------
> From:  "Fields, Christopher J"<cjfields at illinois.edu>;
> Date:  Sun, Mar 24, 2013 01:41 AM
> To:  "Brian Osborne"<briano at bioteam.net>;
> Cc:  "ciel"<58363553 at qq.com>; "Bioperl-L"<bioperl-l at bioperl.org>;
> Subject:  Re: [Bioperl-l] bioperl installation problem
> 
> On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:
> 
> > Hanny,
> > 
> > I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> > 
> >> 
> >> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> >> 
> >> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> >> 
> >> Hanny
> > 
> > Brian O.
> 
> 
> My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.
> 
> chris.




From alexeymorozov1991 at gmail.com  Sun Mar 24 21:00:51 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Mon, 25 Mar 2013 10:00:51 +0900
Subject: [Bioperl-l]
	http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
In-Reply-To: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
References: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
Message-ID: <CAK=7cMMsxCvP+jVYyqDAbaS4_9rycmSVmKUwo-HYTx3nOFA5AQ@mail.gmail.com>

Someone ban the spammer, please.


2013/3/24 sally roberts <elanorbust2 at yahoo.com>

> http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.


From 58363553 at qq.com  Fri Mar 22 12:21:00 2013
From: 58363553 at qq.com (=?ISO-8859-1?B?Y2llbA==?=)
Date: Sat, 23 Mar 2013 00:21:00 +0800
Subject: [Bioperl-l] bioperl installation problem
Message-ID: <tencent_4DDD95B145899AF5173CBF5A@qq.com>

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx


Hanny



From lzwright at gmail.com  Thu Mar 21 17:08:41 2013
From: lzwright at gmail.com (liz wright)
Date: Thu, 21 Mar 2013 17:08:41 -0400
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
Message-ID: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>

Hi, I just force installed bioperl on ubuntu linux as this approach was
proposed as a viable alternative when certain tests fail, but I would like
to check that the fail errors listed below will not significantly impair
bioperl usage as I am new to all this and don't really know how to
interpret the error messages.  Thanks, Liz Wright


* WARNING: Configuration was initially created with Module::Build
  version '0.38' but we are now using version '0.4003'.
  If errors occur, you must re-run the Build.PL or Makefile.PL script.
Will try to install symlinks to /usr/local/bin
  CJFIELDS/BioPerl-1.6.1.tar.gz
  sudo ./Build install  -- OK
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
failure ignored because 'force' in effect
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
failure ignored because 'force' in effect
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
failure ignored because 'force' in effect
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
failure ignored because 'force' in effect


From lzwright at gmail.com  Fri Mar 22 08:44:10 2013
From: lzwright at gmail.com (liz wright)
Date: Fri, 22 Mar 2013 08:44:10 -0400
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>

As a follow up to my previous message, this gives a bit more information as
to why the make tests failed:

  make test had returned bad status, won't install without force
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test NO
 RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
'/usr/bin/perl Build.PL --installdirs site' returned status 512
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness failed
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
not OK (XML::DOM); additionally test harness failed
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
not OK (XML::SAX::Expat)
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
missing
(Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)

On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:

> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect
>
>
>


From carandraug+dev at gmail.com  Mon Mar 25 02:40:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 25 Mar 2013 06:40:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
Message-ID: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>

Hi

I need something to keep a bunch of genes belonging to the same family
organized. It is more than a plain hash since the family can be
divided into multiple ways (subfamilies, types and classes) that
overlap each other, but using a database seems overkill to me. I
couldn't find a module on CPAN that does it so I might write one if no
one suggests an alternative. Basically, with it I wanna be able to do
something like this

  my $histones = Bio::Family->new(
      -classes      => ['canonical', 'variant'],
      -types        => ['H2A', 'H2B', 'H3', 'H4'],
      -subfamilies => [ ... ],
  );

  $histones->add_member ($seqob,
      -class => 'canonical',
      -type  => 'H3',
  );

  @all_members = $histones->members;
  @canonicals  = $histones->class('canonical');

I already wrote a bit of POD for it
http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
on its design before start coding, as I fear it might be too focused
for the problem I have at hand. Could someone give me some advice
about it?

I'm also thinking that maybe I should write some sort of general perl
module, outside the Bio::* namespace.

Thanks,
Carn?



From longbow0 at gmail.com  Mon Mar 25 04:42:38 2013
From: longbow0 at gmail.com (longbow leo)
Date: Mon, 25 Mar 2013 16:42:38 +0800
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
Message-ID: <CAKPXXke637b18wS3DPPrunw1+n-q3NciSvsP=bxEeLDC5n7yVw@mail.gmail.com>

Hi Liz,

There are already "bioperl' and "bioperl-run" packages for ubuntu. It is
not necessary to install bioperl from source code.

Haizhou

On Fri, Mar 22, 2013 at 8:44 PM, liz wright <lzwright at gmail.com> wrote:

> As a follow up to my previous message, this gives a bit more information as
> to why the make tests failed:
>
>   make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test NO
>  RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
> '/usr/bin/perl Build.PL --installdirs site' returned status 512
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
> missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness
> failed
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
> not OK (XML::DOM); additionally test harness failed
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
> not OK (XML::SAX::Expat)
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
> missing
>
> (Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)
>
> On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:
>
> > Hi, I just force installed bioperl on ubuntu linux as this approach was
> > proposed as a viable alternative when certain tests fail, but I would
> like
> > to check that the fail errors listed below will not significantly impair
> > bioperl usage as I am new to all this and don't really know how to
> > interpret the error messages.  Thanks, Liz Wright
> >
> >
> >
> > * WARNING: Configuration was initially created with Module::Build
> >   version '0.38' but we are now using version '0.4003'.
> >   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> > Will try to install symlinks to /usr/local/bin
> >   CJFIELDS/BioPerl-1.6.1.tar.gz
> >   sudo ./Build install  -- OK
> > Failed during this command:
> >  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> > failure ignored because 'force' in effect
> >  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> > failure ignored because 'force' in effect
> >  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TODDR/XML-Parser-2.41.tar.gz                 : make NO
> >  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> > failure ignored because 'force' in effect
> >  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> > failure ignored because 'force' in effect
> >
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From l.m.timmermans at students.uu.nl  Mon Mar 25 07:19:36 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Mon, 25 Mar 2013 12:19:36 +0100
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>

On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect

Most of those are XML modules that need an external XML library. Force
installing won't solve that problem. Installing expat (on my ubuntu
that'd be libexpat1) should be the solution. Odds are the other
failures are dependent failures that will also disappear.

Leon


From cjfields at illinois.edu  Mon Mar 25 08:54:21 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:54:21 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>

IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:

https://metacpan.org/module/Bio::Cluster::FamilyI

My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

chris

On Mar 25, 2013, at 1:40 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I need something to keep a bunch of genes belonging to the same family
> organized. It is more than a plain hash since the family can be
> divided into multiple ways (subfamilies, types and classes) that
> overlap each other, but using a database seems overkill to me. I
> couldn't find a module on CPAN that does it so I might write one if no
> one suggests an alternative. Basically, with it I wanna be able to do
> something like this
> 
>  my $histones = Bio::Family->new(
>      -classes      => ['canonical', 'variant'],
>      -types        => ['H2A', 'H2B', 'H3', 'H4'],
>      -subfamilies => [ ... ],
>  );
> 
>  $histones->add_member ($seqob,
>      -class => 'canonical',
>      -type  => 'H3',
>  );
> 
>  @all_members = $histones->members;
>  @canonicals  = $histones->class('canonical');
> 
> I already wrote a bit of POD for it
> http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
> on its design before start coding, as I fear it might be too focused
> for the problem I have at hand. Could someone give me some advice
> about it?
> 
> I'm also thinking that maybe I should write some sort of general perl
> module, outside the Bio::* namespace.
> 
> Thanks,
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 25 08:56:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:56:37 +0000
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1733@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 6:19 AM, Leon Timmermans <l.m.timmermans at students.uu.nl> wrote:

> On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
>> Hi, I just force installed bioperl on ubuntu linux as this approach was
>> proposed as a viable alternative when certain tests fail, but I would like
>> to check that the fail errors listed below will not significantly impair
>> bioperl usage as I am new to all this and don't really know how to
>> interpret the error messages.  Thanks, Liz Wright
>> 
>> 
>> * WARNING: Configuration was initially created with Module::Build
>>  version '0.38' but we are now using version '0.4003'.
>>  If errors occur, you must re-run the Build.PL or Makefile.PL script.
>> Will try to install symlinks to /usr/local/bin
>>  CJFIELDS/BioPerl-1.6.1.tar.gz
>>  sudo ./Build install  -- OK
>> Failed during this command:
>> LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
>> failure ignored because 'force' in effect
>> KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
>> failure ignored because 'force' in effect
>> BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TODDR/XML-Parser-2.41.tar.gz                 : make NO
>> MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
>> failure ignored because 'force' in effect
>> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
>> failure ignored because 'force' in effect
> 
> Most of those are XML modules that need an external XML library. Force
> installing won't solve that problem. Installing expat (on my ubuntu
> that'd be libexpat1) should be the solution. Odds are the other
> failures are dependent failures that will also disappear.
> 
> Leon

Also, the version on CPAN has been updated to handle 'optional' dependencies; AcePerl for instance is pretty much in maintenance mode (maybe deprecated) and hasn't been updated in years.

chris




From fossandonc at hotmail.com  Mon Mar 25 09:29:48 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 25 Mar 2013 10:29:48 -0300
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <000201ce2959$17ed7830$47c86890$@qq.com>
References: <000201ce2959$17ed7830$47c86890$@qq.com>
Message-ID: <SNT133-ds57FF786B3A8DB70E8F9FACFD70@phx.gbl>

Hi,
I use Windows but I dropped ActivePerl some time ago in preference of
Strawberry Perl (http://strawberryperl.com/), which have better support for
installation directly from CPAN via command line.

I'm not sure if I understood correctly but you installed new Perl 5.16 over
the old 5.10?? In that case I would recommend to completely uninstall the
previous Perl version and then install the new clean Perl version.

On the other hand, the error message points to a problem connecting to the
Uwinnipeg server, so maybe they are down (in fact I just tried on my browser
and received the same error so they have problems with their servers), maybe
use Bribes instead; you don?t need to add ALL the repos anyway, just be sure
to add the http://bioperl.org/DIST, which contains the
"BioPerl-1.6.1-ppm.tar.gz", the last ActivePerl release that can be install
using the Perl Package Manager.

If you want to install the latest version, you will have to ditch the PPM,
type CPAN in command line and use that interface to get the
"BioPerl-1.6.901"
(http://www.bioperl.org/wiki/Installing_BioPerl_on_Windows#Installation_usin
g_CPAN_or_manual_installation). Beware that BioPerl will always give some
tests errors when installing that way, so you have to add "force" when
installing and everything will be fine.

Hope that helps,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de ciel
Enviado el: viernes, 22 de marzo de 2013 13:21
Para: bioperl-l
Asunto: [Bioperl-l] bioperl installation problem

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl
version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version
ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as
:"failed 503 Service temporarily Unavailable", how can I deal with this
problem? thx


Hanny

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hartzell at alerce.com  Mon Mar 25 12:23:32 2013
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 25 Mar 2013 09:23:32 -0700
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <20816.31236.737983.55186@gargle.gargle.HOWL>

Carn? Draug writes:
 > [...]
 > So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
 > Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
 > give some feedback if it's adequate for the rest of the project.
 > 
 > https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

Looks wonderful!

I use a "private" section that I think corresponds to what you call
"internal".  Is there a BioPerl tradition one way or the other?

You might make the SYNOPSIS just a tad less confusing if you point
some meaningful text into the text sections of the GenerateSection
parts, something like "text = Info about mailing lists goes here".  I
scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
lists" had an empty attribute and the other two had nonsense text.  It
looks like FEEDBACK is just an empty level 1 header, but
otherwise....

 > To minimize the number of files added to each distro, I also wrote
 > another plugin which the PluginBundle uses. I wrote it today so you're
 > likely to not have it installed yet.
 > 
 > https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

I can see that being useful. In the name, did you mean "interpolated"
(which you use further down) where you say "interpreted"?

This is a useful contribution!

g.



From cjfields at illinois.edu  Mon Mar 25 12:46:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 16:46:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <20816.31236.737983.55186@gargle.gargle.HOWL>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:

> Carn? Draug writes:
>> [...]
>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>> give some feedback if it's adequate for the rest of the project.
>> 
>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
> 
> Looks wonderful!
> 
> I use a "private" section that I think corresponds to what you call
> "internal".  Is there a BioPerl tradition one way or the other?

Not really, but there probably should be a more standard way of doing this.

> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".  I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....
> 
>> To minimize the number of files added to each distro, I also wrote
>> another plugin which the PluginBundle uses. I wrote it today so you're
>> likely to not have it installed yet.
>> 
>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
> 
> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?
> 
> This is a useful contribution!
> 
> g.

Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

chris




From carandraug+dev at gmail.com  Mon Mar 25 21:13:36 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 01:13:36 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
	<118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2F4yaXPR7ySHQ2jy0UjA5-FhfrWgNvkoF=0DKq5nzHeg@mail.gmail.com>

On 25 March 2013 16:23, George Hartzell <hartzell at alerce.com> wrote:
> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".

I don't understand your suggestion. Could you explain it again please?

> I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....

It's not empty. Feedback is level 1, which contains three level 2
headings for mailing list, support and reporting bugs. The code being
generated should match exactly the feedback section of all current
BioPerl modules. See the feedback section of the Bio::DB::BiblioI that
I recently released with this set up:

https://metacpan.org/module/Bio::DB::BiblioI#FEEDBACK

and compare with the old release of Bio::SeqIO

https://metacpan.org/module/Bio::SeqIO#FEEDBACK

> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?

Yes, that's what I meant. I have just pushed the fix, thank you.

On 25 March 2013 16:46, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:
>
>> Carn? Draug writes:
>>> [...]
>>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>>> give some feedback if it's adequate for the rest of the project.
>>>
>>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>>
>> Looks wonderful!
>>
>> I use a "private" section that I think corresponds to what you call
>> "internal".  Is there a BioPerl tradition one way or the other?
>
> Not really, but there probably should be a more standard way of doing this.

I think the large majority of the modules have a head1 APPENDIX that
says "Internal methods are usually preceded with a _" which contained
each method and attribute by the same order they appear on the code
inside a head2. I just followed the name that was already there
"internal", but it's very easy to change. At the moment, what I set up
recognizes the following:

=attr (for attributes)
=method
=func (for functions)
=internal (internal methods)

It doesn't matter the order they appear on the source, PodWeaver will
group and reorder them. It is easy to change the keywords, and add or
remove the groups. Just let me know what the bundle should be doing.
Take a look at

https://github.com/bioperl/Bio-Biblio/blob/master/lib/Bio/DB/BiblioI.pm

which generates

https://metacpan.org/module/Bio::DB::BiblioI

>>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
>>
>> [...]
>>
>> This is a useful contribution!
>>
>
> Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

I wrote another plugin the day after to generate the legal section
which is mainly aimed at BioPerl and distributions with many modules,
where the authors and copyright owners are not always the same. It
takes the copyright information from a block of comments in each
source file.

https://metacpan.org/module/Pod::Weaver::Section::Legal::Complicated

And yesterday the contributors plugin was released again after also
implementing the option to find the names of contributors in the
source of individual files

https://metacpan.org/module/Pod::Weaver::Section::Contributors

I can easily make the changes on our pluginbundles, or write new ones.
And authors from other packages are usually happy to receive patches
so it's also easy to expand on the ones that already exist. The only
problem left is defining what a BioPerl POD should look like. The pod
weaver pluginbundle as it is now, is just what looked appropriate to
me. But would be great if someone could comment on it so adjustments
to it can be made.

Carn?



From amelia.ireland at gmod.org  Mon Mar 25 19:55:23 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Mon, 25 Mar 2013 16:55:23 -0700
Subject: [Bioperl-l] [Gmod-gbrowse] Last day for early registration for
	GMOD 2013
In-Reply-To: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
References: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
Message-ID: <CAALsq01L4pRuOTsHh-wxmHuKBs24g3Q=DW2ngqaYq4386FAmHQ@mail.gmail.com>

GMOD is very pleased to announce the keynote speaker for the 2013 GMOD
community meeting is Dr. Kentaro Yoshida from the Sainsbury Lab (
http://tsl.ac.uk), talking about the Open Ash Dieback effort. This
pioneering bioinformatics project is employing two increasingly important
paradigms--open access to data and crowdsourcing--to gather genetic
analyses of ash and a fungal pathogen that is threatening tree populations
in the UK. Expect an interesting and inspiring talk!

Online registration: http://gmod2013.eventbrite.com

If you are interested in attending remotely, we will be using Go To Meeting
(http://gotomeeting.com) to allow people to attend virtually. Please email
me if you would like to join in.

Look forward to seeing you all in Cambridge!


On Wed, Mar 20, 2013 at 7:28 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi,
>
> With several guest speakers, including Jane Lomax from GO, Joseph
> Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
> Centre, this GMOD meeting is shaping up to be a very intersting
> meeting indeed.  Today (March 21) is the last day to register with the
> early registration pricing.  To register, go to
>
>   http://gmod2013.eventbrite.com/
>
> I look forward to seeing you next month (April 5-6) in Cambridge,
> England.  For more information about GMOD 2013, go to
>
>   http://www.gmod.org/wiki/April_2013_GMOD_Meeting
>
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


From carandraug+dev at gmail.com  Mon Mar 25 23:48:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 03:48:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2VDEt5OeKsZdNegygdTv_ZPJXcVXO6JS65sFjVCVKKZg@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI

This module mentions Bio::Cluster::Family but I can't seem to find it anywhere.

> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I think I was overcomplicating, this class might do what I want
thought in a different way. My idea of a family of genes doesn't
really match it, but I should be able to work with it by mixing it
with Set::Object.

Thank you,
Carn?



From briano at bioteam.net  Tue Mar 26 13:51:07 2013
From: briano at bioteam.net (Brian Osborne)
Date: Tue, 26 Mar 2013 13:51:07 -0400
Subject: [Bioperl-l] Wiki details
Message-ID: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>

All,

I'm looking at various module pages in the Wiki and it seems that all links are broken. For example, the "<biblio>" parser tag does not work, parser functions like #setvar aren't working and because of this the link to CPAN is broken, and so on. I'm guessing that some upgrade did not restore custom code or install extensions used in the earlier version, and Special:Version confirms this, this code is not installed.

If someone would like to contact me privately and give me credentials I can take a look at the MediaWiki directory, see if I can fix this.

Brian O.




From p.j.a.cock at googlemail.com  Tue Mar 26 14:10:10 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 26 Mar 2013 18:10:10 +0000
Subject: [Bioperl-l] Wiki details
In-Reply-To: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
References: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
Message-ID: <CAKVJ-_5nOp8sXBhLRJ2Kvrzyf0rUGjTfs=PMd7pX_CqYAQ6djg@mail.gmail.com>

On Tue, Mar 26, 2013 at 5:51 PM, Brian Osborne <briano at bioteam.net> wrote:
> All,
>
> I'm looking at various module pages in the Wiki and it seems that all
> links are broken. For example, the "<biblio>" parser tag does not work,
> parser functions like #setvar aren't working and because of this the link to
> CPAN is broken, and so on. I'm guessing that some upgrade did not restore
> custom code or install extensions used in the earlier version, and
> Special:Version confirms this, this code is not installed.
>
> If someone would like to contact me privately and give me credentials I
> can take a look at the MediaWiki directory, see if I can fix this.
>
> Brian O.

Hi Brian,

I was aware of issues with the  "<biblio>" plugin, but not all of this.
Most likely this is from the server move at the end of 2012,
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Assuming someone senior from BioPerl (or Chris Dag?) will vouch
for you, we'd ask you to join the root-l mailing list where OBF server
admin stuff happens. We'll need a preferred username (e.g. briano
or bosborne) and your SSH public key (the new server does not
accept simple username/password logins).

Regards,

Peter
(With his OBF hat on)


From antony.vincent.1 at ulaval.ca  Tue Mar 26 19:24:20 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 16:24:20 -0700 (PDT)
Subject: [Bioperl-l]  One letter protein sequence to three letters
Message-ID: <35222270.post@talk.nabble.com>


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I
try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From Russell.Smithies at agresearch.co.nz  Tue Mar 26 19:44:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 12:44:35 +1300
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAA77@exchsth.agresearch.co.nz>

You're passing an ordinary String to Bio::SeqUtils->seq3 (that's what $hsp->query_string returns) but  I think it needs to be a Bio::PrimarySeqI compliant object.

try this:

$seqobj = Bio::PrimarySeq->new ( -seq => $hsp->query_string);
$polypeptide_3char = Bio::SeqUtils->seq3($seqobj);


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Wednesday, 27 March 2013 12:24 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] One letter protein sequence to three letters


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");  my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
--
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From antony.vincent.1 at ulaval.ca  Tue Mar 26 21:32:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 18:32:09 -0700 (PDT)
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <35222552.post@talk.nabble.com>


Yes! That works and I understand now, thanks for you precious help!
:handshake:

Antony03 wrote:
> 
> Hi!
> 
> I wan't to parse a blastp output for have an hsp with three letters code.
> I try with this:
> 
> my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
>   				    -format => 'fasta' );
>  my $query1 = <$query1_in>; 
>  my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
>   				      -format => 'fasta' );
>  my $query2 = <$query2_in>; 
>  
>  my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>
> "$algo");
>  my $report = $factory->bl2seq($query1, $query2);
> 
> ############################################################################################################
>  while (my $result = $report->next_result) {  # while 1
>     print "Query: ".$result->query_name."\n\n";
>     while (my $hit = $result->next_hit) {     # while 2
>  	while (my $hsp = $hit->next_hsp) {    # while 3
>  
> if ( $hsp->percent_identity >= "$identity" ) 
> 
> 	{ # start of if
> 	
> 	$qseq = $hsp->query_string;
> 	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);
> 
> 	print $polypeptide_3char;
> 
> 	
> 		
> }
>  	} # end of while 3
>     print "\n";
>     }	# end of while 2
>  }	# end of while 3
> 
> And I got this error:
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Not a Bio::PrimarySeqI object but [$self]
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
> STACK: blast_parsing.pl:36
> -----------------------------------------------------------
> I don't understand why my code generate this error!
> 
> Thanks :)
> 

-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222552.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From alexeymorozov1991 at gmail.com  Tue Mar 26 22:34:01 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Wed, 27 Mar 2013 11:34:01 +0900
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <35222552.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
	<35222552.post@talk.nabble.com>
Message-ID: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?


From Russell.Smithies at agresearch.co.nz  Tue Mar 26 22:50:24 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 15:50:24 +1300
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>

Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
Or is there a chance that $identity is going to contain a string rather than a float?

I could be completely wrong of course  ...

--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
Sent: Wednesday, 27 March 2013 3:34 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From cjfields at illinois.edu  Tue Mar 26 23:13:19 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 27 Mar 2013 03:13:19 +0000
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC4070@CHIMBX5.ad.uillinois.edu>

You are correct.   Quotes should be unnecessary in this case, percent identities are calculated I believe from the midline.

chris

On Mar 26, 2013, at 9:50 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
> Or is there a chance that $identity is going to contain a string rather than a float?
> 
> I could be completely wrong of course  ...
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
> Sent: Wednesday, 27 March 2013 3:34 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters
> 
> Well, there is one little thing I don't get. Why is
> 
> if ( $hsp->percent_identity >= "$identity" )
> 
> any better than
> 
> if ( $hsp->percent_identity >= $identity)
> 
> Ie what do quotes do?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From adsj at novozymes.com  Wed Mar 27 08:19:01 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:19:01 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
Message-ID: <87li99593e.fsf@topper.koldfront.dk>

We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
with drawing panels that have tracks with split locations - an exception
is thrown in 2.24.

Here are the outputs of the test-script I've made:

  Bio::Graphics::VERSION: 1.995
  Simple location  ... ok
  Join location  ... ok

and

  Bio::Graphics::VERSION: 2.24
  Simple location  ... ok
  Join location  ... Can't locate object method "has_tag" via package "Bio::Location::Simple" at /usr/share/perl5/Bio/Graphics/Glyph.pm line 706, <DATA> line 192.

The test script looks like this:

== =
#!/usr/bin/perl

use strict;
use warnings;

use Bio::Graphics;

use Bio::SeqFeature::Generic;
use Bio::Factory::FTLocationFactory;

print "Bio::Graphics::VERSION: $Bio::Graphics::VERSION\n";

test_panel_with_location('1..12',              'Simple location');
test_panel_with_location('join(1..10,15..20)', 'Join location');

sub test_panel_with_location {
    my ($location_string, $msg)=@_;

    print "$msg  ... ";
    my $location=Bio::Factory::FTLocationFactory->from_string($location_string);
    my $seq=Bio::SeqFeature::Generic->new;
    $seq->location($location);

    my $panel=Bio::Graphics::Panel->new(-length=>500, -width=>500);
    $panel->add_track($seq);
    eval { $panel->png };
    print $@ || "ok\n";
}
== =

Am I doing something wrong in the script, or is this a regression in
Bio::Graphics somewhere?


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From adsj at novozymes.com  Wed Mar 27 08:33:53 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:33:53 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
In-Reply-To: <87li99593e.fsf@topper.koldfront.dk> ("Adam =?iso-8859-1?Q?Sj?=
	=?iso-8859-1?Q?=F8gren=22's?= message of
	"Wed, 27 Mar 2013 13:19:01 +0100")
References: <87li99593e.fsf@topper.koldfront.dk>
Message-ID: <87hajx58em.fsf@topper.koldfront.dk>

adsj at novozymes.com (Adam Sj?gren) writes:

> We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
> with drawing panels that have tracks with split locations - an exception
> is thrown in 2.24.

[...]

Ahh, this has been fixed between 2.24 and 2.32 - (we upgraded to 2.24
because that is the version in the latest Ubuntu LTS).

2.32 works fine:

  Bio::Graphics::VERSION: 2.32
  Simple location  ... ok
  Join location  ... ok

Sorry for the noise.


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From carandraug+dev at gmail.com  Thu Mar 28 10:55:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 14:55:48 +0000
Subject: [Bioperl-l]  Google Summer of Code - BioPerl proposals
Message-ID: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>

On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
> Just a heads-up, if there are any students interested in the Google Summer of
> Code, the Open Bioinformatics Foundation is planning on participating again
> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
> looking for prospective projects.
>
> We're open for any project ideas this year, so let us know what you would like
> to do!

Hi

I had already mentioned that I would like to finish the split of the
project into smaller distributions. Is it acceptable to finish
projects from previous years? I noticed that the wiki page for BioPerl
projects is still empty for this year. Should I fill it? Would someone
be able to mentor that?

Carn?



From carandraug+dev at gmail.com  Thu Mar 28 12:23:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 16:23:18 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_32AU=Vc1yZofWyLM+CVQj0Xa6et+7rKHrXSHVU-TY2sA@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI
>
> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I'm looking at these now and thinking of making the split from live
into a separate distribution now. But I'm unsure about two of the
files

Bio/ClusterIO/dbsnp.pm
Bio/Cluster/SequenceFamily.pm

Would you agree that these would fit better into a Bio-Variations and
Bio-Seq distribution?

Carn?



From hlapp at drycafe.net  Sat Mar 30 13:24:26 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 30 Mar 2013 12:24:26 -0500
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
Message-ID: <723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>

Hi Carn?,

Not sure I've missed a response to this. If indeed there hasn't been one, let me just chime in non-authoritatively that in principle there's nothing wrong with picking up past pieces. I would argue you'd have to make a convincing argument as to why and how you'd surmount the hurdles that brought the previous project to a premature end (or why it ran out of time and you won't), and as to how it's desirability has not diminished since then even though nobody else picked it up.

If you want to apply as a student, you don't strictly have to put it up on the wiki, but it'd be prudent to discuss your ideas on this list prior to submission. Presumably you were planning that anyway, though.

-hilmar

Sent with a tap.

On Mar 28, 2013, at 9:55 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
>> Just a heads-up, if there are any students interested in the Google Summer of
>> Code, the Open Bioinformatics Foundation is planning on participating again
>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>> looking for prospective projects.
>> 
>> We're open for any project ideas this year, so let us know what you would like
>> to do!
> 
> Hi
> 
> I had already mentioned that I would like to finish the split of the
> project into smaller distributions. Is it acceptable to finish
> projects from previous years? I noticed that the wiki page for BioPerl
> projects is still empty for this year. Should I fill it? Would someone
> be able to mentor that?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From briano at bioteam.net  Sun Mar 31 10:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 10:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 11:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 11:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From cjfields at illinois.edu  Sun Mar 31 20:34:16 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Apr 2013 00:34:16 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>

I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.  

chris

On Mar 30, 2013, at 12:24 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Hi Carn?,
> 
> Not sure I've missed a response to this. If indeed there hasn't been one, let me just chime in non-authoritatively that in principle there's nothing wrong with picking up past pieces. I would argue you'd have to make a convincing argument as to why and how you'd surmount the hurdles that brought the previous project to a premature end (or why it ran out of time and you won't), and as to how it's desirability has not diminished since then even though nobody else picked it up.
> 
> If you want to apply as a student, you don't strictly have to put it up on the wiki, but it'd be prudent to discuss your ideas on this list prior to submission. Presumably you were planning that anyway, though.
> 
> -hilmar
> 
> Sent with a tap.
> 
> On Mar 28, 2013, at 9:55 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
> 
>> On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
>>> Just a heads-up, if there are any students interested in the Google Summer of
>>> Code, the Open Bioinformatics Foundation is planning on participating again
>>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>>> looking for prospective projects.
>>> 
>>> We're open for any project ideas this year, so let us know what you would like
>>> to do!
>> 
>> Hi
>> 
>> I had already mentioned that I would like to finish the split of the
>> project into smaller distributions. Is it acceptable to finish
>> projects from previous years? I noticed that the wiki page for BioPerl
>> projects is still empty for this year. Should I fill it? Would someone
>> be able to mentor that?
>> 
>> Carn?
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Sun Mar 31 22:05:19 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 1 Apr 2013 03:05:19 +0100
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>

On 1 April 2013 01:34, Fields, Christopher J <cjfields at illinois.edu> wrote:
> I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.

Why did the project ran out of time 2 years ago? The blog posts about
it are very few and don't sound too bad. It mentions having prepared a
couple of them, but none was actually ever released. Instead, the
source was also kept in bioperl-live and seems to have already
branched. Is there any reason for this? It was my understanding that
splitting the project is still desirable, from a discussion back in
February

http://article.gmane.org/gmane.comp.lang.perl.bio.general/26395

it just happens that no one has picked it up yet.

I think splitting bioperl-live into subdistributions and make a new
1.70 release of each of them is perfectly doable over a summer. And I
say this after having split and release Bio-Biblio. This is one of my
itches with BioPerl. I have been using it for almost 3 years, but have
never seen a release. I would like to make new releases of everything,
no changes at the start, but take them to the point that "dzil
release" does everything. Make it really easy for anyone to come in
and contribute and even easier for a maintainer to make a new release
after receiving a contribution. Is this desirable for the project?

Carn?



From cjfields at illinois.edu  Sun Mar 31 23:28:55 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Apr 2013 03:28:55 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC8BD8@CHIMBX5.ad.uillinois.edu>

On Mar 31, 2013, at 9:05 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 1 April 2013 01:34, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.
> 
> Why did the project ran out of time 2 years ago? The blog posts about
> it are very few and don't sound too bad. It mentions having prepared a
> couple of them, but none was actually ever released. Instead, the
> source was also kept in bioperl-live and seems to have already
> branched. Is there any reason for this? It was my understanding that
> splitting the project is still desirable, from a discussion back in
> February
> 
> http://article.gmane.org/gmane.comp.lang.perl.bio.general/26395
> 
> it just happens that no one has picked it up yet.

The project actually made a lot of headway; the particular pieces moved out (Bio::Root, Bio::Factory, etc) worked fine, but we never followed up on exactly what to do next on master branch.  It's perfectly feasible for someone to go ahead and finish the initial part of that (in fact, I believe there were some branches that started along this path but never merged back in).

FWIW, Sheena also started the Dist::Zilla bundle you have been working on as well, with the same intent you have.  So the fundamental groundwork is there.

> I think splitting bioperl-live into subdistributions and make a new
> 1.70 release of each of them is perfectly doable over a summer. And I
> say this after having split and release Bio-Biblio. This is one of my
> itches with BioPerl. I have been using it for almost 3 years, but have
> never seen a release. I would like to make new releases of everything,
> no changes at the start, but take them to the point that "dzil
> release" does everything. Make it really easy for anyone to come in
> and contribute and even easier for a maintainer to make a new release
> after receiving a contribution. Is this desirable for the project?
> 
> Carn?


The last Bioperl release was in 2011 IIRC, so we're long overdue, but it's not quite 3 yrs :)  

Hilmar's point is pretty valid, namely that a case would have to be made as to why the initial run at it wasn't completed, or why it would work better this time.  We're not suggesting that this can't be done, but the above point would have to be answered.  Frankly, the project has been pretty reliant on me for releases, so it's perfectly valid to point out the modules haven't made it out yet b/c I haven't made a release since then.  From that point of view, this would be a continuation of that work, maybe with the intent/focus on making code releases much easier.

Regarding updating Bioperl to use Dist::Zilla amongst other modern perl tools (Moose included), yes, it is very much our wish/intent to have this, in any way possible.  But I don't think we can call it BioPerl v1.7, simply based on past release cycles; we're somewhat bound by deprecations, etc.  We really need a clean break.  

So, my general feeling is that while we are cleaving out code and releasing the independent dist and core, we should re-christen core as 1.9 (e.g. pre-v2).  We move to v2 when we feel we're at the right point.  Each of the individual distributions would have to start with their own versions, anything greater than the point where they left the core/live distribution should work.  I agree with you in that I don't think it would take a long time, but we also have bioperl-run in the mix (and in many cases it would make sense to combine wrappers with the proper parsers), so simply cleaving out from one repo may not be the best approach.

With that in mind, my point was meant to indicate we can also start afresh with a section of the code that you would like to focus on, using some of the same ideas (pulling out the relevant modules you want to work on).  This might be an attainable goal in the minds of GSoC reviewers and might suit your particular needs (for instance, if you had a research project reliant on such code).  I'm supportive either way, and I don't think you'll have a problem finding a mentor if you need one.

chris






From l.m.timmermans at students.uu.nl  Fri Mar  1 16:49:58 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Fri, 1 Mar 2013 22:49:58 +0100
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
Message-ID: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>

On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
> Greetings,
>
> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>
> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>
> Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetw!
>  ork::RandomFactory -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA::ESEfinder -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameSubs -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::interpro -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::berkeleydb -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::entrezgene -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tinyseq -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::chadoxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (opt!
>  ional_features -> Bio::SeqIO::game::gameWriter -> requires) [Validatio
> n: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::FileCache -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::bsml_sax -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Primer3 -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::HtSNP -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Compatible -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Taxonomy::entrez -> requires) [Validation: 1.2], Expected a ma!
>  p structure from string or file. (optional_features -> Bio::SeqIO::agave -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::TagHaplotype -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::SeqFeature::Store::FeatureFileLoader -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::Protein* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::blastxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::EUtilities -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Draw::Cladogram -> requires) [Validation: 1!
>  .2], Expected a map structure from string or file. (optional_features
> -> Bio::Tools::SeqPattern -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tigrxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Collection -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Draw::Pictogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::Writer::BSMLResultWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::HIVQuery -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::TreeIO::svggraph -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::eutils -> requires) [Validation: 1.2], Expected a map structure from string or file. (opti!
>  onal_features -> Bio::PhyloNetwork -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern::BackTranslate -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::GenBank -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Variation::IO::xml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::GraphViz -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Annotated -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::NCBIHelper -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::HIV -> requires) [Validation: 1.2], Expected a map structure from string or file. (!
>  optional_features -> Bio::Tools::Analysis::DNA* -> requires) [Validati
> on: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Run::RemoteBlast -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::excel -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::ClusterIO::dbsnp -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Microarray::Tools::ReseqChip -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::soap -> requires) [Validation: 1.2]
> at /usr/local/lib/perl5/5.10.1/Module/Build/Base.pm line 4559
>
> Could not create MYMETA files
> Creating new 'Build' script for 'BioPerl' version '1.006001'

What versions of Module::Build and CPAN::Meta are you using?

> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.

Yeah, 1.6.1 equals 1.006001. See also
http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
Do note that it is no longer the lastest release, latest is 1.6.901
and a new release is expected on a short notice.

Leon



From cjfields at illinois.edu  Fri Mar  1 18:11:39 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 1 Mar 2013 23:11:39 +0000
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
	<CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6E70B5F7@CHIMBX5.ad.uillinois.edu>

On Mar 1, 2013, at 3:49 PM, Leon Timmermans <l.m.timmermans at students.uu.nl>
 wrote:

> On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
>> Greetings,
>> 
>> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>> 
>> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>> ?.
> 
>> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.
> 
> Yeah, 1.6.1 equals 1.006001. See also
> http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
> Do note that it is no longer the lastest release, latest is 1.6.901
> and a new release is expected on a short notice.
> 
> Leon

Yup, hoping to work on it tonight and tomorrow.  Travis-CI indicates all normal tests are passing, I'll run through a few remaining ones.  Some we can't address directly; there are a number of warnings popping up I can't do anything about (they originate from Graph).

chris


From pcantalupo at gmail.com  Sat Mar  2 12:28:15 2013
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Sat, 2 Mar 2013 12:28:15 -0500
Subject: [Bioperl-l] Fix for Bug #3376 broke somewhere else
In-Reply-To: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
References: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
Message-ID: <CAJqbkv5-cXLh_cMa3rWoOVv7PijY2Orq=Smvqd3Xij887iVhMg@mail.gmail.com>

Hi Francisco,

Nice catch. Please submit a new bug report for this and reference bug
3376. Please provide a minimal hmmer output file, a script and the
expected output. Then, I'll look into it and fix the bug.

Thank you,

Paul

Paul Cantalupo
University of Pittsburgh


On Thu, Feb 28, 2013 at 10:36 AM, Francisco J. Ossand?n
<fossandonc at hotmail.com> wrote:
> Hi,
> I was re-checking Bug #3302 using the Bio::SearchIO modules of the
> repository and found that now it can't parse a Hmmer2 file that was
> previously fine. After tracking the problem, I discovered that a change in a
> regular expression to fix another bug broke the parse.
>
> The fix for the Bug #3376 consisted in adding an extra condition to omit
> lines where end of domain indicator is split across lines
> (https://redmine.open-bio.org/issues/3376):
> TEST: domain 1 of 1, from 8 to 97: score 184.7, E = 2.5e-56
>                    *->svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDn
>                       sv+qqqq+  +    +vtAiAiAigYRYRYRAv Wn GsLs G nDn
>         Test     8    SVYQQQQGGSA----MVTAIAIAIGYRYRYRAVVWNKGSLSTGTNDN 50
>
>                    DnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr<-
>                    DnDq +d LYtiYYsvtv +ss+p q+v+HHHaH+asstkiiiki P
>         Test    51 DNDQAAD-LYTIYYSVTVSASSWPGQSVTHHHAHPASSTKIIIKIAPS   97
>
>                    *
>
>         Test     -   -
> This case is characterized by the 2 dashes in the line...
>
> So the expression added in hmmer2.pm - ?next_result?
> (https://github.com/bioperl/bioperl-live/commit/142e5d79e3a6593db32bf0af9904
> 8f47d01bd3f2):
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\-\s+\-\s*$/ ) ### <--- This regex was
> designed for bug 3376
>                         {
>                             next;
>                         }
>
> But the expression used is too broad because it uses the "^.+" just before
> the 2 dashes, and it broke these lines parsing, where is full of dashes:
>                    KyACrqCdtiVQAPaPakpIErGiptaGLLArvlVSKyaEHlPLYRQsEI
>
>   lcl|gi|340     - -------------------------------------------------- -
>
>                    yaRqGVeiaRstLadWVgrtgarLaPLvdALaeyVLkeGklHADeTPVqV
>                          +i  s L   V++ + r
>   lcl|gi|340 60938 ------AIMISGLIHGVSARCLRF-------------------------- 60955
>
> I think a reasonable fix that still fixes the original bug and restore the
> function for this case is to add an extra \s+ in the regex just before the
> first dash, so the expression makes sure that the first dash is the one that
> comes AFTER the description (and is replacing the usual coordinate number)
> and is not the last of an alignment or a series of dashes like the one
> above:
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\s+\-\s+\-\s*$/ ) ### <--- Tweaked regex
>                         {
>                             next;
>                         }
> I tested it and it works fine, hope you find the fix acceptable.
>
> Cheers,
>
> --
> Francisco J. Ossandon
> Bioinformatician.
> Ph.D. Candidate, University Andres Bello.
> Center for Bioinformatics and Genome Biology,
> Fundacion Ciencia para la Vida.
> Santiago, Chile.
> www.cienciavida.cl/CBGB.htm
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hlapp at drycafe.net  Sun Mar  3 12:53:34 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sun, 3 Mar 2013 12:53:34 -0500
Subject: [Bioperl-l] GSoC 2013 is ON
Message-ID: <F68E8168-80A5-4681-9912-8655998A9F40@drycafe.net>

Forwarding on behalf of Pjotr Prins, who just volunteered to serve as OBF's GSoC admin for this year.

~~~

Game on! GSoC 2013 is ON. I am running with the OBF project
administration this year for the Google Summer of code (GSoC). 
First and foremost I want to thank Robert Buels and others for making
OBF/GSoC a success in the previous three years! This year, Robert, Chris
Fields and Hilmar Lapp will act as backup administrators.

The deadline for the OBF application for GSoC2013 as a mentoring
organisation is Friday March 29! See

 http://www.google-melange.com/gsoc/events/google/gsoc2013

Similar to previous years, each Bio* project needs to update and add project
ideas on the project's individual OBF wiki page and create links from the main
OBF page at

 http://www.open-bio.org/wiki/Google_Summer_of_Code

(we will update the main information on that page soon).

So, for each of the OBF projects that wants to do GSoC again this
year:

1. Update the list of project ideas on your project's GSoC page (BioPython,
  BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done
  or no longer relevant, etc. For an example see

    http://bioruby.open-bio.org/wiki/Google_Summer_of_Code

2. Update the final list of project ideas on the main OBF GSoC page
  to match.

    http://www.open-bio.org/wiki/Google_Summer_of_Code

3. Register with gsoc at lists.open-bio.org

4. Announce it on that list when you are ready :)

Anyone can submit a project idea! Former GSoC students are especially
encouraged to contribute ideas to the mailing lists.

Please have the updates done by Friday March 22nd. The number and quality of
the project ideas are part of the evaluation process for whether OBF is
accepted as a Summer of Code organisation again this year, so let's come up
with some good ones!

Pj. (Pjotr Prins)

Important dates: 

 * March 22nd: Finalise project ideas
 * March 29th: Deadline OBF mentoring organisation submission to Google

http://www.open-bio.org/wiki/Google_Summer_of_Code



From carandraug+dev at gmail.com  Sun Mar  3 20:58:41 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 01:58:41 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <512B3DCB.7050008@uni-wuerzburg.de>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
Message-ID: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>

On 25 February 2013 10:32, Andreas Leimbach
<andreas.leimbach at uni-wuerzburg.de> wrote:
> On 25.2.13 11:08, Carn? Draug wrote:
>>
>> I'm writing a perl module to write a description of the variance
>> between 2 sequences as described on
>> http://www.hgvs.org/mutnomen/recs-prot.html
>>
>> Basically, given 2 sequences, would returns something like "p.Lys2del
>> p.His25_Met26insGln" if those are the differences. It also accounts
>> for the existence of - characters on the sequences that may come from
>> their alignment.
>>
>> My question is, where on the project tree should I place the module?
>>
>> Also, is there something already written that would convert from 1 to
>> 3 letter code?
>>
> for your last question:
> You can convert aa strings from one to three letter code with
> 'Bio::SeqUtils'.

Thank you. I have never used Bio::SeqUtils. Not only does solve my
problem, but also seems to be the right place to insert my code.

If no one objects, I'll add a new method to Bio::SeqUtils named
"describe_mutation".

Carn?



From cjfields at illinois.edu  Sun Mar  3 22:45:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 03:45:45 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 7:58 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 25 February 2013 10:32, Andreas Leimbach
> <andreas.leimbach at uni-wuerzburg.de> wrote:
>> On 25.2.13 11:08, Carn? Draug wrote:
>>> 
>>> I'm writing a perl module to write a description of the variance
>>> between 2 sequences as described on
>>> http://www.hgvs.org/mutnomen/recs-prot.html
>>> 
>>> Basically, given 2 sequences, would returns something like "p.Lys2del
>>> p.His25_Met26insGln" if those are the differences. It also accounts
>>> for the existence of - characters on the sequences that may come from
>>> their alignment.
>>> 
>>> My question is, where on the project tree should I place the module?
>>> 
>>> Also, is there something already written that would convert from 1 to
>>> 3 letter code?
>>> 
>> for your last question:
>> You can convert aa strings from one to three letter code with
>> 'Bio::SeqUtils'.
> 
> Thank you. I have never used Bio::SeqUtils. Not only does solve my
> problem, but also seems to be the right place to insert my code.
> 
> If no one objects, I'll add a new method to Bio::SeqUtils named
> "describe_mutation".
> 
> Carn?

I'm fine with that; at some point it might be worth thinking about whether we need to organize the various *Utils modules a bit better.  As most of these export methods, they would be good targets for reorganization at some point (maybe into a general Bio::Utils namespace).

chris



From carandraug+dev at gmail.com  Sun Mar  3 23:15:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 04:15:51 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>

On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
> [...] at some point it might be worth thinking about whether we need to
> organize the various *Utils modules a bit better.  As most of these export
> methods, they would be good targets for reorganization at some point
> (maybe into a general Bio::Utils namespace).

Do you mean placing all of them into a separate Util distribution? I
think it makes more sense to keep them close to what they deal with.

If it's just moving them all into Bio::Utils:: may be a good idea. At
the moment there's not much of a model for their naming. I found these
ones (am I missing anything that does not have Utils on the name?)

Bio/Coordinate/Utils.pm
Bio/SeqUtils.pm
Bio/Search/SearchUtils.pm
Bio/Search/BlastUtils.pm
Bio/Search/Tiling/MapTileUtils.pm

Also, only the last one seems to export anything.

Carn?



From cjfields at illinois.edu  Sun Mar  3 23:50:15 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 04:50:15 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> [...] at some point it might be worth thinking about whether we need to
>> organize the various *Utils modules a bit better.  As most of these export
>> methods, they would be good targets for reorganization at some point
>> (maybe into a general Bio::Utils namespace).
> 
> Do you mean placing all of them into a separate Util distribution? I
> think it makes more sense to keep them close to what they deal with.

No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

> If it's just moving them all into Bio::Utils:: may be a good idea. At
> the moment there's not much of a model for their naming. I found these
> ones (am I missing anything that does not have Utils on the name?)
> 
> Bio/Coordinate/Utils.pm
> Bio/SeqUtils.pm
> Bio/Search/SearchUtils.pm
> Bio/Search/BlastUtils.pm
> Bio/Search/Tiling/MapTileUtils.pm
> 
> Also, only the last one seems to export anything.
> 
> Carn?


A few mentioned above.  I don't think they have to be object classes, their entire purpose is to add functionality, so a full-blown class is probably a bit overkill (no one is likely to override their behavior).  

I could also see subdividing these up: DNA, RNA, and protein specific methods as well (for instance the 1->3 letter amino acid conversions, which would never be used on DNA).  It just depends how fine-grained we want to get.  

chris


From cjfields at illinois.edu  Tue Mar  5 09:46:34 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 5 Mar 2013 14:46:34 +0000
Subject: [Bioperl-l] Quick update on BioPerl release
In-Reply-To: <511C14AA.9030107@gmail.com>
References: <118F034CF4C3EF48A96F86CE585B94BF6CE24CF5@CHIMBX5.ad.uillinois.edu>
	<511C14AA.9030107@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F79C09@CHIMBX5.ad.uillinois.edu>

Just a note to keep everyone updated: the upcoming BioPerl release hasn't dropped off my (our) radar, but it will slip probably to the beginning of next week, likely Sunday-Monday CST.  There are a couple of changes/fixes that I would like to see going in (namely the recent HMMER fixes on master among others), and not insignificantly I've been tied up with a few $job-related tasks that have eaten up my time.

chris

On Feb 13, 2013, at 4:33 PM, Florent Angly <florent.angly at gmail.com> wrote:

> On 14/02/13 01:18, Fields, Christopher J wrote:
>> I*highly*  recommend using X.Y versioning for simplicity (e.g. no more 3-point versions)
> Yes, I support the X.Y versioning as well.
> Florent
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From clarsen at vecna.com  Tue Mar  5 15:55:05 2013
From: clarsen at vecna.com (Chris Larsen)
Date: Tue, 5 Mar 2013 15:55:05 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
	->1.6.1) ?
Message-ID: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>

Hello BioPerl-l,

Issue with partial codon translation. 

At our bioinformatics resource center we are using BioPerl to translate partial sequences to amino acids. This is necessary in the case of certain virus GenBank files, which are typically untranslated from polyprotein into their final mature peptide format, and no amino acid sequence is given in the source file. We need to make one from our mat_peptide generator. However our developers are finding that in their migration from BioPerl 1.6.0 to 1.6.1, the final amino acid generated from a partial nucleotide sequence is now being dropped, and this is resulting in several hundred files being altered relative to legacy. Here is an example:

In the hepC virus genome : AB014488

The nucleotide sequence (only) is given:

caagctgtca tggacatggt ggcgggggcc cactggggag tcctagcggg ccttgcctac
tattccatgg tggggaactg ggctaaggtt ttgattgtga tgctactctt cgccggcgtt
gacgggcata cccgcgtgac ggggggggtg caaggccacg tcacctctac actcacgtcc
ctctttagac ctggggcgtc ccagaaaatt cagcttgtaa acaccaatgg cagttggcac
atcaacagga ctgccctgaa ctgcaatgac tccctccaaa ctgggttcct tgccgcgctg
ttctacacac acaagttcaa cgcgtccgga tgcccggagc gcatggccag ctgccgctcc
attgacaagt tcgaccaggg atggggtccc atcacttatg cccaacctga caactcggac
cagaggccgt attgctggca ctatgcacct cgacagtgtg gtatcgtacc cgcgtcgcag
gtgtgcggtc cagtgtattg cttcacccca agccctgttg tggtggggac gaccgatcgt
tccggtgccc ctacgtataa ctgggg

where this ends in the partial codon of 'gg'. (Dont bother, this is 188 and 2/3 aa). A biologist might know that this terminus is always going to be a Glycine, G, since the third position is irrelevant, and so we would like to extend the partial codon into another amino acid in the last 'E2' protein encoded by this genome fragment. It's not sequenced but we can infer. The viral proteins are so short, it really matters! We want that G (and SPTAVRL). However the newer BioPerl version is not giving us the last amino acid. The functionality appears to be turned off, or a default argument was changed?  Issue with -complete ?

Sorry, not good quite enough in (bio)perl to find the solution myself. Only know it is not working now, and am trying to prevent the DBA from stabbing me in the neck with a spork because 4% of the records are now diff in the new pipeline. (Partial seqs, exactly 2 of 3 bp,  non-stop terminus in the available CDS). They are not telling me that errors don't occur within a string, only at the terminus, in viral polyproteins, and only when is not a stop codon. Ergo, color me confused.

I believe this is being handled by:

Bio::Tools::CodonTable and $obj->translate().

where the docs state the method:

"Returns a string of one letter amino acid codes from 
           nucleotide sequence input. The imput (sic) can be of any length. 
(...)
if the codon is two nucleotides long and if by adding
               an a third character 'N', it codes for a single amino
               acid (with exceptions above), return that, otherwise
               return empty string."

But I defer to the much larger bioperl-l wisdom. Sorry for the complexity. The options for them seem to be to continue using the 1.6.0 version to generate the longer better string, and 1.6.1 for everything else; but I'd rather the DBA team just uses one version of BioPerl. They could also update their version to 1.6.9. But, migrating a whole industrial pipeline to a new version for a production system also isnt trivial, so rather than hoping blindly for the fix in v1.6.9, I am asking here if the functionality works for others, and for which versions, and if its truly a bug, or has been fixed or changed, and as of what version. It would be great if one tiny piece could be replaced and the whole problem vanishes...But we may find it is our problem too. 

Hoping we just have to turn on this changed functionality, but we also want to see the issue documented. Cannot find the solution in BIO's docs. Sorry Brian!

I just want all the extra [SPTAVRLG] we can get. Any guidance I will graciously convey back to the team and try to work it out.

Thanks,

Chris

PS: Chris F and Amir discuss : highly related issue: http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html

"why should CodonTable::translate() automatically 'complete' the translation for incomplete codons by default?  I would consider this a bug."
 
-- 

Christopher Larsen, Ph.D.
Sr. Scientist / Grants Manager
Vecna Medical
Phone: (240) 965-4525
Fax: (240) 547-6133

clarsen at vecna dot com
http://vecna.com

Better Technology, Better World (TM)

The contents of this message may be privileged and confidential. Therefore, if this message has been received in error, please delete it. Your receipt of this message is not intended to waive any applicable privilege. Please do not disseminate this message without the permission of the author.









From Amir_Karger at hms.harvard.edu  Wed Mar  6 13:18:13 2013
From: Amir_Karger at hms.harvard.edu (Karger, Amir)
Date: Wed, 6 Mar 2013 13:18:13 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>
Message-ID: <CD5CF244.51003%amir_karger@hms.harvard.edu>

On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:

>Hello BioPerl-l,
>
>A biologist might know that this terminus is always going to be a
>Glycine, G, since the third position is irrelevant, and so we would like
>to extend the partial codon into another amino acid in the last 'E2'
>protein encoded by this genome fragment. It's not sequenced but we can
>infer. The viral proteins are so short, it really matters! We want that G
>(and SPTAVRL). However the newer BioPerl version is not giving us the
>last amino acid. The functionality appears to be turned off, or a default
>argument was changed?  Issue with -complete ?
>
>
>
>PS: Chris F and Amir discuss : highly related issue:
>http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>
>"why should CodonTable::translate() automatically 'complete' the
>translation for incomplete codons by default?  I would consider this a
>bug."

I guess one man's bug is another man's feature.

Sorry to have ruined your pipeline.

-Amir




From cjfields at illinois.edu  Wed Mar  6 14:19:23 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 6 Mar 2013 19:19:23 +0000
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <CD5CF244.51003%amir_karger@hms.harvard.edu>
References: <CD5CF244.51003%amir_karger@hms.harvard.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D8FF30@CHIMBX5.ad.uillinois.edu>

On Mar 6, 2013, at 12:18 PM, "Karger, Amir" <Amir_Karger at hms.harvard.edu> wrote:

> On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:
> 
>> Hello BioPerl-l,
>> 
>> A biologist might know that this terminus is always going to be a
>> Glycine, G, since the third position is irrelevant, and so we would like
>> to extend the partial codon into another amino acid in the last 'E2'
>> protein encoded by this genome fragment. It's not sequenced but we can
>> infer. The viral proteins are so short, it really matters! We want that G
>> (and SPTAVRL). However the newer BioPerl version is not giving us the
>> last amino acid. The functionality appears to be turned off, or a default
>> argument was changed?  Issue with -complete ?
>> 
>> 
>> 
>> PS: Chris F and Amir discuss : highly related issue:
>> http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>> 
>> "why should CodonTable::translate() automatically 'complete' the
>> translation for incomplete codons by default?  I would consider this a
>> bug."
> 
> I guess one man's bug is another man's feature.
> 
> Sorry to have ruined your pipeline.
> 
> -Amir

Chris, Amir,

Just a note: BioPerl is now at 1.6.901 on CPAN (released in 2011) and will be at 1.6.902 sometime next week.  

IIRC (and from back-reading in that thread), the problem was one of consistency, namely that translate() from PrimarySeqI and CodonTable act differently, and that to intuit what is the 'correct' thing to do in this case was possibly wrong from the PrimarySeqI end.  We went the route of least magic and least surprise, namely to return just the translated sequence w/o guessing whether the sequence in question is complete.  

So in my opinion, the old behavior was a bug, and the new behavior is more consistent.  The magic way is still there, though; pass in '-complete => 1'.  I can check that, just in case, to make sure it works.

chris




From a0071251 at nus.edu.sg  Thu Mar  7 00:24:06 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 13:24:06 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
Message-ID: <BBEBCF29-53C3-4BCD-AE6C-33B42D8F5933@nus.edu.sg>



Dear BioPerl,


I have encountered failed tests while installing Bioperl-1.6.901 from CPAN.
i downloaded BioPerl-1.6.901.tar and ran 'tar xvfz BioPerl-1.6.901.tar'
It gave me a message saying 'tar: Error exit delayed from previous errors.' but i moved on to install using 'perl Build.PL'
it gave me a message saying that some files are missing. I just moved on again and eventually when i ran './Build test', it told me that 32//55 test programs failed and 1/2436 subtests failed.
you will find a detailed report of the errors in the attached file.

Please take a look and let me know where i have gone wrong.
I am suspecting that the problem started when i extracted .tar file, but i have no idea how to correct that.

Your help will be much appreciated.
Thank you for your time and help.


Sincerely,
Ah Jung


-------------- next part --------------
A non-text attachment was scrubbed...
Name: error_from_Bioperl_installation
Type: application/octet-stream
Size: 126548 bytes
Desc: error_from_Bioperl_installation
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0003.obj>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ATT00001.txt
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0003.txt>

From a0071251 at nus.edu.sg  Thu Mar  7 01:15:58 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 14:15:58 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
	(continued)
Message-ID: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>



Dear BioPerl,

I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
Hope this helps to clarify the problem further.

Thank you,
Ah Jung

-------------- next part --------------
A non-text attachment was scrubbed...
Name: error2
Type: application/octet-stream
Size: 71030 bytes
Desc: error2
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/363ab81b/attachment-0003.obj>

From scott at scottcain.net  Thu Mar  7 11:01:37 2013
From: scott at scottcain.net (Scott Cain)
Date: Thu, 7 Mar 2013 11:01:37 -0500
Subject: [Bioperl-l] Failed ./Build test while installing
	Bioperl-1.6.901 (continued)
In-Reply-To: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
References: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
Message-ID: <CA+JTaoxRxE5RtZuYwaW1OAG=G+TxkCQO3WC+OpCx7kzKKYoxCA@mail.gmail.com>

Hi Ah Jung,

The first problem you reported was because you didn't download the
whole tar file (the were a warning message that it was truncated, and
then messages that there were files missing); you just needed to
download it again.

For this message, you have this the first time cpan tries to install a module:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/Library/Perl/5.12/darwin-thread-multi-2level'
Do not have write permissions on '/Library/Perl/5.12/darwin-thread-multi-2level'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

When running cpan, you need to either run it as root (ie, "sudo cpan")
or configure it to use a local directory where you do have write
permission.  The former is probably easier, whereas the latter is
probably better.

Scott


On Thu, Mar 7, 2013 at 1:15 AM, Jeon Ah Jung <a0071251 at nus.edu.sg> wrote:
>
>
> Dear BioPerl,
>
> I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
> Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
> Hope this helps to clarify the problem further.
>
> Thank you,
> Ah Jung
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From liyc1989 at gmail.com  Thu Mar  7 17:52:18 2013
From: liyc1989 at gmail.com (yichao li)
Date: Thu, 7 Mar 2013 17:52:18 -0500
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
Message-ID: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>

Hi,

            In the SYSNOPSIS, it says:

my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
  for my $feat ($in->next_feature) {
    # do something with $feat (a Bio::SeqFeature::Annotated object)
  }

  my $out = Bio::FeatureIO(-format=>'bed');
  for my $feat ($seq->get_seqFeatures) {
    $out->write_feature($feat);
  }

Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
'file.bed');*

If not, an error will occur.


------------------------------------
Best wishes,
Yichao
Ohio University Bioinformatics Lab
Phone: (740)-591-1289


From ragowthaman at gmail.com  Fri Mar  8 14:41:38 2013
From: ragowthaman at gmail.com (gowtham)
Date: Fri, 8 Mar 2013 11:41:38 -0800
Subject: [Bioperl-l] Writing alignment objects read via Bio::DB::Sam
Message-ID: <CAMvwBZnuEYHCFqOwyGuTPs9CZRxWhsGhJfpSzQ_Mrm4CO5mMJA@mail.gmail.com>

Hi Every One,
I'm using Bio::DB::Sam->new(-bam='') method to read a bam file. And I am
able to query individual values of each alignment record. For example
'XM','AS', and 'AS' tags, or alignment start end positions etc. After
filtering these records for some values (eg, mismatches), i would like to
write them back into a "SAM" (preferable BAM) format.

I am not able to find a method that writes the record. Can someone help me
with this?

Though, I am able to open a new bam file for  writing using
Bio::DB::Bam->open(my.bam, 'w'), I dont know how to convert the SAM
alignment i read from (Bio::DB::SAM) to be written using this.

write1() does not accept alignment object read by Bio::DB::SAM, it accepts
objects read only by Bio::DB::BAM.


Thanks very much in advance,
Gowthaman
-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).


From witch.of.agnessi at gmail.com  Fri Mar  8 20:24:01 2013
From: witch.of.agnessi at gmail.com (witch.of.agnessi at gmail.com)
Date: Fri, 8 Mar 2013 17:24:01 -0800 (PST)
Subject: [Bioperl-l] How to find 'is_a'/'part_of' relationship using
	GO::Termfinder
Message-ID: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>

Hello All,

I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
 node. I wonder How I can extract the type of relationship,
like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
any better way to do this in Bioperl?

Thanks in advance


 


From antony.vincent.1 at ulaval.ca  Fri Mar  8 22:56:59 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Fri, 8 Mar 2013 19:56:59 -0800 (PST)
Subject: [Bioperl-l]  sh: 1: Syntax error: "(" unexpected
Message-ID: <35154292.post@talk.nabble.com>


Hi!

I'm trying to use emboss program (water or needle) with a bioperl script. I
got this error when I try the script: sh: 1: Syntax error: "(" unexpected

Here is the script:

#!/usr/bin/perl 

 # get an EMBOSS factory
  use Bio::Factory::EMBOSS;
  use Bio::AlignIO;
  use Bio::SeqIO;
  $f = Bio::Factory::EMBOSS -> new();
  # get an EMBOSS application  object from the factory
  $water = $f->program('water');
    $inputfilename = "krt1.fasta";
    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
                             '-format' => 'fasta');

    $inputfilename2 = "krt2.fasta";
    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
                             '-format' => 'fasta');
  # here is an example of running the application -
  # water can compare 1 sequence against 1 or more sequences
  # in a database using Smith-Waterman
  #this would be a list of seqs to compare 
                       # (could be just 1)
  my $wateroutfile = 'out.water';
  $water->run({-sequences => $seq_to_test,
               -seqall    => \@seqs_to_check,
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => $wateroutfile});
  # now you might want to get the alignment
  
  my $alnin = Bio::AlignIO->new(-format => 'emboss',
                                       -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }

Have you an idea of what can do this error?

Thanks!
-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From l.m.timmermans at students.uu.nl  Sat Mar  9 08:43:54 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Sat, 9 Mar 2013 14:43:54 +0100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>

On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected

The error suggests the script is interpreted by the shell instead of
perl. Are you sure the hashbang (#!) is the absolute first thing in
the file. No whitespace or BOM character in the front?

Leon


From carandraug+dev at gmail.com  Sat Mar  9 09:03:50 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:03:50 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>

On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>  wrote:
>
>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> [...] at some point it might be worth thinking about whether we need to
>>> organize the various *Utils modules a bit better.  As most of these export
>>> methods, they would be good targets for reorganization at some point
>>> (maybe into a general Bio::Utils namespace).
>>
>> Do you mean placing all of them into a separate Util distribution? I
>> think it makes more sense to keep them close to what they deal with.
>
> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

How would you define exportable? I usually don't like the idea of
having functions exported by default. Specially since it's so easy for
the user to load them themselves.

Carn?



From carandraug+dev at gmail.com  Sat Mar  9 09:47:08 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:47:08 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
	Bio::DB::EUtilities ?
Message-ID: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>

Hi

I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
module, part of bioperl-live, seems to be re-implementing pieces of
Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

According to Bio::DB::Biblio::eutils documentation, it should not be
used directly, instead should be used through Bio::DB::Biblio. This
means that it could be replaced by Bio::DB::EUtilities without any
disturbance (other than adding a dependency and as long as users have
been respecting the recommendations).

Carn?



From cjfields at illinois.edu  Sat Mar  9 10:07:20 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:07:20 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate
	of	Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
> module, part of bioperl-live, seems to be re-implementing pieces of
> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.

> According to Bio::DB::Biblio::eutils documentation, it should not be
> used directly, instead should be used through Bio::DB::Biblio. This
> means that it could be replaced by Bio::DB::EUtilities without any
> disturbance (other than adding a dependency and as long as users have
> been respecting the recommendations).
> 
> Carn?

Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

chris


From cjfields at illinois.edu  Sat Mar  9 10:05:33 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:05:33 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94D74@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:03 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>> wrote:
>> 
>>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> [...] at some point it might be worth thinking about whether we need to
>>>> organize the various *Utils modules a bit better.  As most of these export
>>>> methods, they would be good targets for reorganization at some point
>>>> (maybe into a general Bio::Utils namespace).
>>> 
>>> Do you mean placing all of them into a separate Util distribution? I
>>> think it makes more sense to keep them close to what they deal with.
>> 
>> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?
> 
> How would you define exportable? I usually don't like the idea of
> having functions exported by default. Specially since it's so easy for
> the user to load them themselves.
> 
> Carn?

Yes, I agree (no export by default).

chris


From carandraug+dev at gmail.com  Sat Mar  9 16:20:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 21:20:51 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>

On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>> module, part of bioperl-live, seems to be re-implementing pieces of
>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>
> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>
>> According to Bio::DB::Biblio::eutils documentation, it should not be
>> used directly, instead should be used through Bio::DB::Biblio. This
>> means that it could be replaced by Bio::DB::EUtilities without any
>> disturbance (other than adding a dependency and as long as users have
>> been respecting the recommendations).
>>
>> Carn?
>
> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

So I was looking at this but seems that would cause an issue with
circular dependency. Not at module level, but at distribution level
(Bio-Eutilities is dependent on bioperl-live and bioperl-live
dependent on Bio-EUtilities because of Bio::DB::Biblio).

This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
Could this be done and a separate distribution created for it? None of
the empty repositories seems fitting for it.

Carn?



From cjfields at illinois.edu  Sat Mar  9 17:06:41 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 22:06:41 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>


On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>>> module, part of bioperl-live, seems to be re-implementing pieces of
>>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>> 
>> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>> 
>>> According to Bio::DB::Biblio::eutils documentation, it should not be
>>> used directly, instead should be used through Bio::DB::Biblio. This
>>> means that it could be replaced by Bio::DB::EUtilities without any
>>> disturbance (other than adding a dependency and as long as users have
>>> been respecting the recommendations).
>>> 
>>> Carn?
>> 
>> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).
> 
> So I was looking at this but seems that would cause an issue with
> circular dependency. Not at module level, but at distribution level
> (Bio-Eutilities is dependent on bioperl-live and bioperl-live
> dependent on Bio-EUtilities because of Bio::DB::Biblio).
> 
> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
> Could this be done and a separate distribution created for it? None of
> the empty repositories seems fitting for it.
> 
> Carn?

Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

chris





From carandraug+dev at gmail.com  Sat Mar  9 22:06:02 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 10 Mar 2013 03:06:02 +0000
Subject: [Bioperl-l] graphics of gene distribution through a genome interval
Message-ID: <CAPOrs_1BwNeGLse000t6rmNEhneP_svosM2KYhMO+8OO6JrZ-w@mail.gmail.com>

Hi everyone

I was wondering if anyone knows any tools to produce this type of
diagram? http://picpaste.com/1fqB4e8h.png It a piece of genome with
some gene positions marked. And it has nice "zoom-in boxes" around
some more cluttered regions. I've seen these more than once but do not
know how to generate one. Could someone give me a pointer?

Thanks,
Carn?



From antony.vincent.1 at ulaval.ca  Sun Mar 10 09:17:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 06:17:09 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From Russell.Smithies at agresearch.co.nz  Sun Mar 10 16:30:36 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 11 Mar 2013 09:30:36 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>

I'll get in first and say it's best to 'use strict', and 'use warnings'  ;-)

Perhaps some of the params to water have changed? It looks like it wants filenames, not objects.
I get the same errors with your code - which I think is coming from water.

If I do this it seems to work OK:
---------------------------------------
#!/usr/bin/perl

# get an EMBOSS factory
use Bio::Factory::EMBOSS;
use Bio::AlignIO;
use Bio::SeqIO;

use strict;
use warnings;

my $f = Bio::Factory::EMBOSS -> new();
# get an EMBOSS application  object from the factory
my $water = $f->program('water');
my $wateroutfile = 'out.water';
$water->run({  -verbose => 1,
               -asequence => 'krt1.fasta',
               -bsequence => 'krt2.fasta',
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => 'out.water'});
------------------------------------------------


illustrious$ cat out.water
########################################
# Program: water
# Rundate: Mon 11 Mar 2013 09:29:36
# Commandline: water
#    -gapopen 10.0
#    -gapextend 0.5
#    -outfile out.water
#    -asequence krt1.fasta
#    -verbose 1
#    -bsequence krt2.fasta
#    -auto
# Align_format: srspair
# Report_file: out.water
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: K2C1_HUMAN
# 2: K22E_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     436/667 (65.4%)
# Similarity:   499/667 (74.8%)
# Gaps:          78/667 (11.7%)
# Score: 2023.5
#
#
#=======================================

K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR     45
                     ||.|.|.:|..|.||     |||||||.:....||:|||
K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------     39

K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG     91
                      .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA     86

K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG    130
                     ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG    136

K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR    179
                     | ||||.|||         ||||.||::||||||||||::|||||.||::
K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ    177

K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP    229
                     ||||||:|||:|||||||||||||||||||||||||||::..||..||||
K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP    227

K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN    279
                     .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA    277

K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ    329
                     |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS    327

K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE    379
                     :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE    377

K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA    429
                     ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA    427

K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI    479
                     |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI    477

K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG    521
                     ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG    525

K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS    568
                        ||||.||.|||||||...||.||.||| ||.        |||| |||
K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS    565

K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR    616
                     |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG    610

K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
                     |..|||    |||||||
K22E_HUMAN       611 GYGSGG----GGSSSVK    623


#---------------------------------------
#---------------------------------------



--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Monday, 11 March 2013 2:17 a.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From antony.vincent.1 at ulaval.ca  Sun Mar 10 17:59:51 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 14:59:51 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
	<35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
Message-ID: <35158468.post@talk.nabble.com>


That's works! Thanks a lot!

Smithies, Russell wrote:
> 
> I'll get in first and say it's best to 'use strict', and 'use warnings' 
> ;-)
> 
> Perhaps some of the params to water have changed? It looks like it wants
> filenames, not objects.
> I get the same errors with your code - which I think is coming from water.
> 
> If I do this it seems to work OK:
> ---------------------------------------
> #!/usr/bin/perl
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> 
> use strict;
> use warnings;
> 
> my $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> my $water = $f->program('water');
> my $wateroutfile = 'out.water';
> $water->run({  -verbose => 1,
>                -asequence => 'krt1.fasta',
>                -bsequence => 'krt2.fasta',
>                -gapopen   => '10.0',
>                -gapextend => '0.5',
>                -outfile   => 'out.water'});
> ------------------------------------------------
> 
> 
> illustrious$ cat out.water
> ########################################
> # Program: water
> # Rundate: Mon 11 Mar 2013 09:29:36
> # Commandline: water
> #    -gapopen 10.0
> #    -gapextend 0.5
> #    -outfile out.water
> #    -asequence krt1.fasta
> #    -verbose 1
> #    -bsequence krt2.fasta
> #    -auto
> # Align_format: srspair
> # Report_file: out.water
> ########################################
> 
> #=======================================
> #
> # Aligned_sequences: 2
> # 1: K2C1_HUMAN
> # 2: K22E_HUMAN
> # Matrix: EBLOSUM62
> # Gap_penalty: 10.0
> # Extend_penalty: 0.5
> #
> # Length: 667
> # Identity:     436/667 (65.4%)
> # Similarity:   499/667 (74.8%)
> # Gaps:          78/667 (11.7%)
> # Score: 2023.5
> #
> #
> #=======================================
> 
> K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR    
> 45
>                      ||.|.|.:|..|.||     |||||||.:....||:|||
> K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------    
> 39
> 
> K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG    
> 91
>                       .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
> K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA    
> 86
> 
> K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG   
> 130
>                      ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
> K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG   
> 136
> 
> K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR   
> 179
>                      | ||||.|||         ||||.||::||||||||||::|||||.||::
> K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ   
> 177
> 
> K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP   
> 229
>                      ||||||:|||:|||||||||||||||||||||||||||::..||..||||
> K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP   
> 227
> 
> K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN   
> 279
>                      .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
> K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA   
> 277
> 
> K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ   
> 329
>                      |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
> K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS   
> 327
> 
> K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE   
> 379
>                      :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
> K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE   
> 377
> 
> K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA   
> 429
>                      ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
> K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA   
> 427
> 
> K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI   
> 479
>                      |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
> K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI   
> 477
> 
> K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG   
> 521
>                      ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
> K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG   
> 525
> 
> K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS   
> 568
>                         ||||.||.|||||||...||.||.||| ||.        |||| |||
> K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS   
> 565
> 
> K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR   
> 616
>                      |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
> K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG   
> 610
> 
> K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
>                      |..|||    |||||||
> K22E_HUMAN       611 GYGSGG----GGSSSVK    623
> 
> 
> #---------------------------------------
> #---------------------------------------
> 
> 
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Monday, 11 March 2013 2:17 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it
> like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this
> why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl
>>> script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context:
> http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35158468.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From liamelbourne at me.com  Sat Mar  9 04:18:34 2013
From: liamelbourne at me.com (Liam Elbourne)
Date: Sat, 09 Mar 2013 20:18:34 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <7A059EB2-147A-4B26-B321-DEB40D1693EC@me.com>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
>  use Bio::Factory::EMBOSS;
>  use Bio::AlignIO;
>  use Bio::SeqIO;
>  $f = Bio::Factory::EMBOSS -> new();
>  # get an EMBOSS application  object from the factory
>  $water = $f->program('water');
>    $inputfilename = "krt1.fasta";
>    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                             '-format' => 'fasta');
> 
>    $inputfilename2 = "krt2.fasta";
>    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                             '-format' => 'fasta');
>  # here is an example of running the application -
>  # water can compare 1 sequence against 1 or more sequences
>  # in a database using Smith-Waterman
>  #this would be a list of seqs to compare 
>                       # (could be just 1)
>  my $wateroutfile = 'out.water';
>  $water->run({-sequences => $seq_to_test,
>               -seqall    => \@seqs_to_check,
>               -gapopen   => '10.0',
>               -gapextend => '0.5',
>               -outfile   => $wateroutfile});
>  # now you might want to get the alignment
> 
>  my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                       -file   => $wateroutfile);
> 
>  while ( my $aln = $alnin->next_aln ) {
>      # process the alignment -- these will be Bio::SimpleAlign objects
>  }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From antony.vincent.1 at ulaval.ca  Sat Mar  9 13:24:43 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 10:24:43 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From liam.elbourne at mq.edu.au  Sat Mar  9 06:39:44 2013
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Sat, 9 Mar 2013 22:39:44 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <0C3E5EF2-9A20-4C33-94B7-93F242E69704@mq.edu.au>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> $water = $f->program('water');
>   $inputfilename = "krt1.fasta";
>   $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                            '-format' => 'fasta');
> 
>   $inputfilename2 = "krt2.fasta";
>   @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                            '-format' => 'fasta');
> # here is an example of running the application -
> # water can compare 1 sequence against 1 or more sequences
> # in a database using Smith-Waterman
> #this would be a list of seqs to compare 
>                      # (could be just 1)
> my $wateroutfile = 'out.water';
> $water->run({-sequences => $seq_to_test,
>              -seqall    => \@seqs_to_check,
>              -gapopen   => '10.0',
>              -gapextend => '0.5',
>              -outfile   => $wateroutfile});
> # now you might want to get the alignment
> 
> my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                      -file   => $wateroutfile);
> 
> while ( my $aln = $alnin->next_aln ) {
>     # process the alignment -- these will be Bio::SimpleAlign objects
> }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 235 bytes
Desc: Message signed with OpenPGP using GPGMail
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130309/0fd852ec/attachment-0003.bin>

From antony.vincent.1 at ulaval.ca  Sat Mar  9 21:59:26 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 18:59:26 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From sidd.basu at gmail.com  Mon Mar 11 13:16:45 2013
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Mon, 11 Mar 2013 12:16:45 -0500
Subject: [Bioperl-l] Re: How to find 'is_a'/'part_of' relationship
	using	GO::Termfinder
In-Reply-To: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
References: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
Message-ID: <513e1181.aade320a.5bee.ffff87da@mx.google.com>

Hi, 

On Fri, 08 Mar 2013, witch.of.agnessi at gmail.com wrote:

> Hello All,
> 
> I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
>  node. I wonder How I can extract the type of relationship,
> like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
> any better way to do this in Bioperl?

You could use the Bioperl's ontology module in this case. For example,  here is how
you could start with ...

1. Parse gene_ontology obo file with Bio::OntologyIO
https://metacpan.org/module/Bio::OntologyIO

2. Once you get the ontology object(Bio::Ontology::Ontology), you could
use the *find_terms*
https://metacpan.org/module/Bio::Ontology::Ontology#find_terms
to get your term objects.

3. Then use the graph lookup methods
   such as *get_relationships*, get_child_terms, get_parent_terms,
   get_ancestor_terms that takes a term and relationship objects to extract
   whatever connection you are looking for. 

Hope this helps, 
-siddhartha


   


> 
> Thanks in advance
> 
> 
>  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From Russell.Smithies at agresearch.co.nz  Mon Mar 11 14:09:56 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 12 Mar 2013 07:09:56 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>

I suspect that there's several versions of water and the parameters have changed.
This is the version I'm using and I can reproduce the errors:

intrepid$ water -h
Smith-Waterman local alignment of sequences
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -gapopen            float      [10.0 for any sequence] The gap open penalty
                                  is the score taken away when a gap is
                                  created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value assumes you are using the EBLOSUM62
                                  matrix for protein sequences, and the
                                  EDNAFULL matrix for nucleotide sequences.
                                  (Number from 0.000 to 100.000)
   -gapextend          float      [0.5 for any sequence] The gap extension
                                  penalty is added to the standard gap penalty
                                  for each base or residue in the gap. This
                                  is how long gaps are penalized. Usually you
                                  will expect a few long gaps rather than many
                                  short gaps, so the gap extension penalty
                                  should be lower than the gap penalty. An
                                  exception is where one or both sequences are
                                  single reads with possible sequencing
                                  errors in which case you would expect many
                                  single base gaps. You can get this result by
                                  setting the gap open penalty to zero (or
                                  very low) and using the gap extension
                                  penalty to control gap scoring. (Number from
                                  0.000 to 10.000)
  [-outfile]           align      [*.water] Output alignment file name
                                  (default -aformat srspair)

   Additional (Optional) qualifiers:
   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.

   Advanced (Unprompted) qualifiers:
   -[no]brief          boolean    [Y] Brief identity and similarity

   General qualifiers:
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Sunday, 10 March 2013 3:59 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From cjfields at illinois.edu  Mon Mar 11 16:57:59 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 11 Mar 2013 20:57:59 +0000
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
References: <35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D96D47@CHIMBX5.ad.uillinois.edu>

I think the EMBOSS code checks the ACD file for whatever version of EMBOSS is installed, parses the parameters out of that, and uses those for input.  I don't remember if it accepts a Bio::Seq as input (I don't recall it doing so), but if it does then we should file that as a bug.

chris

On Mar 11, 2013, at 1:09 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> I suspect that there's several versions of water and the parameters have changed.
> This is the version I'm using and I can reproduce the errors:
> 
> intrepid$ water -h
> Smith-Waterman local alignment of sequences
> Version: EMBOSS:6.5.0.0
> 
>   Standard (Mandatory) qualifiers:
>  [-asequence]         sequence   Sequence filename and optional format, or
>                                  reference (input USA)
>  [-bsequence]         seqall     Sequence(s) filename and optional format, or
>                                  reference (input USA)
>   -gapopen            float      [10.0 for any sequence] The gap open penalty
>                                  is the score taken away when a gap is
>                                  created. The best value depends on the
>                                  choice of comparison matrix. The default
>                                  value assumes you are using the EBLOSUM62
>                                  matrix for protein sequences, and the
>                                  EDNAFULL matrix for nucleotide sequences.
>                                  (Number from 0.000 to 100.000)
>   -gapextend          float      [0.5 for any sequence] The gap extension
>                                  penalty is added to the standard gap penalty
>                                  for each base or residue in the gap. This
>                                  is how long gaps are penalized. Usually you
>                                  will expect a few long gaps rather than many
>                                  short gaps, so the gap extension penalty
>                                  should be lower than the gap penalty. An
>                                  exception is where one or both sequences are
>                                  single reads with possible sequencing
>                                  errors in which case you would expect many
>                                  single base gaps. You can get this result by
>                                  setting the gap open penalty to zero (or
>                                  very low) and using the gap extension
>                                  penalty to control gap scoring. (Number from
>                                  0.000 to 10.000)
>  [-outfile]           align      [*.water] Output alignment file name
>                                  (default -aformat srspair)
> 
>   Additional (Optional) qualifiers:
>   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
>                                  This is the scoring matrix file used when
>                                  comparing sequences. By default it is the
>                                  file 'EBLOSUM62' (for proteins) or the file
>                                  'EDNAFULL' (for nucleic sequences). These
>                                  files are found in the 'data' directory of
>                                  the EMBOSS installation.
> 
>   Advanced (Unprompted) qualifiers:
>   -[no]brief          boolean    [Y] Brief identity and similarity
> 
>   General qualifiers:
>   -help               boolean    Report command line options and exit. More
>                                  information on associated and general
>                                  qualifiers can be found with -help -verbose
> 
> 
> --Russell
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Sunday, 10 March 2013 3:59 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From bosborne11 at verizon.net  Tue Mar 12 11:04:36 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 12 Mar 2013 11:04:36 -0400
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
In-Reply-To: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
References: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
Message-ID: <C262A6D6-3967-4290-90FF-738A1A8CCC3F@verizon.net>

Yichao,

Fixed. Thank you for pointing that out.

Brian O.


On Mar 7, 2013, at 5:52 PM, yichao li <liyc1989 at gmail.com> wrote:

> Hi,
> 
>            In the SYSNOPSIS, it says:
> 
> my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
>  for my $feat ($in->next_feature) {
>    # do something with $feat (a Bio::SeqFeature::Annotated object)
>  }
> 
>  my $out = Bio::FeatureIO(-format=>'bed');
>  for my $feat ($seq->get_seqFeatures) {
>    $out->write_feature($feat);
>  }
> 
> Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
> 'file.bed');*
> 
> If not, an error will occur.
> 
> 
> ------------------------------------
> Best wishes,
> Yichao
> Ohio University Bioinformatics Lab
> Phone: (740)-591-1289
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Tue Mar 12 18:43:05 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 12 Mar 2013 22:43:05 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>

On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>> Could this be done and a separate distribution created for it? None of
>> the empty repositories seems fitting for it.
>>
>
> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

Could you (or some other admin) prepare a separate Bio-biblio
repository? I'm splitting them now and need a repo to push into.

Thanks,
Carn?



From cjfields at illinois.edu  Tue Mar 12 19:42:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 12 Mar 2013 23:42:11 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>

Done:

https://github.com/bioperl/Bio-Biblio

chris

On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>> Could this be done and a separate distribution created for it? None of
>>> the empty repositories seems fitting for it.
>>> 
>> 
>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
> 
> Could you (or some other admin) prepare a separate Bio-biblio
> repository? I'm splitting them now and need a repo to push into.
> 
> Thanks,
> Carn?




From therealsisterdot at gmail.com  Mon Mar 11 06:31:42 2013
From: therealsisterdot at gmail.com (sisterdot)
Date: Mon, 11 Mar 2013 03:31:42 -0700 (PDT)
Subject: [Bioperl-l] parsing psiblast + ?
Message-ID: <97a3d346-c5dd-41f4-b71d-042cc92f7ee9@googlegroups.com>

hey hey, 

i am using perl v5.10.0 and Bio::SearchIO 1.006901

i would like to use psiblast 2.2.27 + (instead of blastpgp), but parsing 
via  
new Bio::SearchIO(-format => "blast",-file => "$file")
doesn't seem to work well- individual iterations are interpreted as 
separate results.

Bio::SearchIO doesn't seem to really understand "psiblast +" default 
pairwise output, or am i mistaken?
if i am not mistaken, are there alternatives in Bioperl for parsing 
"psiblast +" with the default "-outfmt 0"?

thanks a lot
sis


From scott at scottcain.net  Wed Mar 13 22:51:55 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 13 Mar 2013 22:51:55 -0400
Subject: [Bioperl-l] Early registration for GMOD meeting closes in one week
Message-ID: <CA+JTaozZFOWKcsZ0bDqUS1mD_E2kWLUGi_1bA+bGj6GKb9eJdg@mail.gmail.com>

Hello,

The GMOD meeting is in Cambridge, England on April 5-6 (right before
the Biocurator meeting) and early registration closes March 21 (in one
week).  It is shaping up to be a good meeting with several interesting
talks scheduled.  Please try to make it!  For more information on the
meeting, see the meeting page:

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

and to save some money on your registration, go to

  http://gmod2013.eventbrite.com/

before March 21 to register.

If you'd like to give a talk at the meeting please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From carandraug+dev at gmail.com  Thu Mar 14 19:55:27 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 14 Mar 2013 23:55:27 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>

On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>> Could this be done and a separate distribution created for it? None of
>>>> the empty repositories seems fitting for it.
>>>>
>>>
>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>
>> Could you (or some other admin) prepare a separate Bio-biblio
>> repository? I'm splitting them now and need a repo to push into.
>>
>
> Done:
>
> https://github.com/bioperl/Bio-Biblio

Thanks, I'm trying to prepare a release of the Bio-biblio distribution
soon. I'd like to do a 1.7 release first. One with minimal changes
compared to the current bioperl-live. Could someone give me
co-maintenance of the Bio::Biblio namespace? Or should I just prepare
everything for the release and wait for someone else to just accept
it? Also, the Bio-biblio distribution also has modules on the
Bio::DB::biblio namespace.

Carn?



From carandraug+dev at gmail.com  Thu Mar 14 21:21:16 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 01:21:16 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
Message-ID: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>

Hi

I'm using dist::zilla and found the BioPerl plugin. I noticed that the
bug tracker information is set to

  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
  bugtracker.mailto = bug-${dist}@rt.cpan.org

shouldn't they set for https://redmine.open-bio.org/projects/bioperl?

Carn?



From cjfields at illinois.edu  Thu Mar 14 21:59:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 01:59:53 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1CF@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 6:55 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>>> Could this be done and a separate distribution created for it? None of
>>>>> the empty repositories seems fitting for it.
>>>>> 
>>>> 
>>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>> 
>>> Could you (or some other admin) prepare a separate Bio-biblio
>>> repository? I'm splitting them now and need a repo to push into.
>>> 
>> 
>> Done:
>> 
>> https://github.com/bioperl/Bio-Biblio
> 
> Thanks, I'm trying to prepare a release of the Bio-biblio distribution
> soon. I'd like to do a 1.7 release first. One with minimal changes
> compared to the current bioperl-live. Could someone give me
> co-maintenance of the Bio::Biblio namespace? Or should I just prepare
> everything for the release and wait for someone else to just accept
> it? Also, the Bio-biblio distribution also has modules on the
> Bio::DB::biblio namespace.
> 
> Carn?

That's fine; you can actually do a point release (say, 1.7) and list the proper Bio::* dependencies you need.  I wouldn't list Bio::Root::Root specifically.  

Does anyone here have a problem with Carn? taking co-maintenance of these modules on CPAN?  Please speak up over the next few days, otherwise I'll go ahead and grant it.  Would be nice to have someone looking after these.

chris


From cjfields at illinois.edu  Thu Mar 14 22:00:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:00:43 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>

Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?

chris

On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
> bug tracker information is set to
> 
>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>  bugtracker.mailto = bug-${dist}@rt.cpan.org
> 
> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Thu Mar 14 22:04:23 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 02:04:23 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>

On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>> bug tracker information is set to
>>
>>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>  bugtracker.mailto = bug-${dist}@rt.cpan.org
>>
>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>
>> Carn?
>>
>
> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>
> chris

Yes it is. But only the version 0.01.



From cjfields at illinois.edu  Thu Mar 14 22:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:41:28 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>> bug tracker information is set to
>>> 
>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>> 
>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>> 
>>> Carn?
>>> 
>> 
>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>> 
>> chris
> 
> Yes it is. But only the version 0.01.

Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

chris


From carandraug+dev at gmail.com  Thu Mar 14 23:15:11 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 03:15:11 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>

On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>> bug tracker information is set to
>>>>
>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>
>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>
>>>> Carn?
>>>>
>>>
>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>
>>> chris
>>
>> Yes it is. But only the version 0.01.
>
> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

I think I got it working with the BioPerl bundle. It passes all tests.
Now I was trying to set Pod::Weaver to write the feedback section
automatically but might be better to set it up as pasrt of the BioPerl
bundle.

Carn?



From fossandonc at hotmail.com  Fri Mar 15 10:26:44 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 11:26:44 -0300
Subject: [Bioperl-l] Bug #2936
Message-ID: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>

Hello,

Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven?t
received any feedback yet.

https://redmine.open-bio.org/issues/2936

 

Probably everybody is busy, so I would like to ask only if the proposed fix
is acceptable. If the fix were fine, I could prepare changes in my forked
repo, add tests (in ?t/Seq/PrimarySeq.t????) and make a pull request. What
do you think?

 

Cheers,

 

--

Francisco J. Ossandon

Bioinformatician.

Ph.D. Candidate, University Andres Bello.

Center for Bioinformatics and Genome Biology,

Fundacion Ciencia para la Vida.

Santiago, Chile.

 <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm

 




From cjfields at illinois.edu  Fri Mar 15 10:46:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 14:46:11 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9FAFE@CHIMBX5.ad.uillinois.edu>

Sure, a pull request would be good.  I suggest making sure you are in sync with the 'master' branch first, but I don't think you'll run into conflicts with that.  

My guess is we'll need to pull this into a branch and test rigorously first if it is to go into a bioperl 1.6.  One of the (many?) problems with Bio::Location is that it assumes all features are on linear chromosomes, so there is quite a bit of logic/magic built-in with that assumption that tends to be wrong (e.g. sort order of sublocations and so on, which breaks split locations).  

Frankly, I think we could really simplify this logic so that it is less magic, less fuzzy, and it would bite us in the ass a lot less, but of course this breaks backcompat.  So, my feeling is such fixes would be handled better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com> wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven't
> received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the proposed fix
> is acceptable. If the fix were fine, I could prepare changes in my forked
> repo, add tests (in "t/Seq/PrimarySeq.t"???) and make a pull request. What
> do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From mastarr9 at gmail.com  Fri Mar 15 00:54:49 2013
From: mastarr9 at gmail.com (Matt)
Date: Thu, 14 Mar 2013 23:54:49 -0500
Subject: [Bioperl-l] using a bioperl module after installing.
Message-ID: <5142A999.7090308@gmail.com>

I used "fink" to install bioperl. I see that the installation had no 
problems and that the Bio/SeqIO module exists in hard 
drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually 
make any use of bioperl in a script.

On the bioperl wiki I see that this common error message comes from the 
module sometimes not being installed but, in my case, I think that it is 
installed but "lost".  How can I reinstall or move or change the path to 
make bioperl actually work?
Thanks!

Information:

  * perl v5.10.0
  * Bioperl-pm5.10.0
  * OSX 10.6.8
  * Goal: To simply use a bioperl module
  * The code that gives the error (Using komodo edit):
      o #!/usr/bin/perl -w
        use strict;
        require Bio::SeqiO;
  * The error message:
      o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
        /Library/Perl/Updates/5.10.0
        /System/Library/Perl/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/5.10.0
        /Library/Perl/5.10.0/darwin-thread-multi-2level
        /Library/Perl/5.10.0
        /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
        /Network/Library/Perl/5.10.0 /Network/Library/Perl
        /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
        test.pl line 3.



From mhague at mail.sfsu.edu  Fri Mar 15 15:21:45 2013
From: mhague at mail.sfsu.edu (Michael Hague)
Date: Fri, 15 Mar 2013 12:21:45 -0700
Subject: [Bioperl-l] PopGen Question
Message-ID: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>

Hello,
I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:


use Bio::AlignIO;
use Bio::PopGen::Utilities;
use Bio::PopGen::Statistics;
use Bio::PopGen::Population;

my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
                           				 -format => 'fasta');
my $aln1 = $io1->next_aln;


my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
													-include_monomorphic => 1);

my $stats1 = Bio::PopGen::Statistics->new();
my $D1 = $stats1->tajima_D($pop1);
my $theta1  = $stats1->theta($pop1);
my $segsites1 = $stats1->segregating_sites_count($pop1);

print "\nPopulation #1:\n";
print "Number of segregating sites = $segsites1\n";
print "Tajima\'s D = $D1\n";
print "Watterson\'s theta = $theta1\n\n";

However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?

Thanks so much for the help,
Mike



From cjfields at illinois.edu  Fri Mar 15 16:04:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 20:04:37 +0000
Subject: [Bioperl-l] using a bioperl module after installing.
In-Reply-To: <5142A999.7090308@gmail.com>
References: <5142A999.7090308@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA020F@CHIMBX5.ad.uillinois.edu>

Even if you use fink, you may still need to set the PERL5LIB path to point to that location.  Have you done that?

chris
 
On Mar 14, 2013, at 11:54 PM, Matt <mastarr9 at gmail.com> wrote:

> I used "fink" to install bioperl. I see that the installation had no problems and that the Bio/SeqIO module exists in hard drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually make any use of bioperl in a script.
> 
> On the bioperl wiki I see that this common error message comes from the module sometimes not being installed but, in my case, I think that it is installed but "lost".  How can I reinstall or move or change the path to make bioperl actually work?
> Thanks!
> 
> Information:
> 
> * perl v5.10.0
> * Bioperl-pm5.10.0
> * OSX 10.6.8
> * Goal: To simply use a bioperl module
> * The code that gives the error (Using komodo edit):
>     o #!/usr/bin/perl -w
>       use strict;
>       require Bio::SeqiO;
> * The error message:
>     o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
>       /Library/Perl/Updates/5.10.0
>       /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/5.10.0
>       /Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Library/Perl/5.10.0
>       /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Network/Library/Perl/5.10.0 /Network/Library/Perl
>       /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
>       test.pl line 3.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From fossandonc at hotmail.com  Fri Mar 15 17:36:53 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 18:36:53 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <001d01ce2191$60406310$20c12930$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
Message-ID: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>

Ok,  I did the changes and added a pull request in the repository. All the
tests in "t/Seq/PrimarySeq.t" keeps passing (except the TODOs), including
the ones I added. Everything seems fine on my end.

About the Location/Split module, the lines that I don?t agree at all are the
ones that reverse the segment order in to_FTstring:
	# If the split type is join, the order is important;
	# otherwise must be 5'->3' regardless
	my @locs = ($stype eq 'join' && (!$guide && $strand == -1)) ?
	           reverse $self->sub_Location() : $self->sub_Location() ;

It don?t make sense to me to do that, because doing that you get coordinates
that will NOT give you the expected nucleotide sequence. Another thing that
is weird to me is that the sublocations are free to have different strands
values (like the first being positive strand and the second being negative
strand), since I can't think of one example where that can happen in real
genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
have sublocations in opposite strands at the same time and then extract the
sequence, so I wonder if I'm wrong and there are real cases like that...

As you say, those things would have to wait until later, but at least this
particular bug should be closed. =)

Regards,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: viernes, 15 de marzo de 2013 11:46
Para: Francisco J. Ossand?n
CC: bioperl mailing list
Asunto: Re: [Bioperl-l] Bug #2936

Sure, a pull request would be good.  I suggest making sure you are in sync
with the 'master' branch first, but I don't think you'll run into conflicts
with that.  

My guess is we'll need to pull this into a branch and test rigorously first
if it is to go into a bioperl 1.6.  One of the (many?) problems with
Bio::Location is that it assumes all features are on linear chromosomes, so
there is quite a bit of logic/magic built-in with that assumption that tends
to be wrong (e.g. sort order of sublocations and so on, which breaks split
locations).  

Frankly, I think we could really simplify this logic so that it is less
magic, less fuzzy, and it would bite us in the ass a lot less, but of course
this breaks backcompat.  So, my feeling is such fixes would be handled
better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com>
wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but 
> haven't received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the 
> proposed fix is acceptable. If the fix were fine, I could prepare 
> changes in my forked repo, add tests (in "t/Seq/PrimarySeq.t"???) and 
> make a pull request. What do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From p.j.a.cock at googlemail.com  Sat Mar 16 08:46:22 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sat, 16 Mar 2013 12:46:22 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
Message-ID: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>

On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>
> ... Another thing that
> is weird to me is that the sublocations are free to have different strands
> values (like the first being positive strand and the second being negative
> strand), since I can't think of one example where that can happen in real
> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
> have sublocations in opposite strands at the same time and then extract the
> sequence, so I wonder if I'm wrong and there are real cases like that...
>

This is a real biological phenomena - trans-splicing, often in tRNA genes,
for example:
http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced

As a result the BioPerl / BioSQL / Biopython etc location models do have
to cope with this corner case.  Worse, there are examples where pieces
from different chromosomes are spliced together - which is even harder
to deal with - like my favourite pathological example, nad1 in NC_016406
(and NC_016402), which has the following GenBank location string:

join(complement(149815..150200),
complement(295492..295573),complement(293787..293978),
NC_016402.1:6618..6676,181647..181905)

See also:
http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html

Peter



From cjfields at illinois.edu  Sat Mar 16 10:02:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 16 Mar 2013 14:02:12 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA0D59@CHIMBX5.ad.uillinois.edu>

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different strands
>> values (like the first being positive strand and the second being negative
>> strand), since I can't think of one example where that can happen in real
>> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
>> have sublocations in opposite strands at the same time and then extract the
>> sequence, so I wonder if I'm wrong and there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA genes,
> for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do have
> to cope with this corner case.  Worse, there are examples where pieces
> from different chromosomes are spliced together - which is even harder
> to deal with - like my favourite pathological example, nad1 in NC_016406
> (and NC_016402), which has the following GenBank location string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used for Bio::Location deals with cases like this, but there is an assumption made to deal with some cases like this that is wrong for others (say, circular chromosomes where a feature wraps the origin, where sorting messes things up).  It really needs a top to bottom overhaul to be explicit about the join, but such an overhaul will break some expected behavior, hence my suggestion of putting this in a bioperl v2.

chris


From carandraug+dev at gmail.com  Sat Mar 16 18:27:31 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 16 Mar 2013 22:27:31 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
Message-ID: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>

On 15 March 2013 03:15, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>>> bug tracker information is set to
>>>>>
>>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>>
>>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>>
>>>>> Carn?
>>>>>
>>>>
>>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>>
>>>> chris
>>>
>>> Yes it is. But only the version 0.01.
>>
>> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)
>
> I think I got it working with the BioPerl bundle. It passes all tests.
> Now I was trying to set Pod::Weaver to write the feedback section
> automatically but might be better to set it up as pasrt of the BioPerl
> bundle.

I made a bunch of changes to the BioPerl bundle. I didn't touched the
podweaver part, I just wanted to get a feel of it first, as this was
new stuff to me. I replaced some of the code on the bundle with
plugins that have since been written, and renamed the options so that
they match the option names of the plugins being used.

I do believe that these options are an improvement but since it's a
lot of changes and behaves differently from the previous version, I
created a fork and a branch on my own repo. If no one opposes I will
push them to the main repo.

https://github.com/carandraug/dist-zilla-pluginbundle-bioperl/blob/purging/lib/Dist/Zilla/PluginBundle/BioPerl.pm

Carn?



From fossandonc at hotmail.com  Sun Mar 17 23:09:17 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 18 Mar 2013 00:09:17 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>	<001d01ce2191$60406310$20c12930$@illinois.edu>	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
	<000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
Message-ID: <SNT133-ds9166254353FA597757A40CFE80@phx.gbl>

Wow, trans-splicing is a phenomena I was not aware about, thanks for telling
me. Then, the Guide Strand of the Split-location object must always check if
all the sublocations are present in the same strand; so if all sublocations
are positive the Guide have to be positive, if all are negative the Guide
have to be negative as well, and if there is a mix of strands in
sublocations the Guide have to be undef... The changes I made in flip_strand
didn?t check for the strand consistency in the sublocations when setting the
Guide Strand, so I have to add that.

Ok, how about this, in the following lines I will analyze all possibilities
for location coordinates, step by step, from simpler to complex. Please
follow my reasoning in every step and tell me if there is something you
don?t agree, so I can work on the code and use these cases as tests, and
then make another pull request. Let?s see when there is a reversal of the
sublocations order needed and when is not. For this time, I will only check
cases where the DNA comes from the same chromosome/plasmid/contig


One thing to keep in mind is that the flipped coordinates should reconstruct
the reverse-complement (revcom) of the original sequence.

Example sequence used below (fictional 20bp circular plasmid):
AAAAACCCCCGGGGGTTTTT


### Reasoning: For the following cases, where ALL segments are in the same
strand, NO ORDER REVERSAL is needed because for the complement-strand
sequences the code can join all the positive sequences first and then
complement it complete at the final step. Also, since all segments are in
the same strand, Guide Strand have to be set with the same value than the
sublocations.

# Single location
Coordinates: 1..5 => AAAAA
Revcom: complement(1..5) => TTTTT

# Basic split, both locations in same strand
Coords: join(6..10,16..20) => CCCCCTTTTT
Revcom: complement(join(6..10,16..20)) => AAAAAGGGGG

# Cut by origin-split, same strand, single sequence that pass through origin
Coords: join(16..20,1..2) => TTTTTAA
Revcom: complement(join(16..20,1..2)) => TTAAAAA

# Cut by origin-combo split, same strand, 2 sequences with 1st passing
through origin
Coords: join(19..20,1..2,11..13) => TTAAGGG
Revcom: complement(join(19..20,1..2,11..13)) => CCCTTAA 

# Cut by origin-combo split, same strand, 2 sequences with 2nd passing
through origin
Coords: join(6..10,19..20,1..4) => CCCCCTTAAAA
Revcom: complement(join(6..10,19..20,1..4)) => TTTTAAGGGGG


### Reasoning: For the following cases, where segments are in MIXED strands,
ORDER REVERSAL is needed because the code have to complement some segments
and others not, so it have to complement those segments first and then join
them at the last step. Also, since there is no strand consistency in all
segments, Guide Strand have to be set with undef value.

# Trans-splicing, 2 sequences in different strands, 2nd in complement
Coords: join(6..10,complement(16..20)) => CCCCCAAAAA
Revcom: join(16..20,complement(6..10)) => TTTTTGGGGG

# Trans-splicing, 2 sequences in different strands, 1st in complement
Coords: join(complement(16..20),6..10) => AAAAACCCCC
Revcom: join(complement(6..10),16..20) => GGGGGTTTTT

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 2nd in complement
Coords: join(19..20,1..3,complement(11..13)) => TTAAACCC
Revcom: join(11..13,complement(1..3),complement(19..20)) => GGGTTTAA

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 1st in complement
Coords: join(complement(1..3),complement(19..20), 11..13) => TTTAAGGG
Revcom: join(complement(11..13), 19..20,1..3) => CCCTTAAA

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 2nd in complement
Coords: join(6..10,complement(1..2),complement(18..20),) => CCCCCTTAAA
Revcom: join(18..20,1..2, complement(6..10)) => TTTAAGGGGG

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 1st in complement
Coords: join(complement(6..10),18..20,1..2) => GGGGGTTTAA
Revcom: join(complement(1..2),complement(18..20), 6..10) => TTAAACCCCC

####

As summary, Guide Strand must ensure that all the sublocations have the same
strand value set before using that value, and be undef if there is no
consistency (like in trans-splicing); so any new "add_sub_Location" should
check the other sublocations strands and set Guide Strand according to the
consistency. Establishing Guide Strand value from the beginning and updating
it accordingly with any change in the Split location object, should
correctly signal when to reverse the sublocations order and when not.

Thoughts??

Francisco J.  Ossandon


-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: s?bado, 16 de marzo de 2013 11:02
Para: Peter Cock
CC: bioperl mailing list; Francisco J. Ossand?n
Asunto: Re: [Bioperl-l] Bug #2936

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different 
>> strands values (like the first being positive strand and the second 
>> being negative strand), since I can't think of one example where that 
>> can happen in real genomes. In fact one of the tests in PrimarySeq.t 
>> is designed exactly to have sublocations in opposite strands at the 
>> same time and then extract the sequence, so I wonder if I'm wrong and
there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA 
> genes, for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transplice
> d
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do 
> have to cope with this corner case.  Worse, there are examples where 
> pieces from different chromosomes are spliced together - which is even 
> harder to deal with - like my favourite pathological example, nad1 in 
> NC_016406 (and NC_016402), which has the following GenBank location
string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-gen
> bank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used
for Bio::Location deals with cases like this, but there is an assumption
made to deal with some cases like this that is wrong for others (say,
circular chromosomes where a feature wraps the origin, where sorting messes
things up).  It really needs a top to bottom overhaul to be explicit about
the join, but such an overhaul will break some expected behavior, hence my
suggestion of putting this in a bioperl v2.

chris
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From antony.vincent.1 at ulaval.ca  Mon Mar 18 07:43:30 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 04:43:30 -0700 (PDT)
Subject: [Bioperl-l]  Generate a hsp from emboss format?
Message-ID: <35187436.post@talk.nabble.com>


Hi,
I have a script who uses emboss (water) for a dynamic programming alignment.
Is this possible to generate (convert) my result in emboss format in a hsp
(blast) like.

I need (I think) an hsp format because it's much easier for parse only one
of the two strand in the alignment (and this is what I need).

Thanks!
-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35187436.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From p.j.a.cock at googlemail.com  Mon Mar 18 08:00:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 18 Mar 2013 12:00:21 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <35187436.post@talk.nabble.com>
References: <35187436.post@talk.nabble.com>
Message-ID: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>

On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>
> Hi,
> I have a script who uses emboss (water) for a dynamic programming alignment.
> Is this possible to generate (convert) my result in emboss format in a hsp
> (blast) like.
>
> I need (I think) an hsp format because it's much easier for parse only one
> of the two strand in the alignment (and this is what I need).
>
> Thanks!

EMBOSS water (and related tools like needle) support a range of output
formats - have you looked at those yet?

Peter


From cjfields at illinois.edu  Mon Mar 18 13:19:02 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 17:19:02 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>

On Mar 18, 2013, at 7:00 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>> 
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>> 
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>> 
>> Thanks!
> 
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?
> 
> Peter


Antony,

Bio::AlignIO::emboss is supposed to support water/needle output; have you tried that?  Also, I'm not sure what advantage having this in a BLAST-like output would have over other human-readable formats; any reasons you would need this specific output?

chris




From cjfields at illinois.edu  Mon Mar 18 17:26:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 21:26:22 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA3EA4@CHIMBX5.ad.uillinois.edu>

Just a heads-up, if there are any students interested in the Google Summer of Code, the Open Bioinformatics Foundation is planning on participating again this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are looking for prospective projects.  

We're open for any project ideas this year, so let us know what you would like to do!

chris


From antony.vincent.1 at ulaval.ca  Mon Mar 18 17:35:13 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 14:35:13 -0700 (PDT)
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
Message-ID: <35190011.post@talk.nabble.com>


Hi!
For example, with this code I can easily modify only one string:

 #! /usr/bin/perl -w
 
# use strict;
 use Bio::SeqIO;
 use Bio::Tools::Run::StandAloneBlast;
 use Bio::Seq;
 use warnings;
 
###########################################################################################################
# Usage information
die "Usage: $0 <sequence 1> <sequence 2> <BLAST algorithme> <minimum % of
identity>\n", if (@ARGV != 4);
 my ($infile1,$infile2,$algo,$identity) = @ARGV;
##########################################################################################################


 my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if


	print $hsp->algorithm, ": Identity ", 100*$hsp->frac_identical, "\%, Rank
", $hsp->rank, " (evalue:", $hsp->evalue, ")\n";
	print "\t", $hsp->query_string;
	print "\n";
	print "\t", $hsp->homology_string;
	print "\n";
	print "\t", $hsp->hit_string;
	print "\n\n";
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

This is why I want to have this format. Is this possible?
Thanks!


-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35190011.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From p.rice at imperial.ac.uk  Tue Mar 19 06:51:52 2013
From: p.rice at imperial.ac.uk (Peter Rice)
Date: Tue, 19 Mar 2013 10:51:52 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <51484348.5070603@imperial.ac.uk>

On 18/03/2013 12:00, Peter Cock wrote:
> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>>
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>>
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>>
>> Thanks!
>
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?

The full list for the latest EMBOSS release alignment formats is below. 
They are selected by the -aformat qualifier for any application with an 
"align" output.

It would also be relatively simple to add new formats for the next 
release if they would be useful.

Multiple sequence formats:

"fasta",     "Fasta format sequence",
"msf",       "MSF format sequence",
"clustal",   "clustalw format sequence",
"mega",       "Mega format sequence",
"meganon",       "Mega non-interleaved format sequence",
"nexus",   "nexus/paup format sequence",
"nexusnon",   "nexus/paup non-interleaved format sequence",
"phylip",   "phylip format sequence",
"phylipnon", "phylip non-interleaved format sequence",
"selex",       "SELEX format sequence",
"treecon",       "Treecon format sequence",

Multiple alignment formats:

"markx0",    "Pearson MARKX0 format",
"markx1",    "Pearson MARKX1 format",
"markx2",    "Pearson MARKX2 format",
"markx3",    "Pearson MARKX3 format",
"markx10",   "Pearson MARKX10 format",
"match","Start and end of matches between sequence pairs",
"multiple",  "Simple multiple alignment",
"pair",      "Simple pairwise alignment",
"simple",    "Simple multiple alignment",
"sam",       "Sequence alignent/map (SAM) format",
"score",     "Score values for pairs of sequences",
"srs",       "Simple multiple sequence format for SRS",
"srspair",   "Simple pairwise sequence format for SRS",
"tcoffee",   "TCOFFEE program format",

regards,

Peter Rice
EMBOSS Team



From carandraug+dev at gmail.com  Tue Mar 19 19:02:59 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 19 Mar 2013 23:02:59 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
Message-ID: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>

On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
> I do believe that these options are an improvement but since it's a
> lot of changes and behaves differently from the previous version, I
> created a fork and a branch on my own repo. If no one opposes I will
> push them to the main repo.

Pushed.

Carn?



From cjfields at illinois.edu  Tue Mar 19 22:06:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 20 Mar 2013 02:06:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>

On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> I do believe that these options are an improvement but since it's a
>> lot of changes and behaves differently from the previous version, I
>> created a fork and a branch on my own repo. If no one opposes I will
>> push them to the main repo.
> 
> Pushed.
> 
> Carn?

Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

chris


From carandraug+dev at gmail.com  Tue Mar 19 23:09:52 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 20 Mar 2013 03:09:52 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>

On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> I do believe that these options are an improvement but since it's a
>>> lot of changes and behaves differently from the previous version, I
>>> created a fork and a branch on my own repo. If no one opposes I will
>>> push them to the main repo.
>>
>> Pushed.
>>
>> Carn?
>
> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

I was hoping that it would get more use. jhannah/deafferret tells me
that the people who volunteer to do the CPAN work get burned out. With
this properly set up, it should be as simple as running "dzil
release".

I'm also writing a pod weaver plugin bundle for bioperl but would like
some thought on what others think this should be doing.

Carn?



From fs5 at sanger.ac.uk  Wed Mar 20 18:09:40 2013
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Wed, 20 Mar 2013 22:09:40 +0000
Subject: [Bioperl-l] Bio::DB::Sam - finding clipped regions
Message-ID: <514A33A4.3050107@sanger.ac.uk>

Hi,

I need to report all the positions on a reference sequence where aligned 
reads in a bam file have been hard-clipped.
I am using Bio::DB::Sam and I know that I can use callbacks to traverse 
each individual read and get information about its alignment to each 
position on the reference as in

my $sam = Bio::DB::Sam->new(

   -bam  =>$bam,

   -fasta=>$fasta,

);

my $callback = sub {

   my ( $id, $pos, $p ) = @_;

   for my $pileup (@$p) {

     my $aln  = $pileup->alignment;

     my $cigar = $aln->cigar_str;

     # other stuff here

     # ...

  };

$sam->fast_pileup( $sequence_id, $callback );



But I don't see a straight-forward way (accepting that there may not be 
one of course) to ask "is the next base of the read hardclipped".
It's not that difficult to unravel the cigar string and I have the start 
of the alignment for the read, so I can follow the cigar string along to 
the current base on the reference to see what the alignment is there and 
what happens next.
I've just got that feeling that I'm missing something and there is 
probably a better and more efficient way of doing this, maybe with 
another tool? Using samtools mpileup I can get positions of SNPs and 
INDELS but I can't see a way of collecting the hard-clipped positions 
that I need or is that possible somehow (ok, not BioPerl, I know)

Thanks for your help guys!

Frank



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From scott at scottcain.net  Wed Mar 20 22:28:09 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 20 Mar 2013 22:28:09 -0400
Subject: [Bioperl-l] Last day for early registration for GMOD 2013
Message-ID: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>

Hi,

With several guest speakers, including Jane Lomax from GO, Joseph
Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
Centre, this GMOD meeting is shaping up to be a very intersting
meeting indeed.  Today (March 21) is the last day to register with the
early registration pricing.  To register, go to

  http://gmod2013.eventbrite.com/

I look forward to seeing you next month (April 5-6) in Cambridge,
England.  For more information about GMOD 2013, go to

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From sofia at neuro.utah.edu  Thu Mar 21 10:51:43 2013
From: sofia at neuro.utah.edu (Sofia M Robb)
Date: Thu, 21 Mar 2013 14:51:43 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
Message-ID: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>

Hello All,

The following link http://bioperl.org/cgi-bin/deob_interface.cgi results in an internal server error. I hope that someone can point the link in the right direction.

Thanks,
Sofia



From p.j.a.cock at googlemail.com  Thu Mar 21 11:28:03 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 21 Mar 2013 15:28:03 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
In-Reply-To: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
References: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
Message-ID: <CAKVJ-_46=1zbFjLL+ovow4449hZ7qWa+woPz8VkbLLy_LnYNGw@mail.gmail.com>

On Thu, Mar 21, 2013 at 2:51 PM, Sofia M Robb <sofia at neuro.utah.edu> wrote:
> Hello All,
>
> The following link http://bioperl.org/cgi-bin/deob_interface.cgi results
> in an internal server error. I hope that someone can point the link in
> the right direction.
>
> Thanks,
> Sofia

That might be related to the server move at the end of last year.
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Whomever looks after the deobfuscator - please drop the Sys Admin
team an email on the root-l mailing list if you need assistance.

Regards,

Peter


From carandraug+dev at gmail.com  Thu Mar 21 22:11:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 22 Mar 2013 02:11:18 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
Message-ID: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>

On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>> I do believe that these options are an improvement but since it's a
>>>> lot of changes and behaves differently from the previous version, I
>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>> push them to the main repo.
>>>
>>> Pushed.
>>>
>>
>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>
> I'm also writing a pod weaver plugin bundle for bioperl but would like
> some thought on what others think this should be doing.

So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
give some feedback if it's adequate for the rest of the project.

https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

To minimize the number of files added to each distro, I also wrote
another plugin which the PluginBundle uses. I wrote it today so you're
likely to not have it installed yet.

https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Carn?



From jason.stajich at gmail.com  Fri Mar 22 02:19:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 21 Mar 2013 20:19:23 -1000
Subject: [Bioperl-l] PopGen Question
In-Reply-To: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
References: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
Message-ID: <F6333CA1-8FAD-4022-BC5B-19FB51CE95AC@gmail.com>

Once you convert it into the population object ($pop1) you can iterate through the markers and request the allele frequency from each of these.

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/Population.html
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/MarkerI.html

 for my $name ( $population->get_marker_names ) {
   my $marker = $population->get_Marker($name);
   print "marker $marker\n";
   my %af = $marker->get_Allele_Frequencies;
   foreach my $allele ( keys %af ) {
      print "$allele $af{$allele}\n";
   }
  }


unfortunately the wiki code seems to be messed up for autolinking out to the pdoc documentation so some of the links on the bioperl website don't get properly made.  something to be fixed I hope.

Jason
On Mar 15, 2013, at 9:21 AM, Michael Hague <mhague at mail.sfsu.edu> wrote:

> Hello,
> I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:
> 
> 
> use Bio::AlignIO;
> use Bio::PopGen::Utilities;
> use Bio::PopGen::Statistics;
> use Bio::PopGen::Population;
> 
> my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
>                           				 -format => 'fasta');
> my $aln1 = $io1->next_aln;
> 
> 
> my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
> 													-include_monomorphic => 1);
> 
> my $stats1 = Bio::PopGen::Statistics->new();
> my $D1 = $stats1->tajima_D($pop1);
> my $theta1  = $stats1->theta($pop1);
> my $segsites1 = $stats1->segregating_sites_count($pop1);
> 
> print "\nPopulation #1:\n";
> print "Number of segregating sites = $segsites1\n";
> print "Tajima\'s D = $D1\n";
> print "Watterson\'s theta = $theta1\n\n";
> 
> However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?
> 
> Thanks so much for the help,
> Mike
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From briano at bioteam.net  Sat Mar 23 11:21:58 2013
From: briano at bioteam.net (Brian Osborne)
Date: Sat, 23 Mar 2013 11:21:58 -0400
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
Message-ID: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>

Hanny,

I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.

> 
> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> 
> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> 
> Hanny

Brian O.




From cjfields at illinois.edu  Sat Mar 23 13:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 23 Mar 2013 17:41:28 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
	<7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DBFE3F@CHIMBX5.ad.uillinois.edu>

On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:

> Hanny,
> 
> I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> 
>> 
>> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
>> 
>> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
>> 
>> Hanny
> 
> Brian O.


My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.

chris


From carandraug+dev at gmail.com  Sat Mar 23 21:20:04 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 01:20:04 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
Message-ID: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>

Hi everyone

just announcing that Bio-Biblio version 1.70 just got released.

This release has minimum changes, mainly the split from bioperl-live.
As part of the release with Dist::Zilla, a few changes were made to
the documentation and all source use the utf8 pragma.

Carn?



From hlapp at drycafe.net  Sat Mar 23 21:21:49 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 23 Mar 2013 21:21:49 -0400
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
Message-ID: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>

Congrats, great job! -hilmar

On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:

> Hi everyone
> 
> just announcing that Bio-Biblio version 1.70 just got released.
> 
> This release has minimum changes, mainly the split from bioperl-live.
> As part of the release with Dist::Zilla, a few changes were made to
> the documentation and all source use the utf8 pragma.
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From cjfields at illinois.edu  Sat Mar 23 21:59:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 01:59:31 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
	<7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC01CB@CHIMBX5.ad.uillinois.edu>

Agreed, great job!

I may go ahead and pull these from the v1 branch, just to make sure they don't clobber your release.  

chris

On Mar 23, 2013, at 8:21 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Congrats, great job! -hilmar
> 
> On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:
> 
>> Hi everyone
>> 
>> just announcing that Bio-Biblio version 1.70 just got released.
>> 
>> This release has minimum changes, mainly the split from bioperl-live.
>> As part of the release with Dist::Zilla, a few changes were made to
>> the documentation and all source use the utf8 pragma.
>> 
>> Carn?
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Sat Mar 23 23:54:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 03:54:48 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <CAPOrs_0OkB+FgrraMSsMztweCxoyZ7GbHyGEKbO18GA1a2wiow@mail.gmail.com>

On 22 March 2013 02:11, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>> I do believe that these options are an improvement but since it's a
>>>>> lot of changes and behaves differently from the previous version, I
>>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>>> push them to the main repo.
>>>>
>>>> Pushed.
>>>>
>>>
>>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>>
>> I'm also writing a pod weaver plugin bundle for bioperl but would like
>> some thought on what others think this should be doing.
>
> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
> give some feedback if it's adequate for the rest of the project.
>
> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>
> To minimize the number of files added to each distro, I also wrote
> another plugin which the PluginBundle uses. I wrote it today so you're
> likely to not have it installed yet.
>
> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Could a new release of this pluginbundle be made? I have made a lot of
changes to it but I believe it's ready for "production". I used it to
release Bio-biblio and seems to have worked fine. I tried to set it up
so that all it's needed to do is:

1 - change version number on the dist.ini file (there's no need to
commit this change, the PluginBundle will take care of that)
2 - run dzil release

Carn?



From elanorbust2 at yahoo.com  Sun Mar 24 06:14:32 2013
From: elanorbust2 at yahoo.com (sally roberts)
Date: Sun, 24 Mar 2013 03:14:32 -0700 (PDT)
Subject: [Bioperl-l] http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
Message-ID: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>

http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html


From cjfields at illinois.edu  Sun Mar 24 10:32:38 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 14:32:38 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_75F1512441D48A74101FEE2D@qq.com>
References: <tencent_75F1512441D48A74101FEE2D@qq.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC07D0@CHIMBX5.ad.uillinois.edu>

ActivePerl as of a few years or so ago could install modules directly from CPAN.  Have you tried that?  Also, any reason you are using ActivePerl on Linux?  Lots of very nice options out there for linux, including  perlbrew:

http://perlbrew.pl/

The problem we historically have with Windows support is that very few of our developers use it (let alone have access to a Windows machine).  If anyone wants to take this on I would be more than supportive.

chris

On Mar 24, 2013, at 5:44 AM, ciel <58363553 at qq.com> wrote:

> 
> Thanks!
> 
> So, since their web site migrration , I guess I couldn't install bioperl temporary whether in windows or linux. 
> 
> Hanny  
> 
> ------------------ Original ------------------
> From:  "Fields, Christopher J"<cjfields at illinois.edu>;
> Date:  Sun, Mar 24, 2013 01:41 AM
> To:  "Brian Osborne"<briano at bioteam.net>;
> Cc:  "ciel"<58363553 at qq.com>; "Bioperl-L"<bioperl-l at bioperl.org>;
> Subject:  Re: [Bioperl-l] bioperl installation problem
> 
> On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:
> 
> > Hanny,
> > 
> > I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> > 
> >> 
> >> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> >> 
> >> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> >> 
> >> Hanny
> > 
> > Brian O.
> 
> 
> My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.
> 
> chris.




From alexeymorozov1991 at gmail.com  Sun Mar 24 21:00:51 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Mon, 25 Mar 2013 10:00:51 +0900
Subject: [Bioperl-l]
	http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
In-Reply-To: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
References: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
Message-ID: <CAK=7cMMsxCvP+jVYyqDAbaS4_9rycmSVmKUwo-HYTx3nOFA5AQ@mail.gmail.com>

Someone ban the spammer, please.


2013/3/24 sally roberts <elanorbust2 at yahoo.com>

> http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.


From 58363553 at qq.com  Fri Mar 22 12:21:00 2013
From: 58363553 at qq.com (=?ISO-8859-1?B?Y2llbA==?=)
Date: Sat, 23 Mar 2013 00:21:00 +0800
Subject: [Bioperl-l] bioperl installation problem
Message-ID: <tencent_4DDD95B145899AF5173CBF5A@qq.com>

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx


Hanny



From lzwright at gmail.com  Thu Mar 21 17:08:41 2013
From: lzwright at gmail.com (liz wright)
Date: Thu, 21 Mar 2013 17:08:41 -0400
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
Message-ID: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>

Hi, I just force installed bioperl on ubuntu linux as this approach was
proposed as a viable alternative when certain tests fail, but I would like
to check that the fail errors listed below will not significantly impair
bioperl usage as I am new to all this and don't really know how to
interpret the error messages.  Thanks, Liz Wright


* WARNING: Configuration was initially created with Module::Build
  version '0.38' but we are now using version '0.4003'.
  If errors occur, you must re-run the Build.PL or Makefile.PL script.
Will try to install symlinks to /usr/local/bin
  CJFIELDS/BioPerl-1.6.1.tar.gz
  sudo ./Build install  -- OK
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
failure ignored because 'force' in effect
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
failure ignored because 'force' in effect
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
failure ignored because 'force' in effect
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
failure ignored because 'force' in effect


From lzwright at gmail.com  Fri Mar 22 08:44:10 2013
From: lzwright at gmail.com (liz wright)
Date: Fri, 22 Mar 2013 08:44:10 -0400
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>

As a follow up to my previous message, this gives a bit more information as
to why the make tests failed:

  make test had returned bad status, won't install without force
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test NO
 RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
'/usr/bin/perl Build.PL --installdirs site' returned status 512
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness failed
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
not OK (XML::DOM); additionally test harness failed
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
not OK (XML::SAX::Expat)
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
missing
(Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)

On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:

> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect
>
>
>


From carandraug+dev at gmail.com  Mon Mar 25 02:40:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 25 Mar 2013 06:40:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
Message-ID: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>

Hi

I need something to keep a bunch of genes belonging to the same family
organized. It is more than a plain hash since the family can be
divided into multiple ways (subfamilies, types and classes) that
overlap each other, but using a database seems overkill to me. I
couldn't find a module on CPAN that does it so I might write one if no
one suggests an alternative. Basically, with it I wanna be able to do
something like this

  my $histones = Bio::Family->new(
      -classes      => ['canonical', 'variant'],
      -types        => ['H2A', 'H2B', 'H3', 'H4'],
      -subfamilies => [ ... ],
  );

  $histones->add_member ($seqob,
      -class => 'canonical',
      -type  => 'H3',
  );

  @all_members = $histones->members;
  @canonicals  = $histones->class('canonical');

I already wrote a bit of POD for it
http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
on its design before start coding, as I fear it might be too focused
for the problem I have at hand. Could someone give me some advice
about it?

I'm also thinking that maybe I should write some sort of general perl
module, outside the Bio::* namespace.

Thanks,
Carn?



From longbow0 at gmail.com  Mon Mar 25 04:42:38 2013
From: longbow0 at gmail.com (longbow leo)
Date: Mon, 25 Mar 2013 16:42:38 +0800
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
Message-ID: <CAKPXXke637b18wS3DPPrunw1+n-q3NciSvsP=bxEeLDC5n7yVw@mail.gmail.com>

Hi Liz,

There are already "bioperl' and "bioperl-run" packages for ubuntu. It is
not necessary to install bioperl from source code.

Haizhou

On Fri, Mar 22, 2013 at 8:44 PM, liz wright <lzwright at gmail.com> wrote:

> As a follow up to my previous message, this gives a bit more information as
> to why the make tests failed:
>
>   make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test NO
>  RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
> '/usr/bin/perl Build.PL --installdirs site' returned status 512
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
> missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness
> failed
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
> not OK (XML::DOM); additionally test harness failed
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
> not OK (XML::SAX::Expat)
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
> missing
>
> (Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)
>
> On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:
>
> > Hi, I just force installed bioperl on ubuntu linux as this approach was
> > proposed as a viable alternative when certain tests fail, but I would
> like
> > to check that the fail errors listed below will not significantly impair
> > bioperl usage as I am new to all this and don't really know how to
> > interpret the error messages.  Thanks, Liz Wright
> >
> >
> >
> > * WARNING: Configuration was initially created with Module::Build
> >   version '0.38' but we are now using version '0.4003'.
> >   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> > Will try to install symlinks to /usr/local/bin
> >   CJFIELDS/BioPerl-1.6.1.tar.gz
> >   sudo ./Build install  -- OK
> > Failed during this command:
> >  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> > failure ignored because 'force' in effect
> >  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> > failure ignored because 'force' in effect
> >  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TODDR/XML-Parser-2.41.tar.gz                 : make NO
> >  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> > failure ignored because 'force' in effect
> >  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> > failure ignored because 'force' in effect
> >
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From l.m.timmermans at students.uu.nl  Mon Mar 25 07:19:36 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Mon, 25 Mar 2013 12:19:36 +0100
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>

On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect

Most of those are XML modules that need an external XML library. Force
installing won't solve that problem. Installing expat (on my ubuntu
that'd be libexpat1) should be the solution. Odds are the other
failures are dependent failures that will also disappear.

Leon


From cjfields at illinois.edu  Mon Mar 25 08:54:21 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:54:21 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>

IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:

https://metacpan.org/module/Bio::Cluster::FamilyI

My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

chris

On Mar 25, 2013, at 1:40 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I need something to keep a bunch of genes belonging to the same family
> organized. It is more than a plain hash since the family can be
> divided into multiple ways (subfamilies, types and classes) that
> overlap each other, but using a database seems overkill to me. I
> couldn't find a module on CPAN that does it so I might write one if no
> one suggests an alternative. Basically, with it I wanna be able to do
> something like this
> 
>  my $histones = Bio::Family->new(
>      -classes      => ['canonical', 'variant'],
>      -types        => ['H2A', 'H2B', 'H3', 'H4'],
>      -subfamilies => [ ... ],
>  );
> 
>  $histones->add_member ($seqob,
>      -class => 'canonical',
>      -type  => 'H3',
>  );
> 
>  @all_members = $histones->members;
>  @canonicals  = $histones->class('canonical');
> 
> I already wrote a bit of POD for it
> http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
> on its design before start coding, as I fear it might be too focused
> for the problem I have at hand. Could someone give me some advice
> about it?
> 
> I'm also thinking that maybe I should write some sort of general perl
> module, outside the Bio::* namespace.
> 
> Thanks,
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 25 08:56:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:56:37 +0000
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1733@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 6:19 AM, Leon Timmermans <l.m.timmermans at students.uu.nl> wrote:

> On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
>> Hi, I just force installed bioperl on ubuntu linux as this approach was
>> proposed as a viable alternative when certain tests fail, but I would like
>> to check that the fail errors listed below will not significantly impair
>> bioperl usage as I am new to all this and don't really know how to
>> interpret the error messages.  Thanks, Liz Wright
>> 
>> 
>> * WARNING: Configuration was initially created with Module::Build
>>  version '0.38' but we are now using version '0.4003'.
>>  If errors occur, you must re-run the Build.PL or Makefile.PL script.
>> Will try to install symlinks to /usr/local/bin
>>  CJFIELDS/BioPerl-1.6.1.tar.gz
>>  sudo ./Build install  -- OK
>> Failed during this command:
>> LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
>> failure ignored because 'force' in effect
>> KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
>> failure ignored because 'force' in effect
>> BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TODDR/XML-Parser-2.41.tar.gz                 : make NO
>> MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
>> failure ignored because 'force' in effect
>> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
>> failure ignored because 'force' in effect
> 
> Most of those are XML modules that need an external XML library. Force
> installing won't solve that problem. Installing expat (on my ubuntu
> that'd be libexpat1) should be the solution. Odds are the other
> failures are dependent failures that will also disappear.
> 
> Leon

Also, the version on CPAN has been updated to handle 'optional' dependencies; AcePerl for instance is pretty much in maintenance mode (maybe deprecated) and hasn't been updated in years.

chris




From fossandonc at hotmail.com  Mon Mar 25 09:29:48 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 25 Mar 2013 10:29:48 -0300
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <000201ce2959$17ed7830$47c86890$@qq.com>
References: <000201ce2959$17ed7830$47c86890$@qq.com>
Message-ID: <SNT133-ds57FF786B3A8DB70E8F9FACFD70@phx.gbl>

Hi,
I use Windows but I dropped ActivePerl some time ago in preference of
Strawberry Perl (http://strawberryperl.com/), which have better support for
installation directly from CPAN via command line.

I'm not sure if I understood correctly but you installed new Perl 5.16 over
the old 5.10?? In that case I would recommend to completely uninstall the
previous Perl version and then install the new clean Perl version.

On the other hand, the error message points to a problem connecting to the
Uwinnipeg server, so maybe they are down (in fact I just tried on my browser
and received the same error so they have problems with their servers), maybe
use Bribes instead; you don?t need to add ALL the repos anyway, just be sure
to add the http://bioperl.org/DIST, which contains the
"BioPerl-1.6.1-ppm.tar.gz", the last ActivePerl release that can be install
using the Perl Package Manager.

If you want to install the latest version, you will have to ditch the PPM,
type CPAN in command line and use that interface to get the
"BioPerl-1.6.901"
(http://www.bioperl.org/wiki/Installing_BioPerl_on_Windows#Installation_usin
g_CPAN_or_manual_installation). Beware that BioPerl will always give some
tests errors when installing that way, so you have to add "force" when
installing and everything will be fine.

Hope that helps,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de ciel
Enviado el: viernes, 22 de marzo de 2013 13:21
Para: bioperl-l
Asunto: [Bioperl-l] bioperl installation problem

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl
version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version
ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as
:"failed 503 Service temporarily Unavailable", how can I deal with this
problem? thx


Hanny

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hartzell at alerce.com  Mon Mar 25 12:23:32 2013
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 25 Mar 2013 09:23:32 -0700
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <20816.31236.737983.55186@gargle.gargle.HOWL>

Carn? Draug writes:
 > [...]
 > So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
 > Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
 > give some feedback if it's adequate for the rest of the project.
 > 
 > https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

Looks wonderful!

I use a "private" section that I think corresponds to what you call
"internal".  Is there a BioPerl tradition one way or the other?

You might make the SYNOPSIS just a tad less confusing if you point
some meaningful text into the text sections of the GenerateSection
parts, something like "text = Info about mailing lists goes here".  I
scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
lists" had an empty attribute and the other two had nonsense text.  It
looks like FEEDBACK is just an empty level 1 header, but
otherwise....

 > To minimize the number of files added to each distro, I also wrote
 > another plugin which the PluginBundle uses. I wrote it today so you're
 > likely to not have it installed yet.
 > 
 > https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

I can see that being useful. In the name, did you mean "interpolated"
(which you use further down) where you say "interpreted"?

This is a useful contribution!

g.



From cjfields at illinois.edu  Mon Mar 25 12:46:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 16:46:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <20816.31236.737983.55186@gargle.gargle.HOWL>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:

> Carn? Draug writes:
>> [...]
>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>> give some feedback if it's adequate for the rest of the project.
>> 
>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
> 
> Looks wonderful!
> 
> I use a "private" section that I think corresponds to what you call
> "internal".  Is there a BioPerl tradition one way or the other?

Not really, but there probably should be a more standard way of doing this.

> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".  I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....
> 
>> To minimize the number of files added to each distro, I also wrote
>> another plugin which the PluginBundle uses. I wrote it today so you're
>> likely to not have it installed yet.
>> 
>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
> 
> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?
> 
> This is a useful contribution!
> 
> g.

Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

chris




From carandraug+dev at gmail.com  Mon Mar 25 21:13:36 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 01:13:36 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
	<118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2F4yaXPR7ySHQ2jy0UjA5-FhfrWgNvkoF=0DKq5nzHeg@mail.gmail.com>

On 25 March 2013 16:23, George Hartzell <hartzell at alerce.com> wrote:
> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".

I don't understand your suggestion. Could you explain it again please?

> I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....

It's not empty. Feedback is level 1, which contains three level 2
headings for mailing list, support and reporting bugs. The code being
generated should match exactly the feedback section of all current
BioPerl modules. See the feedback section of the Bio::DB::BiblioI that
I recently released with this set up:

https://metacpan.org/module/Bio::DB::BiblioI#FEEDBACK

and compare with the old release of Bio::SeqIO

https://metacpan.org/module/Bio::SeqIO#FEEDBACK

> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?

Yes, that's what I meant. I have just pushed the fix, thank you.

On 25 March 2013 16:46, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:
>
>> Carn? Draug writes:
>>> [...]
>>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>>> give some feedback if it's adequate for the rest of the project.
>>>
>>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>>
>> Looks wonderful!
>>
>> I use a "private" section that I think corresponds to what you call
>> "internal".  Is there a BioPerl tradition one way or the other?
>
> Not really, but there probably should be a more standard way of doing this.

I think the large majority of the modules have a head1 APPENDIX that
says "Internal methods are usually preceded with a _" which contained
each method and attribute by the same order they appear on the code
inside a head2. I just followed the name that was already there
"internal", but it's very easy to change. At the moment, what I set up
recognizes the following:

=attr (for attributes)
=method
=func (for functions)
=internal (internal methods)

It doesn't matter the order they appear on the source, PodWeaver will
group and reorder them. It is easy to change the keywords, and add or
remove the groups. Just let me know what the bundle should be doing.
Take a look at

https://github.com/bioperl/Bio-Biblio/blob/master/lib/Bio/DB/BiblioI.pm

which generates

https://metacpan.org/module/Bio::DB::BiblioI

>>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
>>
>> [...]
>>
>> This is a useful contribution!
>>
>
> Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

I wrote another plugin the day after to generate the legal section
which is mainly aimed at BioPerl and distributions with many modules,
where the authors and copyright owners are not always the same. It
takes the copyright information from a block of comments in each
source file.

https://metacpan.org/module/Pod::Weaver::Section::Legal::Complicated

And yesterday the contributors plugin was released again after also
implementing the option to find the names of contributors in the
source of individual files

https://metacpan.org/module/Pod::Weaver::Section::Contributors

I can easily make the changes on our pluginbundles, or write new ones.
And authors from other packages are usually happy to receive patches
so it's also easy to expand on the ones that already exist. The only
problem left is defining what a BioPerl POD should look like. The pod
weaver pluginbundle as it is now, is just what looked appropriate to
me. But would be great if someone could comment on it so adjustments
to it can be made.

Carn?



From amelia.ireland at gmod.org  Mon Mar 25 19:55:23 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Mon, 25 Mar 2013 16:55:23 -0700
Subject: [Bioperl-l] [Gmod-gbrowse] Last day for early registration for
	GMOD 2013
In-Reply-To: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
References: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
Message-ID: <CAALsq01L4pRuOTsHh-wxmHuKBs24g3Q=DW2ngqaYq4386FAmHQ@mail.gmail.com>

GMOD is very pleased to announce the keynote speaker for the 2013 GMOD
community meeting is Dr. Kentaro Yoshida from the Sainsbury Lab (
http://tsl.ac.uk), talking about the Open Ash Dieback effort. This
pioneering bioinformatics project is employing two increasingly important
paradigms--open access to data and crowdsourcing--to gather genetic
analyses of ash and a fungal pathogen that is threatening tree populations
in the UK. Expect an interesting and inspiring talk!

Online registration: http://gmod2013.eventbrite.com

If you are interested in attending remotely, we will be using Go To Meeting
(http://gotomeeting.com) to allow people to attend virtually. Please email
me if you would like to join in.

Look forward to seeing you all in Cambridge!


On Wed, Mar 20, 2013 at 7:28 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi,
>
> With several guest speakers, including Jane Lomax from GO, Joseph
> Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
> Centre, this GMOD meeting is shaping up to be a very intersting
> meeting indeed.  Today (March 21) is the last day to register with the
> early registration pricing.  To register, go to
>
>   http://gmod2013.eventbrite.com/
>
> I look forward to seeing you next month (April 5-6) in Cambridge,
> England.  For more information about GMOD 2013, go to
>
>   http://www.gmod.org/wiki/April_2013_GMOD_Meeting
>
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


From carandraug+dev at gmail.com  Mon Mar 25 23:48:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 03:48:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2VDEt5OeKsZdNegygdTv_ZPJXcVXO6JS65sFjVCVKKZg@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI

This module mentions Bio::Cluster::Family but I can't seem to find it anywhere.

> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I think I was overcomplicating, this class might do what I want
thought in a different way. My idea of a family of genes doesn't
really match it, but I should be able to work with it by mixing it
with Set::Object.

Thank you,
Carn?



From briano at bioteam.net  Tue Mar 26 13:51:07 2013
From: briano at bioteam.net (Brian Osborne)
Date: Tue, 26 Mar 2013 13:51:07 -0400
Subject: [Bioperl-l] Wiki details
Message-ID: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>

All,

I'm looking at various module pages in the Wiki and it seems that all links are broken. For example, the "<biblio>" parser tag does not work, parser functions like #setvar aren't working and because of this the link to CPAN is broken, and so on. I'm guessing that some upgrade did not restore custom code or install extensions used in the earlier version, and Special:Version confirms this, this code is not installed.

If someone would like to contact me privately and give me credentials I can take a look at the MediaWiki directory, see if I can fix this.

Brian O.




From p.j.a.cock at googlemail.com  Tue Mar 26 14:10:10 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 26 Mar 2013 18:10:10 +0000
Subject: [Bioperl-l] Wiki details
In-Reply-To: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
References: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
Message-ID: <CAKVJ-_5nOp8sXBhLRJ2Kvrzyf0rUGjTfs=PMd7pX_CqYAQ6djg@mail.gmail.com>

On Tue, Mar 26, 2013 at 5:51 PM, Brian Osborne <briano at bioteam.net> wrote:
> All,
>
> I'm looking at various module pages in the Wiki and it seems that all
> links are broken. For example, the "<biblio>" parser tag does not work,
> parser functions like #setvar aren't working and because of this the link to
> CPAN is broken, and so on. I'm guessing that some upgrade did not restore
> custom code or install extensions used in the earlier version, and
> Special:Version confirms this, this code is not installed.
>
> If someone would like to contact me privately and give me credentials I
> can take a look at the MediaWiki directory, see if I can fix this.
>
> Brian O.

Hi Brian,

I was aware of issues with the  "<biblio>" plugin, but not all of this.
Most likely this is from the server move at the end of 2012,
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Assuming someone senior from BioPerl (or Chris Dag?) will vouch
for you, we'd ask you to join the root-l mailing list where OBF server
admin stuff happens. We'll need a preferred username (e.g. briano
or bosborne) and your SSH public key (the new server does not
accept simple username/password logins).

Regards,

Peter
(With his OBF hat on)


From antony.vincent.1 at ulaval.ca  Tue Mar 26 19:24:20 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 16:24:20 -0700 (PDT)
Subject: [Bioperl-l]  One letter protein sequence to three letters
Message-ID: <35222270.post@talk.nabble.com>


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I
try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From Russell.Smithies at agresearch.co.nz  Tue Mar 26 19:44:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 12:44:35 +1300
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAA77@exchsth.agresearch.co.nz>

You're passing an ordinary String to Bio::SeqUtils->seq3 (that's what $hsp->query_string returns) but  I think it needs to be a Bio::PrimarySeqI compliant object.

try this:

$seqobj = Bio::PrimarySeq->new ( -seq => $hsp->query_string);
$polypeptide_3char = Bio::SeqUtils->seq3($seqobj);


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Wednesday, 27 March 2013 12:24 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] One letter protein sequence to three letters


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");  my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
--
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From antony.vincent.1 at ulaval.ca  Tue Mar 26 21:32:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 18:32:09 -0700 (PDT)
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <35222552.post@talk.nabble.com>


Yes! That works and I understand now, thanks for you precious help!
:handshake:

Antony03 wrote:
> 
> Hi!
> 
> I wan't to parse a blastp output for have an hsp with three letters code.
> I try with this:
> 
> my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
>   				    -format => 'fasta' );
>  my $query1 = <$query1_in>; 
>  my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
>   				      -format => 'fasta' );
>  my $query2 = <$query2_in>; 
>  
>  my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>
> "$algo");
>  my $report = $factory->bl2seq($query1, $query2);
> 
> ############################################################################################################
>  while (my $result = $report->next_result) {  # while 1
>     print "Query: ".$result->query_name."\n\n";
>     while (my $hit = $result->next_hit) {     # while 2
>  	while (my $hsp = $hit->next_hsp) {    # while 3
>  
> if ( $hsp->percent_identity >= "$identity" ) 
> 
> 	{ # start of if
> 	
> 	$qseq = $hsp->query_string;
> 	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);
> 
> 	print $polypeptide_3char;
> 
> 	
> 		
> }
>  	} # end of while 3
>     print "\n";
>     }	# end of while 2
>  }	# end of while 3
> 
> And I got this error:
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Not a Bio::PrimarySeqI object but [$self]
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
> STACK: blast_parsing.pl:36
> -----------------------------------------------------------
> I don't understand why my code generate this error!
> 
> Thanks :)
> 

-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222552.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From alexeymorozov1991 at gmail.com  Tue Mar 26 22:34:01 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Wed, 27 Mar 2013 11:34:01 +0900
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <35222552.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
	<35222552.post@talk.nabble.com>
Message-ID: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?


From Russell.Smithies at agresearch.co.nz  Tue Mar 26 22:50:24 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 15:50:24 +1300
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>

Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
Or is there a chance that $identity is going to contain a string rather than a float?

I could be completely wrong of course  ...

--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
Sent: Wednesday, 27 March 2013 3:34 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From cjfields at illinois.edu  Tue Mar 26 23:13:19 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 27 Mar 2013 03:13:19 +0000
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC4070@CHIMBX5.ad.uillinois.edu>

You are correct.   Quotes should be unnecessary in this case, percent identities are calculated I believe from the midline.

chris

On Mar 26, 2013, at 9:50 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
> Or is there a chance that $identity is going to contain a string rather than a float?
> 
> I could be completely wrong of course  ...
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
> Sent: Wednesday, 27 March 2013 3:34 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters
> 
> Well, there is one little thing I don't get. Why is
> 
> if ( $hsp->percent_identity >= "$identity" )
> 
> any better than
> 
> if ( $hsp->percent_identity >= $identity)
> 
> Ie what do quotes do?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From adsj at novozymes.com  Wed Mar 27 08:19:01 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:19:01 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
Message-ID: <87li99593e.fsf@topper.koldfront.dk>

We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
with drawing panels that have tracks with split locations - an exception
is thrown in 2.24.

Here are the outputs of the test-script I've made:

  Bio::Graphics::VERSION: 1.995
  Simple location  ... ok
  Join location  ... ok

and

  Bio::Graphics::VERSION: 2.24
  Simple location  ... ok
  Join location  ... Can't locate object method "has_tag" via package "Bio::Location::Simple" at /usr/share/perl5/Bio/Graphics/Glyph.pm line 706, <DATA> line 192.

The test script looks like this:

== =
#!/usr/bin/perl

use strict;
use warnings;

use Bio::Graphics;

use Bio::SeqFeature::Generic;
use Bio::Factory::FTLocationFactory;

print "Bio::Graphics::VERSION: $Bio::Graphics::VERSION\n";

test_panel_with_location('1..12',              'Simple location');
test_panel_with_location('join(1..10,15..20)', 'Join location');

sub test_panel_with_location {
    my ($location_string, $msg)=@_;

    print "$msg  ... ";
    my $location=Bio::Factory::FTLocationFactory->from_string($location_string);
    my $seq=Bio::SeqFeature::Generic->new;
    $seq->location($location);

    my $panel=Bio::Graphics::Panel->new(-length=>500, -width=>500);
    $panel->add_track($seq);
    eval { $panel->png };
    print $@ || "ok\n";
}
== =

Am I doing something wrong in the script, or is this a regression in
Bio::Graphics somewhere?


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From adsj at novozymes.com  Wed Mar 27 08:33:53 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:33:53 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
In-Reply-To: <87li99593e.fsf@topper.koldfront.dk> ("Adam =?iso-8859-1?Q?Sj?=
	=?iso-8859-1?Q?=F8gren=22's?= message of
	"Wed, 27 Mar 2013 13:19:01 +0100")
References: <87li99593e.fsf@topper.koldfront.dk>
Message-ID: <87hajx58em.fsf@topper.koldfront.dk>

adsj at novozymes.com (Adam Sj?gren) writes:

> We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
> with drawing panels that have tracks with split locations - an exception
> is thrown in 2.24.

[...]

Ahh, this has been fixed between 2.24 and 2.32 - (we upgraded to 2.24
because that is the version in the latest Ubuntu LTS).

2.32 works fine:

  Bio::Graphics::VERSION: 2.32
  Simple location  ... ok
  Join location  ... ok

Sorry for the noise.


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From carandraug+dev at gmail.com  Thu Mar 28 10:55:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 14:55:48 +0000
Subject: [Bioperl-l]  Google Summer of Code - BioPerl proposals
Message-ID: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>

On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
> Just a heads-up, if there are any students interested in the Google Summer of
> Code, the Open Bioinformatics Foundation is planning on participating again
> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
> looking for prospective projects.
>
> We're open for any project ideas this year, so let us know what you would like
> to do!

Hi

I had already mentioned that I would like to finish the split of the
project into smaller distributions. Is it acceptable to finish
projects from previous years? I noticed that the wiki page for BioPerl
projects is still empty for this year. Should I fill it? Would someone
be able to mentor that?

Carn?



From carandraug+dev at gmail.com  Thu Mar 28 12:23:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 16:23:18 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_32AU=Vc1yZofWyLM+CVQj0Xa6et+7rKHrXSHVU-TY2sA@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI
>
> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I'm looking at these now and thinking of making the split from live
into a separate distribution now. But I'm unsure about two of the
files

Bio/ClusterIO/dbsnp.pm
Bio/Cluster/SequenceFamily.pm

Would you agree that these would fit better into a Bio-Variations and
Bio-Seq distribution?

Carn?



From hlapp at drycafe.net  Sat Mar 30 13:24:26 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 30 Mar 2013 12:24:26 -0500
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
Message-ID: <723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>

Hi Carn?,

Not sure I've missed a response to this. If indeed there hasn't been one, let me just chime in non-authoritatively that in principle there's nothing wrong with picking up past pieces. I would argue you'd have to make a convincing argument as to why and how you'd surmount the hurdles that brought the previous project to a premature end (or why it ran out of time and you won't), and as to how it's desirability has not diminished since then even though nobody else picked it up.

If you want to apply as a student, you don't strictly have to put it up on the wiki, but it'd be prudent to discuss your ideas on this list prior to submission. Presumably you were planning that anyway, though.

-hilmar

Sent with a tap.

On Mar 28, 2013, at 9:55 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
>> Just a heads-up, if there are any students interested in the Google Summer of
>> Code, the Open Bioinformatics Foundation is planning on participating again
>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>> looking for prospective projects.
>> 
>> We're open for any project ideas this year, so let us know what you would like
>> to do!
> 
> Hi
> 
> I had already mentioned that I would like to finish the split of the
> project into smaller distributions. Is it acceptable to finish
> projects from previous years? I noticed that the wiki page for BioPerl
> projects is still empty for this year. Should I fill it? Would someone
> be able to mentor that?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From briano at bioteam.net  Sun Mar 31 10:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 10:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 11:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 11:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From cjfields at illinois.edu  Sun Mar 31 20:34:16 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Apr 2013 00:34:16 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>

I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.  

chris

On Mar 30, 2013, at 12:24 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Hi Carn?,
> 
> Not sure I've missed a response to this. If indeed there hasn't been one, let me just chime in non-authoritatively that in principle there's nothing wrong with picking up past pieces. I would argue you'd have to make a convincing argument as to why and how you'd surmount the hurdles that brought the previous project to a premature end (or why it ran out of time and you won't), and as to how it's desirability has not diminished since then even though nobody else picked it up.
> 
> If you want to apply as a student, you don't strictly have to put it up on the wiki, but it'd be prudent to discuss your ideas on this list prior to submission. Presumably you were planning that anyway, though.
> 
> -hilmar
> 
> Sent with a tap.
> 
> On Mar 28, 2013, at 9:55 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
> 
>> On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
>>> Just a heads-up, if there are any students interested in the Google Summer of
>>> Code, the Open Bioinformatics Foundation is planning on participating again
>>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>>> looking for prospective projects.
>>> 
>>> We're open for any project ideas this year, so let us know what you would like
>>> to do!
>> 
>> Hi
>> 
>> I had already mentioned that I would like to finish the split of the
>> project into smaller distributions. Is it acceptable to finish
>> projects from previous years? I noticed that the wiki page for BioPerl
>> projects is still empty for this year. Should I fill it? Would someone
>> be able to mentor that?
>> 
>> Carn?
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Sun Mar 31 22:05:19 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 1 Apr 2013 03:05:19 +0100
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>

On 1 April 2013 01:34, Fields, Christopher J <cjfields at illinois.edu> wrote:
> I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.

Why did the project ran out of time 2 years ago? The blog posts about
it are very few and don't sound too bad. It mentions having prepared a
couple of them, but none was actually ever released. Instead, the
source was also kept in bioperl-live and seems to have already
branched. Is there any reason for this? It was my understanding that
splitting the project is still desirable, from a discussion back in
February

http://article.gmane.org/gmane.comp.lang.perl.bio.general/26395

it just happens that no one has picked it up yet.

I think splitting bioperl-live into subdistributions and make a new
1.70 release of each of them is perfectly doable over a summer. And I
say this after having split and release Bio-Biblio. This is one of my
itches with BioPerl. I have been using it for almost 3 years, but have
never seen a release. I would like to make new releases of everything,
no changes at the start, but take them to the point that "dzil
release" does everything. Make it really easy for anyone to come in
and contribute and even easier for a maintainer to make a new release
after receiving a contribution. Is this desirable for the project?

Carn?



From cjfields at illinois.edu  Sun Mar 31 23:28:55 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Apr 2013 03:28:55 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
	<723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74DC843A@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1XpkvttJ+YpBnE3+7Qm39PRW-cnc9C9A_8tw+u9H8zwA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC8BD8@CHIMBX5.ad.uillinois.edu>

On Mar 31, 2013, at 9:05 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 1 April 2013 01:34, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be done for bioperl-run, bioperl-live, etc.
> 
> Why did the project ran out of time 2 years ago? The blog posts about
> it are very few and don't sound too bad. It mentions having prepared a
> couple of them, but none was actually ever released. Instead, the
> source was also kept in bioperl-live and seems to have already
> branched. Is there any reason for this? It was my understanding that
> splitting the project is still desirable, from a discussion back in
> February
> 
> http://article.gmane.org/gmane.comp.lang.perl.bio.general/26395
> 
> it just happens that no one has picked it up yet.

The project actually made a lot of headway; the particular pieces moved out (Bio::Root, Bio::Factory, etc) worked fine, but we never followed up on exactly what to do next on master branch.  It's perfectly feasible for someone to go ahead and finish the initial part of that (in fact, I believe there were some branches that started along this path but never merged back in).

FWIW, Sheena also started the Dist::Zilla bundle you have been working on as well, with the same intent you have.  So the fundamental groundwork is there.

> I think splitting bioperl-live into subdistributions and make a new
> 1.70 release of each of them is perfectly doable over a summer. And I
> say this after having split and release Bio-Biblio. This is one of my
> itches with BioPerl. I have been using it for almost 3 years, but have
> never seen a release. I would like to make new releases of everything,
> no changes at the start, but take them to the point that "dzil
> release" does everything. Make it really easy for anyone to come in
> and contribute and even easier for a maintainer to make a new release
> after receiving a contribution. Is this desirable for the project?
> 
> Carn?


The last Bioperl release was in 2011 IIRC, so we're long overdue, but it's not quite 3 yrs :)  

Hilmar's point is pretty valid, namely that a case would have to be made as to why the initial run at it wasn't completed, or why it would work better this time.  We're not suggesting that this can't be done, but the above point would have to be answered.  Frankly, the project has been pretty reliant on me for releases, so it's perfectly valid to point out the modules haven't made it out yet b/c I haven't made a release since then.  From that point of view, this would be a continuation of that work, maybe with the intent/focus on making code releases much easier.

Regarding updating Bioperl to use Dist::Zilla amongst other modern perl tools (Moose included), yes, it is very much our wish/intent to have this, in any way possible.  But I don't think we can call it BioPerl v1.7, simply based on past release cycles; we're somewhat bound by deprecations, etc.  We really need a clean break.  

So, my general feeling is that while we are cleaving out code and releasing the independent dist and core, we should re-christen core as 1.9 (e.g. pre-v2).  We move to v2 when we feel we're at the right point.  Each of the individual distributions would have to start with their own versions, anything greater than the point where they left the core/live distribution should work.  I agree with you in that I don't think it would take a long time, but we also have bioperl-run in the mix (and in many cases it would make sense to combine wrappers with the proper parsers), so simply cleaving out from one repo may not be the best approach.

With that in mind, my point was meant to indicate we can also start afresh with a section of the code that you would like to focus on, using some of the same ideas (pulling out the relevant modules you want to work on).  This might be an attainable goal in the minds of GSoC reviewers and might suit your particular needs (for instance, if you had a research project reliant on such code).  I'm supportive either way, and I don't think you'll have a problem finding a mentor if you need one.

chris






From chapmanb at 50mail.com  Fri Mar  1 02:30:01 2013
From: chapmanb at 50mail.com (Brad Chapman)
Date: Thu, 28 Feb 2013 21:30:01 -0500
Subject: [Bioperl-l] Coming soon: BOSC/Broad Hackathon, BOSC Codefest
Message-ID: <874ngvua1i.fsf@fastmail.fm>


Hi all; 
There are some upcoming coding events and conferences of interest to open source
biology programmers:

- BOSC/Broad Interoperability Hackathon -- This is a two day coding session at
  the Broad Institute in Cambridge, MA on April 7-8 focused on improving tool
  interoperability.
  
  Sign up and details: http://j.mp/XJT6ew
  
- Codefest at the Bioinformatics Open Source Conference -- This year BOSC is
  taking place in Berlin from July 19-20 and we'll have a two day coding session
  before the conference. This is the 4th year of Codefests and they've proven to
  be a productive and fun time to work collectively on open source projects.

  Sign up and details: http://www.open-bio.org/wiki/Codefest_2013
  BOSC conference: http://www.open-bio.org/wiki/BOSC_2013

Here are the key dates for the events and abstracts:

April  7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA
April   12, 2013: BOSC abstracts due
July 17-18, 2013: Codefest 2013, Berlin
July 19-20, 2013: BOSC 2013, Berlin

Looking forward to seeing everyone this spring and summer for plenty of fun
science and code,
Brad


From l.m.timmermans at students.uu.nl  Fri Mar  1 21:49:58 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Fri, 1 Mar 2013 22:49:58 +0100
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
Message-ID: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>

On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
> Greetings,
>
> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>
> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>
> Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetw!
>  ork::RandomFactory -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA::ESEfinder -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameSubs -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::interpro -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::berkeleydb -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::entrezgene -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tinyseq -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::chadoxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (opt!
>  ional_features -> Bio::SeqIO::game::gameWriter -> requires) [Validatio
> n: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::FileCache -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::bsml_sax -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Primer3 -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::HtSNP -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Compatible -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Taxonomy::entrez -> requires) [Validation: 1.2], Expected a ma!
>  p structure from string or file. (optional_features -> Bio::SeqIO::agave -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::TagHaplotype -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::SeqFeature::Store::FeatureFileLoader -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::Protein* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::blastxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::EUtilities -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Draw::Cladogram -> requires) [Validation: 1!
>  .2], Expected a map structure from string or file. (optional_features
> -> Bio::Tools::SeqPattern -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tigrxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Collection -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Draw::Pictogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::Writer::BSMLResultWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::HIVQuery -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::TreeIO::svggraph -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::eutils -> requires) [Validation: 1.2], Expected a map structure from string or file. (opti!
>  onal_features -> Bio::PhyloNetwork -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern::BackTranslate -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::GenBank -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Variation::IO::xml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::GraphViz -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Annotated -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::NCBIHelper -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::HIV -> requires) [Validation: 1.2], Expected a map structure from string or file. (!
>  optional_features -> Bio::Tools::Analysis::DNA* -> requires) [Validati
> on: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Run::RemoteBlast -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::excel -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::ClusterIO::dbsnp -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Microarray::Tools::ReseqChip -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::soap -> requires) [Validation: 1.2]
> at /usr/local/lib/perl5/5.10.1/Module/Build/Base.pm line 4559
>
> Could not create MYMETA files
> Creating new 'Build' script for 'BioPerl' version '1.006001'

What versions of Module::Build and CPAN::Meta are you using?

> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.

Yeah, 1.6.1 equals 1.006001. See also
http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
Do note that it is no longer the lastest release, latest is 1.6.901
and a new release is expected on a short notice.

Leon



From cjfields at illinois.edu  Fri Mar  1 23:11:39 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 1 Mar 2013 23:11:39 +0000
Subject: [Bioperl-l] Error when running Build.PL
In-Reply-To: <CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
References: <DC8C6FE0AED292469CF192A00459937BC0F8660B@EDGE-EXCH02.edgebio.com>
	<CAC1jpXDJGXus3H9HHjWqUUK5UQQ39Y-UtQe85VdoRW9OrJZs4g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6E70B5F7@CHIMBX5.ad.uillinois.edu>

On Mar 1, 2013, at 3:49 PM, Leon Timmermans <l.m.timmermans at students.uu.nl>
 wrote:

> On Mon, Feb 25, 2013 at 5:50 PM, Phil Dagosto <PDagosto at edgebio.com> wrote:
>> Greetings,
>> 
>> I downloaded BioPerl 1.6.1 from this location: http://www.bioperl.org/wiki/Getting_BioPerl
>> 
>> When I ran Build.PL with all of the default settings chosen in the interactive mode I got the following error message:
>> ?.
> 
>> I have no idea whether this is a problem or not or if I can proceed. Also, I'm confused by the version number referenced in the last line. 1.006001 is our current version - I thought I was installing version 1.6.1. Are these version numbers equivalent, i.e., are the zeros not meaningful?.
> 
> Yeah, 1.6.1 equals 1.006001. See also
> http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/.
> Do note that it is no longer the lastest release, latest is 1.6.901
> and a new release is expected on a short notice.
> 
> Leon

Yup, hoping to work on it tonight and tomorrow.  Travis-CI indicates all normal tests are passing, I'll run through a few remaining ones.  Some we can't address directly; there are a number of warnings popping up I can't do anything about (they originate from Graph).

chris


From pcantalupo at gmail.com  Sat Mar  2 17:28:15 2013
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Sat, 2 Mar 2013 12:28:15 -0500
Subject: [Bioperl-l] Fix for Bug #3376 broke somewhere else
In-Reply-To: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
References: <SNT133-ds14A180BAFAE068EE359031CFFE0@phx.gbl>
Message-ID: <CAJqbkv5-cXLh_cMa3rWoOVv7PijY2Orq=Smvqd3Xij887iVhMg@mail.gmail.com>

Hi Francisco,

Nice catch. Please submit a new bug report for this and reference bug
3376. Please provide a minimal hmmer output file, a script and the
expected output. Then, I'll look into it and fix the bug.

Thank you,

Paul

Paul Cantalupo
University of Pittsburgh


On Thu, Feb 28, 2013 at 10:36 AM, Francisco J. Ossand?n
<fossandonc at hotmail.com> wrote:
> Hi,
> I was re-checking Bug #3302 using the Bio::SearchIO modules of the
> repository and found that now it can't parse a Hmmer2 file that was
> previously fine. After tracking the problem, I discovered that a change in a
> regular expression to fix another bug broke the parse.
>
> The fix for the Bug #3376 consisted in adding an extra condition to omit
> lines where end of domain indicator is split across lines
> (https://redmine.open-bio.org/issues/3376):
> TEST: domain 1 of 1, from 8 to 97: score 184.7, E = 2.5e-56
>                    *->svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDn
>                       sv+qqqq+  +    +vtAiAiAigYRYRYRAv Wn GsLs G nDn
>         Test     8    SVYQQQQGGSA----MVTAIAIAIGYRYRYRAVVWNKGSLSTGTNDN 50
>
>                    DnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr<-
>                    DnDq +d LYtiYYsvtv +ss+p q+v+HHHaH+asstkiiiki P
>         Test    51 DNDQAAD-LYTIYYSVTVSASSWPGQSVTHHHAHPASSTKIIIKIAPS   97
>
>                    *
>
>         Test     -   -
> This case is characterized by the 2 dashes in the line...
>
> So the expression added in hmmer2.pm - ?next_result?
> (https://github.com/bioperl/bioperl-live/commit/142e5d79e3a6593db32bf0af9904
> 8f47d01bd3f2):
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\-\s+\-\s*$/ ) ### <--- This regex was
> designed for bug 3376
>                         {
>                             next;
>                         }
>
> But the expression used is too broad because it uses the "^.+" just before
> the 2 dashes, and it broke these lines parsing, where is full of dashes:
>                    KyACrqCdtiVQAPaPakpIErGiptaGLLArvlVSKyaEHlPLYRQsEI
>
>   lcl|gi|340     - -------------------------------------------------- -
>
>                    yaRqGVeiaRstLadWVgrtgarLaPLvdALaeyVLkeGklHADeTPVqV
>                          +i  s L   V++ + r
>   lcl|gi|340 60938 ------AIMISGLIHGVSARCLRF-------------------------- 60955
>
> I think a reasonable fix that still fixes the original bug and restore the
> function for this case is to add an extra \s+ in the regex just before the
> first dash, so the expression makes sure that the first dash is the one that
> comes AFTER the description (and is replacing the usual coordinate number)
> and is not the last of an alignment or a series of dashes like the one
> above:
>                         elsif (CORE::length($_) == 0
>                             || ( $count != 1 && /^\s+$/o )
>                             || /^\s+\-?\*\s*$/
>                             || /^.+\s+\-\s+\-\s*$/ ) ### <--- Tweaked regex
>                         {
>                             next;
>                         }
> I tested it and it works fine, hope you find the fix acceptable.
>
> Cheers,
>
> --
> Francisco J. Ossandon
> Bioinformatician.
> Ph.D. Candidate, University Andres Bello.
> Center for Bioinformatics and Genome Biology,
> Fundacion Ciencia para la Vida.
> Santiago, Chile.
> www.cienciavida.cl/CBGB.htm
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hlapp at drycafe.net  Sun Mar  3 17:53:34 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sun, 3 Mar 2013 12:53:34 -0500
Subject: [Bioperl-l] GSoC 2013 is ON
Message-ID: <F68E8168-80A5-4681-9912-8655998A9F40@drycafe.net>

Forwarding on behalf of Pjotr Prins, who just volunteered to serve as OBF's GSoC admin for this year.

~~~

Game on! GSoC 2013 is ON. I am running with the OBF project
administration this year for the Google Summer of code (GSoC). 
First and foremost I want to thank Robert Buels and others for making
OBF/GSoC a success in the previous three years! This year, Robert, Chris
Fields and Hilmar Lapp will act as backup administrators.

The deadline for the OBF application for GSoC2013 as a mentoring
organisation is Friday March 29! See

 http://www.google-melange.com/gsoc/events/google/gsoc2013

Similar to previous years, each Bio* project needs to update and add project
ideas on the project's individual OBF wiki page and create links from the main
OBF page at

 http://www.open-bio.org/wiki/Google_Summer_of_Code

(we will update the main information on that page soon).

So, for each of the OBF projects that wants to do GSoC again this
year:

1. Update the list of project ideas on your project's GSoC page (BioPython,
  BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done
  or no longer relevant, etc. For an example see

    http://bioruby.open-bio.org/wiki/Google_Summer_of_Code

2. Update the final list of project ideas on the main OBF GSoC page
  to match.

    http://www.open-bio.org/wiki/Google_Summer_of_Code

3. Register with gsoc at lists.open-bio.org

4. Announce it on that list when you are ready :)

Anyone can submit a project idea! Former GSoC students are especially
encouraged to contribute ideas to the mailing lists.

Please have the updates done by Friday March 22nd. The number and quality of
the project ideas are part of the evaluation process for whether OBF is
accepted as a Summer of Code organisation again this year, so let's come up
with some good ones!

Pj. (Pjotr Prins)

Important dates: 

 * March 22nd: Finalise project ideas
 * March 29th: Deadline OBF mentoring organisation submission to Google

http://www.open-bio.org/wiki/Google_Summer_of_Code



From carandraug+dev at gmail.com  Mon Mar  4 01:58:41 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 01:58:41 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <512B3DCB.7050008@uni-wuerzburg.de>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
Message-ID: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>

On 25 February 2013 10:32, Andreas Leimbach
<andreas.leimbach at uni-wuerzburg.de> wrote:
> On 25.2.13 11:08, Carn? Draug wrote:
>>
>> I'm writing a perl module to write a description of the variance
>> between 2 sequences as described on
>> http://www.hgvs.org/mutnomen/recs-prot.html
>>
>> Basically, given 2 sequences, would returns something like "p.Lys2del
>> p.His25_Met26insGln" if those are the differences. It also accounts
>> for the existence of - characters on the sequences that may come from
>> their alignment.
>>
>> My question is, where on the project tree should I place the module?
>>
>> Also, is there something already written that would convert from 1 to
>> 3 letter code?
>>
> for your last question:
> You can convert aa strings from one to three letter code with
> 'Bio::SeqUtils'.

Thank you. I have never used Bio::SeqUtils. Not only does solve my
problem, but also seems to be the right place to insert my code.

If no one objects, I'll add a new method to Bio::SeqUtils named
"describe_mutation".

Carn?



From cjfields at illinois.edu  Mon Mar  4 03:45:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 03:45:45 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 7:58 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 25 February 2013 10:32, Andreas Leimbach
> <andreas.leimbach at uni-wuerzburg.de> wrote:
>> On 25.2.13 11:08, Carn? Draug wrote:
>>> 
>>> I'm writing a perl module to write a description of the variance
>>> between 2 sequences as described on
>>> http://www.hgvs.org/mutnomen/recs-prot.html
>>> 
>>> Basically, given 2 sequences, would returns something like "p.Lys2del
>>> p.His25_Met26insGln" if those are the differences. It also accounts
>>> for the existence of - characters on the sequences that may come from
>>> their alignment.
>>> 
>>> My question is, where on the project tree should I place the module?
>>> 
>>> Also, is there something already written that would convert from 1 to
>>> 3 letter code?
>>> 
>> for your last question:
>> You can convert aa strings from one to three letter code with
>> 'Bio::SeqUtils'.
> 
> Thank you. I have never used Bio::SeqUtils. Not only does solve my
> problem, but also seems to be the right place to insert my code.
> 
> If no one objects, I'll add a new method to Bio::SeqUtils named
> "describe_mutation".
> 
> Carn?

I'm fine with that; at some point it might be worth thinking about whether we need to organize the various *Utils modules a bit better.  As most of these export methods, they would be good targets for reorganization at some point (maybe into a general Bio::Utils namespace).

chris



From carandraug+dev at gmail.com  Mon Mar  4 04:15:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 4 Mar 2013 04:15:51 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>

On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
> [...] at some point it might be worth thinking about whether we need to
> organize the various *Utils modules a bit better.  As most of these export
> methods, they would be good targets for reorganization at some point
> (maybe into a general Bio::Utils namespace).

Do you mean placing all of them into a separate Util distribution? I
think it makes more sense to keep them close to what they deal with.

If it's just moving them all into Bio::Utils:: may be a good idea. At
the moment there's not much of a model for their naming. I found these
ones (am I missing anything that does not have Utils on the name?)

Bio/Coordinate/Utils.pm
Bio/SeqUtils.pm
Bio/Search/SearchUtils.pm
Bio/Search/BlastUtils.pm
Bio/Search/Tiling/MapTileUtils.pm

Also, only the last one seems to export anything.

Carn?



From cjfields at illinois.edu  Mon Mar  4 04:50:15 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Mar 2013 04:50:15 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>

On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> [...] at some point it might be worth thinking about whether we need to
>> organize the various *Utils modules a bit better.  As most of these export
>> methods, they would be good targets for reorganization at some point
>> (maybe into a general Bio::Utils namespace).
> 
> Do you mean placing all of them into a separate Util distribution? I
> think it makes more sense to keep them close to what they deal with.

No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

> If it's just moving them all into Bio::Utils:: may be a good idea. At
> the moment there's not much of a model for their naming. I found these
> ones (am I missing anything that does not have Utils on the name?)
> 
> Bio/Coordinate/Utils.pm
> Bio/SeqUtils.pm
> Bio/Search/SearchUtils.pm
> Bio/Search/BlastUtils.pm
> Bio/Search/Tiling/MapTileUtils.pm
> 
> Also, only the last one seems to export anything.
> 
> Carn?


A few mentioned above.  I don't think they have to be object classes, their entire purpose is to add functionality, so a full-blown class is probably a bit overkill (no one is likely to override their behavior).  

I could also see subdividing these up: DNA, RNA, and protein specific methods as well (for instance the 1->3 letter amino acid conversions, which would never be used on DNA).  It just depends how fine-grained we want to get.  

chris


From cjfields at illinois.edu  Tue Mar  5 14:46:34 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 5 Mar 2013 14:46:34 +0000
Subject: [Bioperl-l] Quick update on BioPerl release
In-Reply-To: <511C14AA.9030107@gmail.com>
References: <118F034CF4C3EF48A96F86CE585B94BF6CE24CF5@CHIMBX5.ad.uillinois.edu>
	<511C14AA.9030107@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF72F79C09@CHIMBX5.ad.uillinois.edu>

Just a note to keep everyone updated: the upcoming BioPerl release hasn't dropped off my (our) radar, but it will slip probably to the beginning of next week, likely Sunday-Monday CST.  There are a couple of changes/fixes that I would like to see going in (namely the recent HMMER fixes on master among others), and not insignificantly I've been tied up with a few $job-related tasks that have eaten up my time.

chris

On Feb 13, 2013, at 4:33 PM, Florent Angly <florent.angly at gmail.com> wrote:

> On 14/02/13 01:18, Fields, Christopher J wrote:
>> I*highly*  recommend using X.Y versioning for simplicity (e.g. no more 3-point versions)
> Yes, I support the X.Y versioning as well.
> Florent
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From clarsen at vecna.com  Tue Mar  5 20:55:05 2013
From: clarsen at vecna.com (Chris Larsen)
Date: Tue, 5 Mar 2013 15:55:05 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
	->1.6.1) ?
Message-ID: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>

Hello BioPerl-l,

Issue with partial codon translation. 

At our bioinformatics resource center we are using BioPerl to translate partial sequences to amino acids. This is necessary in the case of certain virus GenBank files, which are typically untranslated from polyprotein into their final mature peptide format, and no amino acid sequence is given in the source file. We need to make one from our mat_peptide generator. However our developers are finding that in their migration from BioPerl 1.6.0 to 1.6.1, the final amino acid generated from a partial nucleotide sequence is now being dropped, and this is resulting in several hundred files being altered relative to legacy. Here is an example:

In the hepC virus genome : AB014488

The nucleotide sequence (only) is given:

caagctgtca tggacatggt ggcgggggcc cactggggag tcctagcggg ccttgcctac
tattccatgg tggggaactg ggctaaggtt ttgattgtga tgctactctt cgccggcgtt
gacgggcata cccgcgtgac ggggggggtg caaggccacg tcacctctac actcacgtcc
ctctttagac ctggggcgtc ccagaaaatt cagcttgtaa acaccaatgg cagttggcac
atcaacagga ctgccctgaa ctgcaatgac tccctccaaa ctgggttcct tgccgcgctg
ttctacacac acaagttcaa cgcgtccgga tgcccggagc gcatggccag ctgccgctcc
attgacaagt tcgaccaggg atggggtccc atcacttatg cccaacctga caactcggac
cagaggccgt attgctggca ctatgcacct cgacagtgtg gtatcgtacc cgcgtcgcag
gtgtgcggtc cagtgtattg cttcacccca agccctgttg tggtggggac gaccgatcgt
tccggtgccc ctacgtataa ctgggg

where this ends in the partial codon of 'gg'. (Dont bother, this is 188 and 2/3 aa). A biologist might know that this terminus is always going to be a Glycine, G, since the third position is irrelevant, and so we would like to extend the partial codon into another amino acid in the last 'E2' protein encoded by this genome fragment. It's not sequenced but we can infer. The viral proteins are so short, it really matters! We want that G (and SPTAVRL). However the newer BioPerl version is not giving us the last amino acid. The functionality appears to be turned off, or a default argument was changed?  Issue with -complete ?

Sorry, not good quite enough in (bio)perl to find the solution myself. Only know it is not working now, and am trying to prevent the DBA from stabbing me in the neck with a spork because 4% of the records are now diff in the new pipeline. (Partial seqs, exactly 2 of 3 bp,  non-stop terminus in the available CDS). They are not telling me that errors don't occur within a string, only at the terminus, in viral polyproteins, and only when is not a stop codon. Ergo, color me confused.

I believe this is being handled by:

Bio::Tools::CodonTable and $obj->translate().

where the docs state the method:

"Returns a string of one letter amino acid codes from 
           nucleotide sequence input. The imput (sic) can be of any length. 
(...)
if the codon is two nucleotides long and if by adding
               an a third character 'N', it codes for a single amino
               acid (with exceptions above), return that, otherwise
               return empty string."

But I defer to the much larger bioperl-l wisdom. Sorry for the complexity. The options for them seem to be to continue using the 1.6.0 version to generate the longer better string, and 1.6.1 for everything else; but I'd rather the DBA team just uses one version of BioPerl. They could also update their version to 1.6.9. But, migrating a whole industrial pipeline to a new version for a production system also isnt trivial, so rather than hoping blindly for the fix in v1.6.9, I am asking here if the functionality works for others, and for which versions, and if its truly a bug, or has been fixed or changed, and as of what version. It would be great if one tiny piece could be replaced and the whole problem vanishes...But we may find it is our problem too. 

Hoping we just have to turn on this changed functionality, but we also want to see the issue documented. Cannot find the solution in BIO's docs. Sorry Brian!

I just want all the extra [SPTAVRLG] we can get. Any guidance I will graciously convey back to the team and try to work it out.

Thanks,

Chris

PS: Chris F and Amir discuss : highly related issue: http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html

"why should CodonTable::translate() automatically 'complete' the translation for incomplete codons by default?  I would consider this a bug."
 
-- 

Christopher Larsen, Ph.D.
Sr. Scientist / Grants Manager
Vecna Medical
Phone: (240) 965-4525
Fax: (240) 547-6133

clarsen at vecna dot com
http://vecna.com

Better Technology, Better World (TM)

The contents of this message may be privileged and confidential. Therefore, if this message has been received in error, please delete it. Your receipt of this message is not intended to waive any applicable privilege. Please do not disseminate this message without the permission of the author.









From Amir_Karger at hms.harvard.edu  Wed Mar  6 18:18:13 2013
From: Amir_Karger at hms.harvard.edu (Karger, Amir)
Date: Wed, 6 Mar 2013 13:18:13 -0500
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <AB5F76C3-6656-4CFC-A7D0-6CED7D8A43B3@vecna.com>
Message-ID: <CD5CF244.51003%amir_karger@hms.harvard.edu>

On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:

>Hello BioPerl-l,
>
>A biologist might know that this terminus is always going to be a
>Glycine, G, since the third position is irrelevant, and so we would like
>to extend the partial codon into another amino acid in the last 'E2'
>protein encoded by this genome fragment. It's not sequenced but we can
>infer. The viral proteins are so short, it really matters! We want that G
>(and SPTAVRL). However the newer BioPerl version is not giving us the
>last amino acid. The functionality appears to be turned off, or a default
>argument was changed?  Issue with -complete ?
>
>
>
>PS: Chris F and Amir discuss : highly related issue:
>http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>
>"why should CodonTable::translate() automatically 'complete' the
>translation for incomplete codons by default?  I would consider this a
>bug."

I guess one man's bug is another man's feature.

Sorry to have ruined your pipeline.

-Amir




From cjfields at illinois.edu  Wed Mar  6 19:19:23 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 6 Mar 2013 19:19:23 +0000
Subject: [Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0
 ->1.6.1) ?
In-Reply-To: <CD5CF244.51003%amir_karger@hms.harvard.edu>
References: <CD5CF244.51003%amir_karger@hms.harvard.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D8FF30@CHIMBX5.ad.uillinois.edu>

On Mar 6, 2013, at 12:18 PM, "Karger, Amir" <Amir_Karger at hms.harvard.edu> wrote:

> On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:
> 
>> Hello BioPerl-l,
>> 
>> A biologist might know that this terminus is always going to be a
>> Glycine, G, since the third position is irrelevant, and so we would like
>> to extend the partial codon into another amino acid in the last 'E2'
>> protein encoded by this genome fragment. It's not sequenced but we can
>> infer. The viral proteins are so short, it really matters! We want that G
>> (and SPTAVRL). However the newer BioPerl version is not giving us the
>> last amino acid. The functionality appears to be turned off, or a default
>> argument was changed?  Issue with -complete ?
>> 
>> 
>> 
>> PS: Chris F and Amir discuss : highly related issue:
>> http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>> 
>> "why should CodonTable::translate() automatically 'complete' the
>> translation for incomplete codons by default?  I would consider this a
>> bug."
> 
> I guess one man's bug is another man's feature.
> 
> Sorry to have ruined your pipeline.
> 
> -Amir

Chris, Amir,

Just a note: BioPerl is now at 1.6.901 on CPAN (released in 2011) and will be at 1.6.902 sometime next week.  

IIRC (and from back-reading in that thread), the problem was one of consistency, namely that translate() from PrimarySeqI and CodonTable act differently, and that to intuit what is the 'correct' thing to do in this case was possibly wrong from the PrimarySeqI end.  We went the route of least magic and least surprise, namely to return just the translated sequence w/o guessing whether the sequence in question is complete.  

So in my opinion, the old behavior was a bug, and the new behavior is more consistent.  The magic way is still there, though; pass in '-complete => 1'.  I can check that, just in case, to make sure it works.

chris




From a0071251 at nus.edu.sg  Thu Mar  7 05:24:06 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 13:24:06 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
Message-ID: <BBEBCF29-53C3-4BCD-AE6C-33B42D8F5933@nus.edu.sg>



Dear BioPerl,


I have encountered failed tests while installing Bioperl-1.6.901 from CPAN.
i downloaded BioPerl-1.6.901.tar and ran 'tar xvfz BioPerl-1.6.901.tar'
It gave me a message saying 'tar: Error exit delayed from previous errors.' but i moved on to install using 'perl Build.PL'
it gave me a message saying that some files are missing. I just moved on again and eventually when i ran './Build test', it told me that 32//55 test programs failed and 1/2436 subtests failed.
you will find a detailed report of the errors in the attached file.

Please take a look and let me know where i have gone wrong.
I am suspecting that the problem started when i extracted .tar file, but i have no idea how to correct that.

Your help will be much appreciated.
Thank you for your time and help.


Sincerely,
Ah Jung


-------------- next part --------------
A non-text attachment was scrubbed...
Name: error_from_Bioperl_installation
Type: application/octet-stream
Size: 126548 bytes
Desc: error_from_Bioperl_installation
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0004.obj>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ATT00001.txt
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/0c559a8d/attachment-0004.txt>

From a0071251 at nus.edu.sg  Thu Mar  7 06:15:58 2013
From: a0071251 at nus.edu.sg (Jeon Ah Jung)
Date: Thu, 7 Mar 2013 14:15:58 +0800
Subject: [Bioperl-l] Failed ./Build test while installing Bioperl-1.6.901
	(continued)
Message-ID: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>



Dear BioPerl,

I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
Hope this helps to clarify the problem further.

Thank you,
Ah Jung

-------------- next part --------------
A non-text attachment was scrubbed...
Name: error2
Type: application/octet-stream
Size: 71030 bytes
Desc: error2
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130307/363ab81b/attachment-0004.obj>

From scott at scottcain.net  Thu Mar  7 16:01:37 2013
From: scott at scottcain.net (Scott Cain)
Date: Thu, 7 Mar 2013 11:01:37 -0500
Subject: [Bioperl-l] Failed ./Build test while installing
	Bioperl-1.6.901 (continued)
In-Reply-To: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
References: <71B61326-04FB-4F03-8F7A-9E671162BCEB@nus.edu.sg>
Message-ID: <CA+JTaoxRxE5RtZuYwaW1OAG=G+TxkCQO3WC+OpCx7kzKKYoxCA@mail.gmail.com>

Hi Ah Jung,

The first problem you reported was because you didn't download the
whole tar file (the were a warning message that it was truncated, and
then messages that there were files missing); you just needed to
download it again.

For this message, you have this the first time cpan tries to install a module:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/Library/Perl/5.12/darwin-thread-multi-2level'
Do not have write permissions on '/Library/Perl/5.12/darwin-thread-multi-2level'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

When running cpan, you need to either run it as root (ie, "sudo cpan")
or configure it to use a local directory where you do have write
permission.  The former is probably easier, whereas the latter is
probably better.

Scott


On Thu, Mar 7, 2013 at 1:15 AM, Jeon Ah Jung <a0071251 at nus.edu.sg> wrote:
>
>
> Dear BioPerl,
>
> I have emailed earlier regarding failed tests while installing Bioperl by downloading .tar file directly.
> Shortly after i tried 'cpan install Bio::Perl' instead, and i am attaching the error messages i received for your information.
> Hope this helps to clarify the problem further.
>
> Thank you,
> Ah Jung
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From liyc1989 at gmail.com  Thu Mar  7 22:52:18 2013
From: liyc1989 at gmail.com (yichao li)
Date: Thu, 7 Mar 2013 17:52:18 -0500
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
Message-ID: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>

Hi,

            In the SYSNOPSIS, it says:

my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
  for my $feat ($in->next_feature) {
    # do something with $feat (a Bio::SeqFeature::Annotated object)
  }

  my $out = Bio::FeatureIO(-format=>'bed');
  for my $feat ($seq->get_seqFeatures) {
    $out->write_feature($feat);
  }

Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
'file.bed');*

If not, an error will occur.


------------------------------------
Best wishes,
Yichao
Ohio University Bioinformatics Lab
Phone: (740)-591-1289


From ragowthaman at gmail.com  Fri Mar  8 19:41:38 2013
From: ragowthaman at gmail.com (gowtham)
Date: Fri, 8 Mar 2013 11:41:38 -0800
Subject: [Bioperl-l] Writing alignment objects read via Bio::DB::Sam
Message-ID: <CAMvwBZnuEYHCFqOwyGuTPs9CZRxWhsGhJfpSzQ_Mrm4CO5mMJA@mail.gmail.com>

Hi Every One,
I'm using Bio::DB::Sam->new(-bam='') method to read a bam file. And I am
able to query individual values of each alignment record. For example
'XM','AS', and 'AS' tags, or alignment start end positions etc. After
filtering these records for some values (eg, mismatches), i would like to
write them back into a "SAM" (preferable BAM) format.

I am not able to find a method that writes the record. Can someone help me
with this?

Though, I am able to open a new bam file for  writing using
Bio::DB::Bam->open(my.bam, 'w'), I dont know how to convert the SAM
alignment i read from (Bio::DB::SAM) to be written using this.

write1() does not accept alignment object read by Bio::DB::SAM, it accepts
objects read only by Bio::DB::BAM.


Thanks very much in advance,
Gowthaman
-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).


From witch.of.agnessi at gmail.com  Sat Mar  9 01:24:01 2013
From: witch.of.agnessi at gmail.com (witch.of.agnessi at gmail.com)
Date: Fri, 8 Mar 2013 17:24:01 -0800 (PST)
Subject: [Bioperl-l] How to find 'is_a'/'part_of' relationship using
	GO::Termfinder
Message-ID: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>

Hello All,

I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
 node. I wonder How I can extract the type of relationship,
like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
any better way to do this in Bioperl?

Thanks in advance


 


From antony.vincent.1 at ulaval.ca  Sat Mar  9 03:56:59 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Fri, 8 Mar 2013 19:56:59 -0800 (PST)
Subject: [Bioperl-l]  sh: 1: Syntax error: "(" unexpected
Message-ID: <35154292.post@talk.nabble.com>


Hi!

I'm trying to use emboss program (water or needle) with a bioperl script. I
got this error when I try the script: sh: 1: Syntax error: "(" unexpected

Here is the script:

#!/usr/bin/perl 

 # get an EMBOSS factory
  use Bio::Factory::EMBOSS;
  use Bio::AlignIO;
  use Bio::SeqIO;
  $f = Bio::Factory::EMBOSS -> new();
  # get an EMBOSS application  object from the factory
  $water = $f->program('water');
    $inputfilename = "krt1.fasta";
    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
                             '-format' => 'fasta');

    $inputfilename2 = "krt2.fasta";
    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
                             '-format' => 'fasta');
  # here is an example of running the application -
  # water can compare 1 sequence against 1 or more sequences
  # in a database using Smith-Waterman
  #this would be a list of seqs to compare 
                       # (could be just 1)
  my $wateroutfile = 'out.water';
  $water->run({-sequences => $seq_to_test,
               -seqall    => \@seqs_to_check,
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => $wateroutfile});
  # now you might want to get the alignment
  
  my $alnin = Bio::AlignIO->new(-format => 'emboss',
                                       -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }

Have you an idea of what can do this error?

Thanks!
-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From l.m.timmermans at students.uu.nl  Sat Mar  9 13:43:54 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Sat, 9 Mar 2013 14:43:54 +0100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>

On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected

The error suggests the script is interpreted by the shell instead of
perl. Are you sure the hashbang (#!) is the absolute first thing in
the file. No whitespace or BOM character in the front?

Leon


From carandraug+dev at gmail.com  Sat Mar  9 14:03:50 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:03:50 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>

On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>  wrote:
>
>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> [...] at some point it might be worth thinking about whether we need to
>>> organize the various *Utils modules a bit better.  As most of these export
>>> methods, they would be good targets for reorganization at some point
>>> (maybe into a general Bio::Utils namespace).
>>
>> Do you mean placing all of them into a separate Util distribution? I
>> think it makes more sense to keep them close to what they deal with.
>
> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?

How would you define exportable? I usually don't like the idea of
having functions exported by default. Specially since it's so easy for
the user to load them themselves.

Carn?



From carandraug+dev at gmail.com  Sat Mar  9 14:47:08 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 14:47:08 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
	Bio::DB::EUtilities ?
Message-ID: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>

Hi

I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
module, part of bioperl-live, seems to be re-implementing pieces of
Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

According to Bio::DB::Biblio::eutils documentation, it should not be
used directly, instead should be used through Bio::DB::Biblio. This
means that it could be replaced by Bio::DB::EUtilities without any
disturbance (other than adding a dependency and as long as users have
been respecting the recommendations).

Carn?



From cjfields at illinois.edu  Sat Mar  9 15:07:20 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:07:20 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate
	of	Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
> module, part of bioperl-live, seems to be re-implementing pieces of
> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?

Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.

> According to Bio::DB::Biblio::eutils documentation, it should not be
> used directly, instead should be used through Bio::DB::Biblio. This
> means that it could be replaced by Bio::DB::EUtilities without any
> disturbance (other than adding a dependency and as long as users have
> been respecting the recommendations).
> 
> Carn?

Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

chris


From cjfields at illinois.edu  Sat Mar  9 15:05:33 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 15:05:33 +0000
Subject: [Bioperl-l] module for description of sequence variants (where
 to place code)
In-Reply-To: <CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
References: <CAPOrs_0X9tF0_4q-KmV_OMu5vPDT7JbRsPZteLf5dYh1n9_vPg@mail.gmail.com>
	<512B3DCB.7050008@uni-wuerzburg.de>
	<CAPOrs_2syf+9_sCndB6v_CW1h0jGMSnGgA2YJquZ2A2W7_CNgg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74954@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_0WKug4bjXAi4bcF=Rv882ye1Lg8DfBMvKRCO6Sm6Awzw@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF72F74C33@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1o=8ZHa9MSxFJto8J2PGUbuu-U+nXeWhVShTSknUL7yg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94D74@CHIMBX5.ad.uillinois.edu>

On Mar 9, 2013, at 8:03 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 3, 2013, at 10:15 PM, Carn? Draug <carandraug+dev at gmail.com>
>> wrote:
>> 
>>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> [...] at some point it might be worth thinking about whether we need to
>>>> organize the various *Utils modules a bit better.  As most of these export
>>>> methods, they would be good targets for reorganization at some point
>>>> (maybe into a general Bio::Utils namespace).
>>> 
>>> Do you mean placing all of them into a separate Util distribution? I
>>> think it makes more sense to keep them close to what they deal with.
>> 
>> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not?
> 
> How would you define exportable? I usually don't like the idea of
> having functions exported by default. Specially since it's so easy for
> the user to load them themselves.
> 
> Carn?

Yes, I agree (no export by default).

chris


From carandraug+dev at gmail.com  Sat Mar  9 21:20:51 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 9 Mar 2013 21:20:51 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>

On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>> module, part of bioperl-live, seems to be re-implementing pieces of
>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>
> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>
>> According to Bio::DB::Biblio::eutils documentation, it should not be
>> used directly, instead should be used through Bio::DB::Biblio. This
>> means that it could be replaced by Bio::DB::EUtilities without any
>> disturbance (other than adding a dependency and as long as users have
>> been respecting the recommendations).
>>
>> Carn?
>
> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).

So I was looking at this but seems that would cause an issue with
circular dependency. Not at module level, but at distribution level
(Bio-Eutilities is dependent on bioperl-live and bioperl-live
dependent on Bio-EUtilities because of Bio::DB::Biblio).

This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
Could this be done and a separate distribution created for it? None of
the empty repositories seems fitting for it.

Carn?



From cjfields at illinois.edu  Sat Mar  9 22:06:41 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 9 Mar 2013 22:06:41 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>


On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 9 March 2013 15:07, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 8:47 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>>> module, part of bioperl-live, seems to be re-implementing pieces of
>>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>> 
>> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>> 
>>> According to Bio::DB::Biblio::eutils documentation, it should not be
>>> used directly, instead should be used through Bio::DB::Biblio. This
>>> means that it could be replaced by Bio::DB::EUtilities without any
>>> disturbance (other than adding a dependency and as long as users have
>>> been respecting the recommendations).
>>> 
>>> Carn?
>> 
>> Right; the intent is at some point to also do something similar with other eutils-related tools (Bio::DB::GenBank, etc).
> 
> So I was looking at this but seems that would cause an issue with
> circular dependency. Not at module level, but at distribution level
> (Bio-Eutilities is dependent on bioperl-live and bioperl-live
> dependent on Bio-EUtilities because of Bio::DB::Biblio).
> 
> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
> Could this be done and a separate distribution created for it? None of
> the empty repositories seems fitting for it.
> 
> Carn?

Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

chris





From carandraug+dev at gmail.com  Sun Mar 10 03:06:02 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 10 Mar 2013 03:06:02 +0000
Subject: [Bioperl-l] graphics of gene distribution through a genome interval
Message-ID: <CAPOrs_1BwNeGLse000t6rmNEhneP_svosM2KYhMO+8OO6JrZ-w@mail.gmail.com>

Hi everyone

I was wondering if anyone knows any tools to produce this type of
diagram? http://picpaste.com/1fqB4e8h.png It a piece of genome with
some gene positions marked. And it has nice "zoom-in boxes" around
some more cluttered regions. I've seen these more than once but do not
know how to generate one. Could someone give me a pointer?

Thanks,
Carn?



From antony.vincent.1 at ulaval.ca  Sun Mar 10 13:17:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 06:17:09 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From Russell.Smithies at agresearch.co.nz  Sun Mar 10 20:30:36 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 11 Mar 2013 09:30:36 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>

I'll get in first and say it's best to 'use strict', and 'use warnings'  ;-)

Perhaps some of the params to water have changed? It looks like it wants filenames, not objects.
I get the same errors with your code - which I think is coming from water.

If I do this it seems to work OK:
---------------------------------------
#!/usr/bin/perl

# get an EMBOSS factory
use Bio::Factory::EMBOSS;
use Bio::AlignIO;
use Bio::SeqIO;

use strict;
use warnings;

my $f = Bio::Factory::EMBOSS -> new();
# get an EMBOSS application  object from the factory
my $water = $f->program('water');
my $wateroutfile = 'out.water';
$water->run({  -verbose => 1,
               -asequence => 'krt1.fasta',
               -bsequence => 'krt2.fasta',
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => 'out.water'});
------------------------------------------------


illustrious$ cat out.water
########################################
# Program: water
# Rundate: Mon 11 Mar 2013 09:29:36
# Commandline: water
#    -gapopen 10.0
#    -gapextend 0.5
#    -outfile out.water
#    -asequence krt1.fasta
#    -verbose 1
#    -bsequence krt2.fasta
#    -auto
# Align_format: srspair
# Report_file: out.water
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: K2C1_HUMAN
# 2: K22E_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     436/667 (65.4%)
# Similarity:   499/667 (74.8%)
# Gaps:          78/667 (11.7%)
# Score: 2023.5
#
#
#=======================================

K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR     45
                     ||.|.|.:|..|.||     |||||||.:....||:|||
K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------     39

K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG     91
                      .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA     86

K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG    130
                     ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG    136

K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR    179
                     | ||||.|||         ||||.||::||||||||||::|||||.||::
K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ    177

K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP    229
                     ||||||:|||:|||||||||||||||||||||||||||::..||..||||
K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP    227

K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN    279
                     .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA    277

K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ    329
                     |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS    327

K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE    379
                     :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE    377

K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA    429
                     ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA    427

K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI    479
                     |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI    477

K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG    521
                     ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG    525

K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS    568
                        ||||.||.|||||||...||.||.||| ||.        |||| |||
K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS    565

K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR    616
                     |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG    610

K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
                     |..|||    |||||||
K22E_HUMAN       611 GYGSGG----GGSSSVK    623


#---------------------------------------
#---------------------------------------



--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Monday, 11 March 2013 2:17 a.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From antony.vincent.1 at ulaval.ca  Sun Mar 10 21:59:51 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sun, 10 Mar 2013 14:59:51 -0700 (PDT)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
	<35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF37337864CFB@exchsth.agresearch.co.nz>
Message-ID: <35158468.post@talk.nabble.com>


That's works! Thanks a lot!

Smithies, Russell wrote:
> 
> I'll get in first and say it's best to 'use strict', and 'use warnings' 
> ;-)
> 
> Perhaps some of the params to water have changed? It looks like it wants
> filenames, not objects.
> I get the same errors with your code - which I think is coming from water.
> 
> If I do this it seems to work OK:
> ---------------------------------------
> #!/usr/bin/perl
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> 
> use strict;
> use warnings;
> 
> my $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> my $water = $f->program('water');
> my $wateroutfile = 'out.water';
> $water->run({  -verbose => 1,
>                -asequence => 'krt1.fasta',
>                -bsequence => 'krt2.fasta',
>                -gapopen   => '10.0',
>                -gapextend => '0.5',
>                -outfile   => 'out.water'});
> ------------------------------------------------
> 
> 
> illustrious$ cat out.water
> ########################################
> # Program: water
> # Rundate: Mon 11 Mar 2013 09:29:36
> # Commandline: water
> #    -gapopen 10.0
> #    -gapextend 0.5
> #    -outfile out.water
> #    -asequence krt1.fasta
> #    -verbose 1
> #    -bsequence krt2.fasta
> #    -auto
> # Align_format: srspair
> # Report_file: out.water
> ########################################
> 
> #=======================================
> #
> # Aligned_sequences: 2
> # 1: K2C1_HUMAN
> # 2: K22E_HUMAN
> # Matrix: EBLOSUM62
> # Gap_penalty: 10.0
> # Extend_penalty: 0.5
> #
> # Length: 667
> # Identity:     436/667 (65.4%)
> # Similarity:   499/667 (74.8%)
> # Gaps:          78/667 (11.7%)
> # Score: 2023.5
> #
> #
> #=======================================
> 
> K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR    
> 45
>                      ||.|.|.:|..|.||     |||||||.:....||:|||
> K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------    
> 39
> 
> K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG    
> 91
>                       .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
> K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA    
> 86
> 
> K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG   
> 130
>                      ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
> K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG   
> 136
> 
> K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR   
> 179
>                      | ||||.|||         ||||.||::||||||||||::|||||.||::
> K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ   
> 177
> 
> K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP   
> 229
>                      ||||||:|||:|||||||||||||||||||||||||||::..||..||||
> K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP   
> 227
> 
> K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN   
> 279
>                      .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
> K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA   
> 277
> 
> K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ   
> 329
>                      |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
> K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS   
> 327
> 
> K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE   
> 379
>                      :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
> K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE   
> 377
> 
> K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA   
> 429
>                      ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
> K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA   
> 427
> 
> K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI   
> 479
>                      |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
> K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI   
> 477
> 
> K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG   
> 521
>                      ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
> K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG   
> 525
> 
> K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS   
> 568
>                         ||||.||.|||||||...||.||.||| ||.        |||| |||
> K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS   
> 565
> 
> K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR   
> 616
>                      |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
> K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG   
> 610
> 
> K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
>                      |..|||    |||||||
> K22E_HUMAN       611 GYGSGG----GGSSSVK    623
> 
> 
> #---------------------------------------
> #---------------------------------------
> 
> 
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Monday, 11 March 2013 2:17 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it
> like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this
> why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl
>>> script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context:
> http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35158468.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From liamelbourne at me.com  Sat Mar  9 09:18:34 2013
From: liamelbourne at me.com (Liam Elbourne)
Date: Sat, 09 Mar 2013 20:18:34 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <7A059EB2-147A-4B26-B321-DEB40D1693EC@me.com>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
>  use Bio::Factory::EMBOSS;
>  use Bio::AlignIO;
>  use Bio::SeqIO;
>  $f = Bio::Factory::EMBOSS -> new();
>  # get an EMBOSS application  object from the factory
>  $water = $f->program('water');
>    $inputfilename = "krt1.fasta";
>    $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                             '-format' => 'fasta');
> 
>    $inputfilename2 = "krt2.fasta";
>    @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                             '-format' => 'fasta');
>  # here is an example of running the application -
>  # water can compare 1 sequence against 1 or more sequences
>  # in a database using Smith-Waterman
>  #this would be a list of seqs to compare 
>                       # (could be just 1)
>  my $wateroutfile = 'out.water';
>  $water->run({-sequences => $seq_to_test,
>               -seqall    => \@seqs_to_check,
>               -gapopen   => '10.0',
>               -gapextend => '0.5',
>               -outfile   => $wateroutfile});
>  # now you might want to get the alignment
> 
>  my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                       -file   => $wateroutfile);
> 
>  while ( my $aln = $alnin->next_aln ) {
>      # process the alignment -- these will be Bio::SimpleAlign objects
>  }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From antony.vincent.1 at ulaval.ca  Sat Mar  9 18:24:43 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 10:24:43 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
References: <35154292.post@talk.nabble.com>
	<CAC1jpXBrXA_gokQLHE4zrnG6aKx7UJEf+8FsoczPu1GBsMUwaQ@mail.gmail.com>
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From liam.elbourne at mq.edu.au  Sat Mar  9 11:39:44 2013
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Sat, 9 Mar 2013 22:39:44 +1100
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35154292.post@talk.nabble.com>
References: <35154292.post@talk.nabble.com>
Message-ID: <0C3E5EF2-9A20-4C33-94B7-93F242E69704@mq.edu.au>

Hi Antony,

How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.

Regards,
Liam.



On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> 
> Hi!
> 
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> Here is the script:
> 
> #!/usr/bin/perl 
> 
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application  object from the factory
> $water = $f->program('water');
>   $inputfilename = "krt1.fasta";
>   $seq_to_test  = Bio::SeqIO->new(-file => $inputfilename ,
>                            '-format' => 'fasta');
> 
>   $inputfilename2 = "krt2.fasta";
>   @seqs_to_check  = Bio::SeqIO->new(-file => $inputfilename2 ,
>                            '-format' => 'fasta');
> # here is an example of running the application -
> # water can compare 1 sequence against 1 or more sequences
> # in a database using Smith-Waterman
> #this would be a list of seqs to compare 
>                      # (could be just 1)
> my $wateroutfile = 'out.water';
> $water->run({-sequences => $seq_to_test,
>              -seqall    => \@seqs_to_check,
>              -gapopen   => '10.0',
>              -gapextend => '0.5',
>              -outfile   => $wateroutfile});
> # now you might want to get the alignment
> 
> my $alnin = Bio::AlignIO->new(-format => 'emboss',
>                                      -file   => $wateroutfile);
> 
> while ( my $aln = $alnin->next_aln ) {
>     # process the alignment -- these will be Bio::SimpleAlign objects
> }
> 
> Have you an idea of what can do this error?
> 
> Thanks!
> -- 
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 235 bytes
Desc: Message signed with OpenPGP using GPGMail
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20130309/0fd852ec/attachment.sig>

From antony.vincent.1 at ulaval.ca  Sun Mar 10 02:59:26 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Sat, 9 Mar 2013 18:59:26 -0800 (PST)
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
Message-ID: <35155738.post@talk.nabble.com>


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why
I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
> 
> The error suggests the script is interpreted by the shell instead of
> perl. Are you sure the hashbang (#!) is the absolute first thing in
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From sidd.basu at gmail.com  Mon Mar 11 17:16:45 2013
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Mon, 11 Mar 2013 12:16:45 -0500
Subject: [Bioperl-l] Re: How to find 'is_a'/'part_of' relationship
	using	GO::Termfinder
In-Reply-To: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
References: <b23a3e91-c178-4f30-9573-a1d9fb9f1c8a@googlegroups.com>
Message-ID: <513e1181.aade320a.5bee.ffff87da@mx.google.com>

Hi, 

On Fri, 08 Mar 2013, witch.of.agnessi at gmail.com wrote:

> Hello All,
> 
> I'm using Perl's GO::Termfinder to find  parent/child nodes of a given 
>  node. I wonder How I can extract the type of relationship,
> like 'is_a', 'part_of' etc. relationship that connects two nodes? Is there 
> any better way to do this in Bioperl?

You could use the Bioperl's ontology module in this case. For example,  here is how
you could start with ...

1. Parse gene_ontology obo file with Bio::OntologyIO
https://metacpan.org/module/Bio::OntologyIO

2. Once you get the ontology object(Bio::Ontology::Ontology), you could
use the *find_terms*
https://metacpan.org/module/Bio::Ontology::Ontology#find_terms
to get your term objects.

3. Then use the graph lookup methods
   such as *get_relationships*, get_child_terms, get_parent_terms,
   get_ancestor_terms that takes a term and relationship objects to extract
   whatever connection you are looking for. 

Hope this helps, 
-siddhartha


   


> 
> Thanks in advance
> 
> 
>  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From Russell.Smithies at agresearch.co.nz  Mon Mar 11 18:09:56 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 12 Mar 2013 07:09:56 +1300
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <35155738.post@talk.nabble.com>
References: <35155738.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>

I suspect that there's several versions of water and the parameters have changed.
This is the version I'm using and I can reproduce the errors:

intrepid$ water -h
Smith-Waterman local alignment of sequences
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -gapopen            float      [10.0 for any sequence] The gap open penalty
                                  is the score taken away when a gap is
                                  created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value assumes you are using the EBLOSUM62
                                  matrix for protein sequences, and the
                                  EDNAFULL matrix for nucleotide sequences.
                                  (Number from 0.000 to 100.000)
   -gapextend          float      [0.5 for any sequence] The gap extension
                                  penalty is added to the standard gap penalty
                                  for each base or residue in the gap. This
                                  is how long gaps are penalized. Usually you
                                  will expect a few long gaps rather than many
                                  short gaps, so the gap extension penalty
                                  should be lower than the gap penalty. An
                                  exception is where one or both sequences are
                                  single reads with possible sequencing
                                  errors in which case you would expect many
                                  single base gaps. You can get this result by
                                  setting the gap open penalty to zero (or
                                  very low) and using the gap extension
                                  penalty to control gap scoring. (Number from
                                  0.000 to 10.000)
  [-outfile]           align      [*.water] Output alignment file name
                                  (default -aformat srspair)

   Additional (Optional) qualifiers:
   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.

   Advanced (Unprompted) qualifiers:
   -[no]brief          boolean    [Y] Brief identity and similarity

   General qualifiers:
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Sunday, 10 March 2013 3:59 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> I'm trying to use emboss program (water or needle) with a bioperl script.
>> I
>> got this error when I try the script: sh: 1: Syntax error: "(" 
>> unexpected
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

--
View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From cjfields at illinois.edu  Mon Mar 11 20:57:59 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 11 Mar 2013 20:57:59 +0000
Subject: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
References: <35155738.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF373379097CB@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D96D47@CHIMBX5.ad.uillinois.edu>

I think the EMBOSS code checks the ACD file for whatever version of EMBOSS is installed, parses the parameters out of that, and uses those for input.  I don't remember if it accepts a Bio::Seq as input (I don't recall it doing so), but if it does then we should file that as a bug.

chris

On Mar 11, 2013, at 1:09 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> I suspect that there's several versions of water and the parameters have changed.
> This is the version I'm using and I can reproduce the errors:
> 
> intrepid$ water -h
> Smith-Waterman local alignment of sequences
> Version: EMBOSS:6.5.0.0
> 
>   Standard (Mandatory) qualifiers:
>  [-asequence]         sequence   Sequence filename and optional format, or
>                                  reference (input USA)
>  [-bsequence]         seqall     Sequence(s) filename and optional format, or
>                                  reference (input USA)
>   -gapopen            float      [10.0 for any sequence] The gap open penalty
>                                  is the score taken away when a gap is
>                                  created. The best value depends on the
>                                  choice of comparison matrix. The default
>                                  value assumes you are using the EBLOSUM62
>                                  matrix for protein sequences, and the
>                                  EDNAFULL matrix for nucleotide sequences.
>                                  (Number from 0.000 to 100.000)
>   -gapextend          float      [0.5 for any sequence] The gap extension
>                                  penalty is added to the standard gap penalty
>                                  for each base or residue in the gap. This
>                                  is how long gaps are penalized. Usually you
>                                  will expect a few long gaps rather than many
>                                  short gaps, so the gap extension penalty
>                                  should be lower than the gap penalty. An
>                                  exception is where one or both sequences are
>                                  single reads with possible sequencing
>                                  errors in which case you would expect many
>                                  single base gaps. You can get this result by
>                                  setting the gap open penalty to zero (or
>                                  very low) and using the gap extension
>                                  penalty to control gap scoring. (Number from
>                                  0.000 to 10.000)
>  [-outfile]           align      [*.water] Output alignment file name
>                                  (default -aformat srspair)
> 
>   Additional (Optional) qualifiers:
>   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
>                                  This is the scoring matrix file used when
>                                  comparing sequences. By default it is the
>                                  file 'EBLOSUM62' (for proteins) or the file
>                                  'EDNAFULL' (for nucleic sequences). These
>                                  files are found in the 'data' directory of
>                                  the EMBOSS installation.
> 
>   Advanced (Unprompted) qualifiers:
>   -[no]brief          boolean    [Y] Brief identity and similarity
> 
>   General qualifiers:
>   -help               boolean    Report command line options and exit. More
>                                  information on associated and general
>                                  qualifiers can be found with -help -verbose
> 
> 
> --Russell
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
> Sent: Sunday, 10 March 2013 3:59 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected
> 
> 
> Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
> this:
> anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
> sh: 1: Syntax error: "(" unexpected
> So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!
> 
> 
> Leon Timmermans-2 wrote:
>> 
>> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
>> wrote:
>>> I'm trying to use emboss program (water or needle) with a bioperl script.
>>> I
>>> got this error when I try the script: sh: 1: Syntax error: "(" 
>>> unexpected
>> 
>> The error suggests the script is interpreted by the shell instead of 
>> perl. Are you sure the hashbang (#!) is the absolute first thing in 
>> the file. No whitespace or BOM character in the front?
>> 
>> Leon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> --
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From bosborne11 at verizon.net  Tue Mar 12 15:04:36 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 12 Mar 2013 11:04:36 -0400
Subject: [Bioperl-l] An error in the SYNOPSIS of Bio::FeatureIO::bed
In-Reply-To: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
References: <CANYeyAC8=J4V5-e+3rjT_1y7YEifQswyYO+jLW54ORwS+tOtkQ@mail.gmail.com>
Message-ID: <C262A6D6-3967-4290-90FF-738A1A8CCC3F@verizon.net>

Yichao,

Fixed. Thank you for pointing that out.

Brian O.


On Mar 7, 2013, at 5:52 PM, yichao li <liyc1989 at gmail.com> wrote:

> Hi,
> 
>            In the SYSNOPSIS, it says:
> 
> my $in =* Bio::FeatureIO(-format => 'bed', -file => 'file.bed');*
>  for my $feat ($in->next_feature) {
>    # do something with $feat (a Bio::SeqFeature::Annotated object)
>  }
> 
>  my $out = Bio::FeatureIO(-format=>'bed');
>  for my $feat ($seq->get_seqFeatures) {
>    $out->write_feature($feat);
>  }
> 
> Actually, it should be *Bio::FeatureIO->new(-format => 'bed', -file =>
> 'file.bed');*
> 
> If not, an error will occur.
> 
> 
> ------------------------------------
> Best wishes,
> Yichao
> Ohio University Bioinformatics Lab
> Phone: (740)-591-1289
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Tue Mar 12 22:43:05 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 12 Mar 2013 22:43:05 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>

On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>> Could this be done and a separate distribution created for it? None of
>> the empty repositories seems fitting for it.
>>
>
> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.

Could you (or some other admin) prepare a separate Bio-biblio
repository? I'm splitting them now and need a repo to push into.

Thanks,
Carn?



From cjfields at illinois.edu  Tue Mar 12 23:42:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 12 Mar 2013 23:42:11 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>

Done:

https://github.com/bioperl/Bio-Biblio

chris

On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>> Could this be done and a separate distribution created for it? None of
>>> the empty repositories seems fitting for it.
>>> 
>> 
>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
> 
> Could you (or some other admin) prepare a separate Bio-biblio
> repository? I'm splitting them now and need a repo to push into.
> 
> Thanks,
> Carn?




From therealsisterdot at gmail.com  Mon Mar 11 10:31:42 2013
From: therealsisterdot at gmail.com (sisterdot)
Date: Mon, 11 Mar 2013 03:31:42 -0700 (PDT)
Subject: [Bioperl-l] parsing psiblast + ?
Message-ID: <97a3d346-c5dd-41f4-b71d-042cc92f7ee9@googlegroups.com>

hey hey, 

i am using perl v5.10.0 and Bio::SearchIO 1.006901

i would like to use psiblast 2.2.27 + (instead of blastpgp), but parsing 
via  
new Bio::SearchIO(-format => "blast",-file => "$file")
doesn't seem to work well- individual iterations are interpreted as 
separate results.

Bio::SearchIO doesn't seem to really understand "psiblast +" default 
pairwise output, or am i mistaken?
if i am not mistaken, are there alternatives in Bioperl for parsing 
"psiblast +" with the default "-outfmt 0"?

thanks a lot
sis


From scott at scottcain.net  Thu Mar 14 02:51:55 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 13 Mar 2013 22:51:55 -0400
Subject: [Bioperl-l] Early registration for GMOD meeting closes in one week
Message-ID: <CA+JTaozZFOWKcsZ0bDqUS1mD_E2kWLUGi_1bA+bGj6GKb9eJdg@mail.gmail.com>

Hello,

The GMOD meeting is in Cambridge, England on April 5-6 (right before
the Biocurator meeting) and early registration closes March 21 (in one
week).  It is shaping up to be a good meeting with several interesting
talks scheduled.  Please try to make it!  For more information on the
meeting, see the meeting page:

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

and to save some money on your registration, go to

  http://gmod2013.eventbrite.com/

before March 21 to register.

If you'd like to give a talk at the meeting please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From carandraug+dev at gmail.com  Thu Mar 14 23:55:27 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 14 Mar 2013 23:55:27 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>

On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>> Could this be done and a separate distribution created for it? None of
>>>> the empty repositories seems fitting for it.
>>>>
>>>
>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>
>> Could you (or some other admin) prepare a separate Bio-biblio
>> repository? I'm splitting them now and need a repo to push into.
>>
>
> Done:
>
> https://github.com/bioperl/Bio-Biblio

Thanks, I'm trying to prepare a release of the Bio-biblio distribution
soon. I'd like to do a 1.7 release first. One with minimal changes
compared to the current bioperl-live. Could someone give me
co-maintenance of the Bio::Biblio namespace? Or should I just prepare
everything for the release and wait for someone else to just accept
it? Also, the Bio-biblio distribution also has modules on the
Bio::DB::biblio namespace.

Carn?



From carandraug+dev at gmail.com  Fri Mar 15 01:21:16 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 01:21:16 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
Message-ID: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>

Hi

I'm using dist::zilla and found the BioPerl plugin. I noticed that the
bug tracker information is set to

  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
  bugtracker.mailto = bug-${dist}@rt.cpan.org

shouldn't they set for https://redmine.open-bio.org/projects/bioperl?

Carn?



From cjfields at illinois.edu  Fri Mar 15 01:59:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 01:59:53 +0000
Subject: [Bioperl-l] is Bio::DB::Biblio::eutils duplicate of
 Bio::DB::EUtilities ?
In-Reply-To: <CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
References: <CAPOrs_1-w5xcQ1vN1kF127M7Tgc-R-AAkmnt8njOoSs4oVymzg@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94DAA@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2=7hj3XSeJVuOyjfwoLg3o5Ek_-Fv0x4iAe94H4AUj0Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D94EE3@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_3kXkVNf3eDV+r74=7ktoEreOEZgvPs7o6NPoQGFC701g@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9C11D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2_FzyUnxhvYWEbg0xqex=4zqKLx5Cecgux=NmKBtiYvQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1CF@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 6:55 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 12 March 2013 23:42, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 12, 2013, at 5:43 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> On 9 March 2013 22:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 9, 2013, at 3:20 PM, Carn? Draug <carandraug+dev at gmail.com>
>>>>> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
>>>>> Could this be done and a separate distribution created for it? None of
>>>>> the empty repositories seems fitting for it.
>>>>> 
>>>> 
>>>> Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself.  Not sure how much it is actually used, tell the truth.
>>> 
>>> Could you (or some other admin) prepare a separate Bio-biblio
>>> repository? I'm splitting them now and need a repo to push into.
>>> 
>> 
>> Done:
>> 
>> https://github.com/bioperl/Bio-Biblio
> 
> Thanks, I'm trying to prepare a release of the Bio-biblio distribution
> soon. I'd like to do a 1.7 release first. One with minimal changes
> compared to the current bioperl-live. Could someone give me
> co-maintenance of the Bio::Biblio namespace? Or should I just prepare
> everything for the release and wait for someone else to just accept
> it? Also, the Bio-biblio distribution also has modules on the
> Bio::DB::biblio namespace.
> 
> Carn?

That's fine; you can actually do a point release (say, 1.7) and list the proper Bio::* dependencies you need.  I wouldn't list Bio::Root::Root specifically.  

Does anyone here have a problem with Carn? taking co-maintenance of these modules on CPAN?  Please speak up over the next few days, otherwise I'll go ahead and grant it.  Would be nice to have someone looking after these.

chris


From cjfields at illinois.edu  Fri Mar 15 02:00:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:00:43 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>

Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?

chris

On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
> bug tracker information is set to
> 
>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>  bugtracker.mailto = bug-${dist}@rt.cpan.org
> 
> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Fri Mar 15 02:04:23 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 02:04:23 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>

On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> Hi
>>
>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>> bug tracker information is set to
>>
>>  bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>  bugtracker.mailto = bug-${dist}@rt.cpan.org
>>
>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>
>> Carn?
>>
>
> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>
> chris

Yes it is. But only the version 0.01.



From cjfields at illinois.edu  Fri Mar 15 02:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 02:41:28 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>

On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>> bug tracker information is set to
>>> 
>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>> 
>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>> 
>>> Carn?
>>> 
>> 
>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>> 
>> chris
> 
> Yes it is. But only the version 0.01.

Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

chris


From carandraug+dev at gmail.com  Fri Mar 15 03:15:11 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 15 Mar 2013 03:15:11 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>

On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>> bug tracker information is set to
>>>>
>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>
>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>
>>>> Carn?
>>>>
>>>
>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>
>>> chris
>>
>> Yes it is. But only the version 0.01.
>
> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)

I think I got it working with the BioPerl bundle. It passes all tests.
Now I was trying to set Pod::Weaver to write the feedback section
automatically but might be better to set it up as pasrt of the BioPerl
bundle.

Carn?



From fossandonc at hotmail.com  Fri Mar 15 14:26:44 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 11:26:44 -0300
Subject: [Bioperl-l] Bug #2936
Message-ID: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>

Hello,

Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven?t
received any feedback yet.

https://redmine.open-bio.org/issues/2936

 

Probably everybody is busy, so I would like to ask only if the proposed fix
is acceptable. If the fix were fine, I could prepare changes in my forked
repo, add tests (in ?t/Seq/PrimarySeq.t????) and make a pull request. What
do you think?

 

Cheers,

 

--

Francisco J. Ossandon

Bioinformatician.

Ph.D. Candidate, University Andres Bello.

Center for Bioinformatics and Genome Biology,

Fundacion Ciencia para la Vida.

Santiago, Chile.

 <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm

 




From cjfields at illinois.edu  Fri Mar 15 14:46:11 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 14:46:11 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74D9FAFE@CHIMBX5.ad.uillinois.edu>

Sure, a pull request would be good.  I suggest making sure you are in sync with the 'master' branch first, but I don't think you'll run into conflicts with that.  

My guess is we'll need to pull this into a branch and test rigorously first if it is to go into a bioperl 1.6.  One of the (many?) problems with Bio::Location is that it assumes all features are on linear chromosomes, so there is quite a bit of logic/magic built-in with that assumption that tends to be wrong (e.g. sort order of sublocations and so on, which breaks split locations).  

Frankly, I think we could really simplify this logic so that it is less magic, less fuzzy, and it would bite us in the ass a lot less, but of course this breaks backcompat.  So, my feeling is such fixes would be handled better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com> wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven't
> received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the proposed fix
> is acceptable. If the fix were fine, I could prepare changes in my forked
> repo, add tests (in "t/Seq/PrimarySeq.t"???) and make a pull request. What
> do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From mastarr9 at gmail.com  Fri Mar 15 04:54:49 2013
From: mastarr9 at gmail.com (Matt)
Date: Thu, 14 Mar 2013 23:54:49 -0500
Subject: [Bioperl-l] using a bioperl module after installing.
Message-ID: <5142A999.7090308@gmail.com>

I used "fink" to install bioperl. I see that the installation had no 
problems and that the Bio/SeqIO module exists in hard 
drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually 
make any use of bioperl in a script.

On the bioperl wiki I see that this common error message comes from the 
module sometimes not being installed but, in my case, I think that it is 
installed but "lost".  How can I reinstall or move or change the path to 
make bioperl actually work?
Thanks!

Information:

  * perl v5.10.0
  * Bioperl-pm5.10.0
  * OSX 10.6.8
  * Goal: To simply use a bioperl module
  * The code that gives the error (Using komodo edit):
      o #!/usr/bin/perl -w
        use strict;
        require Bio::SeqiO;
  * The error message:
      o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
        /Library/Perl/Updates/5.10.0
        /System/Library/Perl/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/5.10.0
        /Library/Perl/5.10.0/darwin-thread-multi-2level
        /Library/Perl/5.10.0
        /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
        /Network/Library/Perl/5.10.0 /Network/Library/Perl
        /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
        /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
        test.pl line 3.



From mhague at mail.sfsu.edu  Fri Mar 15 19:21:45 2013
From: mhague at mail.sfsu.edu (Michael Hague)
Date: Fri, 15 Mar 2013 12:21:45 -0700
Subject: [Bioperl-l] PopGen Question
Message-ID: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>

Hello,
I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:


use Bio::AlignIO;
use Bio::PopGen::Utilities;
use Bio::PopGen::Statistics;
use Bio::PopGen::Population;

my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
                           				 -format => 'fasta');
my $aln1 = $io1->next_aln;


my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
													-include_monomorphic => 1);

my $stats1 = Bio::PopGen::Statistics->new();
my $D1 = $stats1->tajima_D($pop1);
my $theta1  = $stats1->theta($pop1);
my $segsites1 = $stats1->segregating_sites_count($pop1);

print "\nPopulation #1:\n";
print "Number of segregating sites = $segsites1\n";
print "Tajima\'s D = $D1\n";
print "Watterson\'s theta = $theta1\n\n";

However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?

Thanks so much for the help,
Mike



From cjfields at illinois.edu  Fri Mar 15 20:04:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 15 Mar 2013 20:04:37 +0000
Subject: [Bioperl-l] using a bioperl module after installing.
In-Reply-To: <5142A999.7090308@gmail.com>
References: <5142A999.7090308@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA020F@CHIMBX5.ad.uillinois.edu>

Even if you use fink, you may still need to set the PERL5LIB path to point to that location.  Have you done that?

chris
 
On Mar 14, 2013, at 11:54 PM, Matt <mastarr9 at gmail.com> wrote:

> I used "fink" to install bioperl. I see that the installation had no problems and that the Bio/SeqIO module exists in hard drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually make any use of bioperl in a script.
> 
> On the bioperl wiki I see that this common error message comes from the module sometimes not being installed but, in my case, I think that it is installed but "lost".  How can I reinstall or move or change the path to make bioperl actually work?
> Thanks!
> 
> Information:
> 
> * perl v5.10.0
> * Bioperl-pm5.10.0
> * OSX 10.6.8
> * Goal: To simply use a bioperl module
> * The code that gives the error (Using komodo edit):
>     o #!/usr/bin/perl -w
>       use strict;
>       require Bio::SeqiO;
> * The error message:
>     o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
>       /Library/Perl/Updates/5.10.0
>       /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/5.10.0
>       /Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Library/Perl/5.10.0
>       /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>       /Network/Library/Perl/5.10.0 /Network/Library/Perl
>       /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>       /System/Library/Perl/Extras/5.10.0 .) at /Users/Matt/bioperl
>       test.pl line 3.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From fossandonc at hotmail.com  Fri Mar 15 21:36:53 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 15 Mar 2013 18:36:53 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <001d01ce2191$60406310$20c12930$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
Message-ID: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>

Ok,  I did the changes and added a pull request in the repository. All the
tests in "t/Seq/PrimarySeq.t" keeps passing (except the TODOs), including
the ones I added. Everything seems fine on my end.

About the Location/Split module, the lines that I don?t agree at all are the
ones that reverse the segment order in to_FTstring:
	# If the split type is join, the order is important;
	# otherwise must be 5'->3' regardless
	my @locs = ($stype eq 'join' && (!$guide && $strand == -1)) ?
	           reverse $self->sub_Location() : $self->sub_Location() ;

It don?t make sense to me to do that, because doing that you get coordinates
that will NOT give you the expected nucleotide sequence. Another thing that
is weird to me is that the sublocations are free to have different strands
values (like the first being positive strand and the second being negative
strand), since I can't think of one example where that can happen in real
genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
have sublocations in opposite strands at the same time and then extract the
sequence, so I wonder if I'm wrong and there are real cases like that...

As you say, those things would have to wait until later, but at least this
particular bug should be closed. =)

Regards,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: viernes, 15 de marzo de 2013 11:46
Para: Francisco J. Ossand?n
CC: bioperl mailing list
Asunto: Re: [Bioperl-l] Bug #2936

Sure, a pull request would be good.  I suggest making sure you are in sync
with the 'master' branch first, but I don't think you'll run into conflicts
with that.  

My guess is we'll need to pull this into a branch and test rigorously first
if it is to go into a bioperl 1.6.  One of the (many?) problems with
Bio::Location is that it assumes all features are on linear chromosomes, so
there is quite a bit of logic/magic built-in with that assumption that tends
to be wrong (e.g. sort order of sublocations and so on, which breaks split
locations).  

Frankly, I think we could really simplify this logic so that it is less
magic, less fuzzy, and it would bite us in the ass a lot less, but of course
this breaks backcompat.  So, my feeling is such fixes would be handled
better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossand?n <fossandonc at hotmail.com>
wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but 
> haven't received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the 
> proposed fix is acceptable. If the fix were fine, I could prepare 
> changes in my forked repo, add tests (in "t/Seq/PrimarySeq.t"???) and 
> make a pull request. What do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From p.j.a.cock at googlemail.com  Sat Mar 16 12:46:22 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sat, 16 Mar 2013 12:46:22 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
Message-ID: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>

On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>
> ... Another thing that
> is weird to me is that the sublocations are free to have different strands
> values (like the first being positive strand and the second being negative
> strand), since I can't think of one example where that can happen in real
> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
> have sublocations in opposite strands at the same time and then extract the
> sequence, so I wonder if I'm wrong and there are real cases like that...
>

This is a real biological phenomena - trans-splicing, often in tRNA genes,
for example:
http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced

As a result the BioPerl / BioSQL / Biopython etc location models do have
to cope with this corner case.  Worse, there are examples where pieces
from different chromosomes are spliced together - which is even harder
to deal with - like my favourite pathological example, nad1 in NC_016406
(and NC_016402), which has the following GenBank location string:

join(complement(149815..150200),
complement(295492..295573),complement(293787..293978),
NC_016402.1:6618..6676,181647..181905)

See also:
http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html

Peter



From cjfields at illinois.edu  Sat Mar 16 14:02:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 16 Mar 2013 14:02:12 +0000
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>
	<001d01ce2191$60406310$20c12930$@illinois.edu>
	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>
	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA0D59@CHIMBX5.ad.uillinois.edu>

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different strands
>> values (like the first being positive strand and the second being negative
>> strand), since I can't think of one example where that can happen in real
>> genomes. In fact one of the tests in PrimarySeq.t is designed exactly to
>> have sublocations in opposite strands at the same time and then extract the
>> sequence, so I wonder if I'm wrong and there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA genes,
> for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transpliced
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do have
> to cope with this corner case.  Worse, there are examples where pieces
> from different chromosomes are spliced together - which is even harder
> to deal with - like my favourite pathological example, nad1 in NC_016406
> (and NC_016402), which has the following GenBank location string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used for Bio::Location deals with cases like this, but there is an assumption made to deal with some cases like this that is wrong for others (say, circular chromosomes where a feature wraps the origin, where sorting messes things up).  It really needs a top to bottom overhaul to be explicit about the join, but such an overhaul will break some expected behavior, hence my suggestion of putting this in a bioperl v2.

chris


From carandraug+dev at gmail.com  Sat Mar 16 22:27:31 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sat, 16 Mar 2013 22:27:31 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
Message-ID: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>

On 15 March 2013 03:15, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 15 March 2013 02:41, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 14, 2013, at 9:04 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 15 March 2013 02:00, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> On Mar 14, 2013, at 8:21 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> I'm using dist::zilla and found the BioPerl plugin. I noticed that the
>>>>> bug tracker information is set to
>>>>>
>>>>> bugtracker.web    = http://rt.cpan.org/Public/Dist/Display.html?Name=${dist}
>>>>> bugtracker.mailto = bug-${dist}@rt.cpan.org
>>>>>
>>>>> shouldn't they set for https://redmine.open-bio.org/projects/bioperl?
>>>>>
>>>>> Carn?
>>>>>
>>>>
>>>> Yes, that should be redmine.  AFAIK that plugin isn't on CPAN yet, is it?
>>>>
>>>> chris
>>>
>>> Yes it is. But only the version 0.01.
>>
>> Yeah, we'll have to work on the update then.  The dependency curve for dzil isn't for the light-hearted, but I can't recommend it enough :)
>
> I think I got it working with the BioPerl bundle. It passes all tests.
> Now I was trying to set Pod::Weaver to write the feedback section
> automatically but might be better to set it up as pasrt of the BioPerl
> bundle.

I made a bunch of changes to the BioPerl bundle. I didn't touched the
podweaver part, I just wanted to get a feel of it first, as this was
new stuff to me. I replaced some of the code on the bundle with
plugins that have since been written, and renamed the options so that
they match the option names of the plugins being used.

I do believe that these options are an improvement but since it's a
lot of changes and behaves differently from the previous version, I
created a fork and a branch on my own repo. If no one opposes I will
push them to the main repo.

https://github.com/carandraug/dist-zilla-pluginbundle-bioperl/blob/purging/lib/Dist/Zilla/PluginBundle/BioPerl.pm

Carn?



From fossandonc at hotmail.com  Mon Mar 18 03:09:17 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 18 Mar 2013 00:09:17 -0300
Subject: [Bioperl-l] Bug #2936
In-Reply-To: <000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
References: <SNT133-ds1370FDCBD763942BC372B9CFED0@phx.gbl>	<001d01ce2191$60406310$20c12930$@illinois.edu>	<SNT133-ds9FA4CCA72D37BDEA48C90CFED0@phx.gbl>	<CAKVJ-_63Q5r+9mcg+qDgMND6oG8cZ+aAoHyw1HFVeGcfA6=VYw@mail.gmail.com>
	<000a01ce2253$4cf7c7e0$e6e757a0$@illinois.edu>
Message-ID: <SNT133-ds9166254353FA597757A40CFE80@phx.gbl>

Wow, trans-splicing is a phenomena I was not aware about, thanks for telling
me. Then, the Guide Strand of the Split-location object must always check if
all the sublocations are present in the same strand; so if all sublocations
are positive the Guide have to be positive, if all are negative the Guide
have to be negative as well, and if there is a mix of strands in
sublocations the Guide have to be undef... The changes I made in flip_strand
didn?t check for the strand consistency in the sublocations when setting the
Guide Strand, so I have to add that.

Ok, how about this, in the following lines I will analyze all possibilities
for location coordinates, step by step, from simpler to complex. Please
follow my reasoning in every step and tell me if there is something you
don?t agree, so I can work on the code and use these cases as tests, and
then make another pull request. Let?s see when there is a reversal of the
sublocations order needed and when is not. For this time, I will only check
cases where the DNA comes from the same chromosome/plasmid/contig


One thing to keep in mind is that the flipped coordinates should reconstruct
the reverse-complement (revcom) of the original sequence.

Example sequence used below (fictional 20bp circular plasmid):
AAAAACCCCCGGGGGTTTTT


### Reasoning: For the following cases, where ALL segments are in the same
strand, NO ORDER REVERSAL is needed because for the complement-strand
sequences the code can join all the positive sequences first and then
complement it complete at the final step. Also, since all segments are in
the same strand, Guide Strand have to be set with the same value than the
sublocations.

# Single location
Coordinates: 1..5 => AAAAA
Revcom: complement(1..5) => TTTTT

# Basic split, both locations in same strand
Coords: join(6..10,16..20) => CCCCCTTTTT
Revcom: complement(join(6..10,16..20)) => AAAAAGGGGG

# Cut by origin-split, same strand, single sequence that pass through origin
Coords: join(16..20,1..2) => TTTTTAA
Revcom: complement(join(16..20,1..2)) => TTAAAAA

# Cut by origin-combo split, same strand, 2 sequences with 1st passing
through origin
Coords: join(19..20,1..2,11..13) => TTAAGGG
Revcom: complement(join(19..20,1..2,11..13)) => CCCTTAA 

# Cut by origin-combo split, same strand, 2 sequences with 2nd passing
through origin
Coords: join(6..10,19..20,1..4) => CCCCCTTAAAA
Revcom: complement(join(6..10,19..20,1..4)) => TTTTAAGGGGG


### Reasoning: For the following cases, where segments are in MIXED strands,
ORDER REVERSAL is needed because the code have to complement some segments
and others not, so it have to complement those segments first and then join
them at the last step. Also, since there is no strand consistency in all
segments, Guide Strand have to be set with undef value.

# Trans-splicing, 2 sequences in different strands, 2nd in complement
Coords: join(6..10,complement(16..20)) => CCCCCAAAAA
Revcom: join(16..20,complement(6..10)) => TTTTTGGGGG

# Trans-splicing, 2 sequences in different strands, 1st in complement
Coords: join(complement(16..20),6..10) => AAAAACCCCC
Revcom: join(complement(6..10),16..20) => GGGGGTTTTT

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 2nd in complement
Coords: join(19..20,1..3,complement(11..13)) => TTAAACCC
Revcom: join(11..13,complement(1..3),complement(19..20)) => GGGTTTAA

# Trans-splicing w/cut by origin, 2 sequences with 1st passing through
origin, 1st in complement
Coords: join(complement(1..3),complement(19..20), 11..13) => TTTAAGGG
Revcom: join(complement(11..13), 19..20,1..3) => CCCTTAAA

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 2nd in complement
Coords: join(6..10,complement(1..2),complement(18..20),) => CCCCCTTAAA
Revcom: join(18..20,1..2, complement(6..10)) => TTTAAGGGGG

# Trans-splicing w/cut by origin, 2 sequences with 2nd passing through
origin, 1st in complement
Coords: join(complement(6..10),18..20,1..2) => GGGGGTTTAA
Revcom: join(complement(1..2),complement(18..20), 6..10) => TTAAACCCCC

####

As summary, Guide Strand must ensure that all the sublocations have the same
strand value set before using that value, and be undef if there is no
consistency (like in trans-splicing); so any new "add_sub_Location" should
check the other sublocations strands and set Guide Strand according to the
consistency. Establishing Guide Strand value from the beginning and updating
it accordingly with any change in the Split location object, should
correctly signal when to reverse the sublocations order and when not.

Thoughts??

Francisco J.  Ossandon


-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: s?bado, 16 de marzo de 2013 11:02
Para: Peter Cock
CC: bioperl mailing list; Francisco J. Ossand?n
Asunto: Re: [Bioperl-l] Bug #2936

On Mar 16, 2013, at 7:46 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Fri, Mar 15, 2013 at 9:36 PM, Francisco J. Ossand?n wrote:
>> 
>> ... Another thing that
>> is weird to me is that the sublocations are free to have different 
>> strands values (like the first being positive strand and the second 
>> being negative strand), since I can't think of one example where that 
>> can happen in real genomes. In fact one of the tests in PrimarySeq.t 
>> is designed exactly to have sublocations in opposite strands at the 
>> same time and then extract the sequence, so I wonder if I'm wrong and
there are real cases like that...
>> 
> 
> This is a real biological phenomena - trans-splicing, often in tRNA 
> genes, for example:
> http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation#transplice
> d
> 
> As a result the BioPerl / BioSQL / Biopython etc location models do 
> have to cope with this corner case.  Worse, there are examples where 
> pieces from different chromosomes are spliced together - which is even 
> harder to deal with - like my favourite pathological example, nad1 in 
> NC_016406 (and NC_016402), which has the following GenBank location
string:
> 
> join(complement(149815..150200),
> complement(295492..295573),complement(293787..293978),
> NC_016402.1:6618..6676,181647..181905)
> 
> See also:
> http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-gen
> bank-with.html
> 
> Peter

Exactly.  So, in this implementation the problem is the internal logic used
for Bio::Location deals with cases like this, but there is an assumption
made to deal with some cases like this that is wrong for others (say,
circular chromosomes where a feature wraps the origin, where sorting messes
things up).  It really needs a top to bottom overhaul to be explicit about
the join, but such an overhaul will break some expected behavior, hence my
suggestion of putting this in a bioperl v2.

chris
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From antony.vincent.1 at ulaval.ca  Mon Mar 18 11:43:30 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 04:43:30 -0700 (PDT)
Subject: [Bioperl-l]  Generate a hsp from emboss format?
Message-ID: <35187436.post@talk.nabble.com>


Hi,
I have a script who uses emboss (water) for a dynamic programming alignment.
Is this possible to generate (convert) my result in emboss format in a hsp
(blast) like.

I need (I think) an hsp format because it's much easier for parse only one
of the two strand in the alignment (and this is what I need).

Thanks!
-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35187436.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From p.j.a.cock at googlemail.com  Mon Mar 18 12:00:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 18 Mar 2013 12:00:21 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <35187436.post@talk.nabble.com>
References: <35187436.post@talk.nabble.com>
Message-ID: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>

On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>
> Hi,
> I have a script who uses emboss (water) for a dynamic programming alignment.
> Is this possible to generate (convert) my result in emboss format in a hsp
> (blast) like.
>
> I need (I think) an hsp format because it's much easier for parse only one
> of the two strand in the alignment (and this is what I need).
>
> Thanks!

EMBOSS water (and related tools like needle) support a range of output
formats - have you looked at those yet?

Peter


From cjfields at illinois.edu  Mon Mar 18 17:19:02 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 17:19:02 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>

On Mar 18, 2013, at 7:00 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>> 
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>> 
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>> 
>> Thanks!
> 
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?
> 
> Peter


Antony,

Bio::AlignIO::emboss is supposed to support water/needle output; have you tried that?  Also, I'm not sure what advantage having this in a BLAST-like output would have over other human-readable formats; any reasons you would need this specific output?

chris




From cjfields at illinois.edu  Mon Mar 18 21:26:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 18 Mar 2013 21:26:22 +0000
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA3EA4@CHIMBX5.ad.uillinois.edu>

Just a heads-up, if there are any students interested in the Google Summer of Code, the Open Bioinformatics Foundation is planning on participating again this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are looking for prospective projects.  

We're open for any project ideas this year, so let us know what you would like to do!

chris


From antony.vincent.1 at ulaval.ca  Mon Mar 18 21:35:13 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Mon, 18 Mar 2013 14:35:13 -0700 (PDT)
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA29D1@CHIMBX5.ad.uillinois.edu>
Message-ID: <35190011.post@talk.nabble.com>


Hi!
For example, with this code I can easily modify only one string:

 #! /usr/bin/perl -w
 
# use strict;
 use Bio::SeqIO;
 use Bio::Tools::Run::StandAloneBlast;
 use Bio::Seq;
 use warnings;
 
###########################################################################################################
# Usage information
die "Usage: $0 <sequence 1> <sequence 2> <BLAST algorithme> <minimum % of
identity>\n", if (@ARGV != 4);
 my ($infile1,$infile2,$algo,$identity) = @ARGV;
##########################################################################################################


 my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if


	print $hsp->algorithm, ": Identity ", 100*$hsp->frac_identical, "\%, Rank
", $hsp->rank, " (evalue:", $hsp->evalue, ")\n";
	print "\t", $hsp->query_string;
	print "\n";
	print "\t", $hsp->homology_string;
	print "\n";
	print "\t", $hsp->hit_string;
	print "\n\n";
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

This is why I want to have this format. Is this possible?
Thanks!


-- 
View this message in context: http://old.nabble.com/Generate-a-hsp-from-emboss-format--tp35187436p35190011.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From p.rice at imperial.ac.uk  Tue Mar 19 10:51:52 2013
From: p.rice at imperial.ac.uk (Peter Rice)
Date: Tue, 19 Mar 2013 10:51:52 +0000
Subject: [Bioperl-l] Generate a hsp from emboss format?
In-Reply-To: <CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
References: <35187436.post@talk.nabble.com>
	<CAKVJ-_5TXxUu-AfiVN7SsV9co_ZyHM3OkYc486gA1cgxNBF0+w@mail.gmail.com>
Message-ID: <51484348.5070603@imperial.ac.uk>

On 18/03/2013 12:00, Peter Cock wrote:
> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>>
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>>
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>>
>> Thanks!
>
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?

The full list for the latest EMBOSS release alignment formats is below. 
They are selected by the -aformat qualifier for any application with an 
"align" output.

It would also be relatively simple to add new formats for the next 
release if they would be useful.

Multiple sequence formats:

"fasta",     "Fasta format sequence",
"msf",       "MSF format sequence",
"clustal",   "clustalw format sequence",
"mega",       "Mega format sequence",
"meganon",       "Mega non-interleaved format sequence",
"nexus",   "nexus/paup format sequence",
"nexusnon",   "nexus/paup non-interleaved format sequence",
"phylip",   "phylip format sequence",
"phylipnon", "phylip non-interleaved format sequence",
"selex",       "SELEX format sequence",
"treecon",       "Treecon format sequence",

Multiple alignment formats:

"markx0",    "Pearson MARKX0 format",
"markx1",    "Pearson MARKX1 format",
"markx2",    "Pearson MARKX2 format",
"markx3",    "Pearson MARKX3 format",
"markx10",   "Pearson MARKX10 format",
"match","Start and end of matches between sequence pairs",
"multiple",  "Simple multiple alignment",
"pair",      "Simple pairwise alignment",
"simple",    "Simple multiple alignment",
"sam",       "Sequence alignent/map (SAM) format",
"score",     "Score values for pairs of sequences",
"srs",       "Simple multiple sequence format for SRS",
"srspair",   "Simple pairwise sequence format for SRS",
"tcoffee",   "TCOFFEE program format",

regards,

Peter Rice
EMBOSS Team



From carandraug+dev at gmail.com  Tue Mar 19 23:02:59 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 19 Mar 2013 23:02:59 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
Message-ID: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>

On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
> I do believe that these options are an improvement but since it's a
> lot of changes and behaves differently from the previous version, I
> created a fork and a branch on my own repo. If no one opposes I will
> push them to the main repo.

Pushed.

Carn?



From cjfields at illinois.edu  Wed Mar 20 02:06:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 20 Mar 2013 02:06:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>

On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> I do believe that these options are an improvement but since it's a
>> lot of changes and behaves differently from the previous version, I
>> created a fork and a branch on my own repo. If no one opposes I will
>> push them to the main repo.
> 
> Pushed.
> 
> Carn?

Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

chris


From carandraug+dev at gmail.com  Wed Mar 20 03:09:52 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 20 Mar 2013 03:09:52 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>

On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>
>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>> I do believe that these options are an improvement but since it's a
>>> lot of changes and behaves differently from the previous version, I
>>> created a fork and a branch on my own repo. If no one opposes I will
>>> push them to the main repo.
>>
>> Pushed.
>>
>> Carn?
>
> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.

I was hoping that it would get more use. jhannah/deafferret tells me
that the people who volunteer to do the CPAN work get burned out. With
this properly set up, it should be as simple as running "dzil
release".

I'm also writing a pod weaver plugin bundle for bioperl but would like
some thought on what others think this should be doing.

Carn?



From fs5 at sanger.ac.uk  Wed Mar 20 22:09:40 2013
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Wed, 20 Mar 2013 22:09:40 +0000
Subject: [Bioperl-l] Bio::DB::Sam - finding clipped regions
Message-ID: <514A33A4.3050107@sanger.ac.uk>

Hi,

I need to report all the positions on a reference sequence where aligned 
reads in a bam file have been hard-clipped.
I am using Bio::DB::Sam and I know that I can use callbacks to traverse 
each individual read and get information about its alignment to each 
position on the reference as in

my $sam = Bio::DB::Sam->new(

   -bam  =>$bam,

   -fasta=>$fasta,

);

my $callback = sub {

   my ( $id, $pos, $p ) = @_;

   for my $pileup (@$p) {

     my $aln  = $pileup->alignment;

     my $cigar = $aln->cigar_str;

     # other stuff here

     # ...

  };

$sam->fast_pileup( $sequence_id, $callback );



But I don't see a straight-forward way (accepting that there may not be 
one of course) to ask "is the next base of the read hardclipped".
It's not that difficult to unravel the cigar string and I have the start 
of the alignment for the read, so I can follow the cigar string along to 
the current base on the reference to see what the alignment is there and 
what happens next.
I've just got that feeling that I'm missing something and there is 
probably a better and more efficient way of doing this, maybe with 
another tool? Using samtools mpileup I can get positions of SNPs and 
INDELS but I can't see a way of collecting the hard-clipped positions 
that I need or is that possible somehow (ok, not BioPerl, I know)

Thanks for your help guys!

Frank



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From scott at scottcain.net  Thu Mar 21 02:28:09 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 20 Mar 2013 22:28:09 -0400
Subject: [Bioperl-l] Last day for early registration for GMOD 2013
Message-ID: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>

Hi,

With several guest speakers, including Jane Lomax from GO, Joseph
Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
Centre, this GMOD meeting is shaping up to be a very intersting
meeting indeed.  Today (March 21) is the last day to register with the
early registration pricing.  To register, go to

  http://gmod2013.eventbrite.com/

I look forward to seeing you next month (April 5-6) in Cambridge,
England.  For more information about GMOD 2013, go to

  http://www.gmod.org/wiki/April_2013_GMOD_Meeting

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From sofia at neuro.utah.edu  Thu Mar 21 14:51:43 2013
From: sofia at neuro.utah.edu (Sofia M Robb)
Date: Thu, 21 Mar 2013 14:51:43 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
Message-ID: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>

Hello All,

The following link http://bioperl.org/cgi-bin/deob_interface.cgi results in an internal server error. I hope that someone can point the link in the right direction.

Thanks,
Sofia



From p.j.a.cock at googlemail.com  Thu Mar 21 15:28:03 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 21 Mar 2013 15:28:03 +0000
Subject: [Bioperl-l] Deobfuscator Internal Server Error
In-Reply-To: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
References: <1055C7B6DBAFEE48B720DAF9762C0AA23B8EA735@X-MB4.xds.umail.utah.edu>
Message-ID: <CAKVJ-_46=1zbFjLL+ovow4449hZ7qWa+woPz8VkbLLy_LnYNGw@mail.gmail.com>

On Thu, Mar 21, 2013 at 2:51 PM, Sofia M Robb <sofia at neuro.utah.edu> wrote:
> Hello All,
>
> The following link http://bioperl.org/cgi-bin/deob_interface.cgi results
> in an internal server error. I hope that someone can point the link in
> the right direction.
>
> Thanks,
> Sofia

That might be related to the server move at the end of last year.
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Whomever looks after the deobfuscator - please drop the Sys Admin
team an email on the root-l mailing list if you need assistance.

Regards,

Peter


From carandraug+dev at gmail.com  Fri Mar 22 02:11:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 22 Mar 2013 02:11:18 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
Message-ID: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>

On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>
>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>> I do believe that these options are an improvement but since it's a
>>>> lot of changes and behaves differently from the previous version, I
>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>> push them to the main repo.
>>>
>>> Pushed.
>>>
>>
>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>
> I'm also writing a pod weaver plugin bundle for bioperl but would like
> some thought on what others think this should be doing.

So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
give some feedback if it's adequate for the rest of the project.

https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

To minimize the number of files added to each distro, I also wrote
another plugin which the PluginBundle uses. I wrote it today so you're
likely to not have it installed yet.

https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Carn?



From jason.stajich at gmail.com  Fri Mar 22 06:19:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 21 Mar 2013 20:19:23 -1000
Subject: [Bioperl-l] PopGen Question
In-Reply-To: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
References: <1F31D4A1-DB04-46C9-8867-56D45FE4EAE5@mail.sfsu.edu>
Message-ID: <F6333CA1-8FAD-4022-BC5B-19FB51CE95AC@gmail.com>

Once you convert it into the population object ($pop1) you can iterate through the markers and request the allele frequency from each of these.

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/Population.html
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PopGen/MarkerI.html

 for my $name ( $population->get_marker_names ) {
   my $marker = $population->get_Marker($name);
   print "marker $marker\n";
   my %af = $marker->get_Allele_Frequencies;
   foreach my $allele ( keys %af ) {
      print "$allele $af{$allele}\n";
   }
  }


unfortunately the wiki code seems to be messed up for autolinking out to the pdoc documentation so some of the links on the bioperl website don't get properly made.  something to be fixed I hope.

Jason
On Mar 15, 2013, at 9:21 AM, Michael Hague <mhague at mail.sfsu.edu> wrote:

> Hello,
> I'm trying to calculate some diversity statistics for an aligned dataset in BioPerl. My aligned dataset is a fasta file. I've been able to import the file and calculate Tajima's D and theta using the following script:
> 
> 
> use Bio::AlignIO;
> use Bio::PopGen::Utilities;
> use Bio::PopGen::Statistics;
> use Bio::PopGen::Population;
> 
> my $io1 = Bio::AlignIO->new(-file   => 'Callisaurus_cytb_final.fas',
>                           				 -format => 'fasta');
> my $aln1 = $io1->next_aln;
> 
> 
> my $pop1 = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln1,
> 													-include_monomorphic => 1);
> 
> my $stats1 = Bio::PopGen::Statistics->new();
> my $D1 = $stats1->tajima_D($pop1);
> my $theta1  = $stats1->theta($pop1);
> my $segsites1 = $stats1->segregating_sites_count($pop1);
> 
> print "\nPopulation #1:\n";
> print "Number of segregating sites = $segsites1\n";
> print "Tajima\'s D = $D1\n";
> print "Watterson\'s theta = $theta1\n\n";
> 
> However, I would like to also calculate haplotype diversity. To the best of my knowledge, I haven't found a BioPerl module that explicitly calculate haplotype diversity. Is there a relatively simple way to do this in BioPerl? I haven't even found a way to count allele frequencies from my alignment file. It that possible in BioPerl?
> 
> Thanks so much for the help,
> Mike
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From briano at bioteam.net  Sat Mar 23 15:21:58 2013
From: briano at bioteam.net (Brian Osborne)
Date: Sat, 23 Mar 2013 11:21:58 -0400
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
Message-ID: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>

Hanny,

I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.

> 
> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> 
> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> 
> Hanny

Brian O.




From cjfields at illinois.edu  Sat Mar 23 17:41:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 23 Mar 2013 17:41:28 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
References: <tencent_5E123CAD0FA07A6C5F551917@qq.com>
	<7A546450-2C68-4DEC-856F-AB9DA9CC9583@verizon.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DBFE3F@CHIMBX5.ad.uillinois.edu>

On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:

> Hanny,
> 
> I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> 
>> 
>> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
>> 
>> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
>> 
>> Hanny
> 
> Brian O.


My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.

chris


From carandraug+dev at gmail.com  Sun Mar 24 01:20:04 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 01:20:04 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
Message-ID: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>

Hi everyone

just announcing that Bio-Biblio version 1.70 just got released.

This release has minimum changes, mainly the split from bioperl-live.
As part of the release with Dist::Zilla, a few changes were made to
the documentation and all source use the utf8 pragma.

Carn?



From hlapp at drycafe.net  Sun Mar 24 01:21:49 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 23 Mar 2013 21:21:49 -0400
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
Message-ID: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>

Congrats, great job! -hilmar

On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:

> Hi everyone
> 
> just announcing that Bio-Biblio version 1.70 just got released.
> 
> This release has minimum changes, mainly the split from bioperl-live.
> As part of the release with Dist::Zilla, a few changes were made to
> the documentation and all source use the utf8 pragma.
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From cjfields at illinois.edu  Sun Mar 24 01:59:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 01:59:31 +0000
Subject: [Bioperl-l] new release of Bio-Biblio - version 1.70
In-Reply-To: <7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
References: <CAPOrs_3ZvcPOfaEmSKL3xswDwjYGbNzY9mFKoqpOygrtbGRNXg@mail.gmail.com>
	<7B814843-B822-44AF-B4C9-6916D7C04580@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC01CB@CHIMBX5.ad.uillinois.edu>

Agreed, great job!

I may go ahead and pull these from the v1 branch, just to make sure they don't clobber your release.  

chris

On Mar 23, 2013, at 8:21 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Congrats, great job! -hilmar
> 
> On Mar 23, 2013, at 9:20 PM, Carn? Draug wrote:
> 
>> Hi everyone
>> 
>> just announcing that Bio-Biblio version 1.70 just got released.
>> 
>> This release has minimum changes, mainly the split from bioperl-live.
>> As part of the release with Dist::Zilla, a few changes were made to
>> the documentation and all source use the utf8 pragma.
>> 
>> Carn?
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Sun Mar 24 03:54:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Sun, 24 Mar 2013 03:54:48 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <CAPOrs_0OkB+FgrraMSsMztweCxoyZ7GbHyGEKbO18GA1a2wiow@mail.gmail.com>

On 22 March 2013 02:11, Carn? Draug <carandraug+dev at gmail.com> wrote:
> On 20 March 2013 03:09, Carn? Draug <carandraug+dev at gmail.com> wrote:
>> On 20 March 2013 02:06, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>> On Mar 19, 2013, at 6:02 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>
>>>> On 16 March 2013 22:27, Carn? Draug <carandraug+dev at gmail.com> wrote:
>>>>> I do believe that these options are an improvement but since it's a
>>>>> lot of changes and behaves differently from the previous version, I
>>>>> created a fork and a branch on my own repo. If no one opposes I will
>>>>> push them to the main repo.
>>>>
>>>> Pushed.
>>>>
>>>
>>> Thanks Carn?.  I don't think there will be any complaints; we're probably the primary users, so any improvement is good.
>>
>> I'm also writing a pod weaver plugin bundle for bioperl but would like
>> some thought on what others think this should be doing.
>
> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
> give some feedback if it's adequate for the rest of the project.
>
> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>
> To minimize the number of files added to each distro, I also wrote
> another plugin which the PluginBundle uses. I wrote it today so you're
> likely to not have it installed yet.
>
> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

Could a new release of this pluginbundle be made? I have made a lot of
changes to it but I believe it's ready for "production". I used it to
release Bio-biblio and seems to have worked fine. I tried to set it up
so that all it's needed to do is:

1 - change version number on the dist.ini file (there's no need to
commit this change, the PluginBundle will take care of that)
2 - run dzil release

Carn?



From elanorbust2 at yahoo.com  Sun Mar 24 10:14:32 2013
From: elanorbust2 at yahoo.com (sally roberts)
Date: Sun, 24 Mar 2013 03:14:32 -0700 (PDT)
Subject: [Bioperl-l] http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
Message-ID: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>

http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html


From cjfields at illinois.edu  Sun Mar 24 14:32:38 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 24 Mar 2013 14:32:38 +0000
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <tencent_75F1512441D48A74101FEE2D@qq.com>
References: <tencent_75F1512441D48A74101FEE2D@qq.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC07D0@CHIMBX5.ad.uillinois.edu>

ActivePerl as of a few years or so ago could install modules directly from CPAN.  Have you tried that?  Also, any reason you are using ActivePerl on Linux?  Lots of very nice options out there for linux, including  perlbrew:

http://perlbrew.pl/

The problem we historically have with Windows support is that very few of our developers use it (let alone have access to a Windows machine).  If anyone wants to take this on I would be more than supportive.

chris

On Mar 24, 2013, at 5:44 AM, ciel <58363553 at qq.com> wrote:

> 
> Thanks!
> 
> So, since their web site migrration , I guess I couldn't install bioperl temporary whether in windows or linux. 
> 
> Hanny  
> 
> ------------------ Original ------------------
> From:  "Fields, Christopher J"<cjfields at illinois.edu>;
> Date:  Sun, Mar 24, 2013 01:41 AM
> To:  "Brian Osborne"<briano at bioteam.net>;
> Cc:  "ciel"<58363553 at qq.com>; "Bioperl-L"<bioperl-l at bioperl.org>;
> Subject:  Re: [Bioperl-l] bioperl installation problem
> 
> On Mar 23, 2013, at 10:21 AM, Brian Osborne <briano at bioteam.net> wrote:
> 
> > Hanny,
> > 
> > I'm the wrong person to ask, I really don't know much about installing Perl on Windows. However, someone on bioperl-l might know.
> > 
> >> 
> >> I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.
> >> 
> >> when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx
> >> 
> >> Hanny
> > 
> > Brian O.
> 
> 
> My guess is the PPM repository is down due to the recent web site migration to AWS.  We'll have to check how easy this would be to bring back up.
> 
> chris.




From alexeymorozov1991 at gmail.com  Mon Mar 25 01:00:51 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Mon, 25 Mar 2013 10:00:51 +0900
Subject: [Bioperl-l]
	http://www.fhste.com.br/inscricoes/nbproject/wijgh.html
In-Reply-To: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
References: <1364120072.6623.YahooMailNeo@web163506.mail.gq1.yahoo.com>
Message-ID: <CAK=7cMMsxCvP+jVYyqDAbaS4_9rycmSVmKUwo-HYTx3nOFA5AQ@mail.gmail.com>

Someone ban the spammer, please.


2013/3/24 sally roberts <elanorbust2 at yahoo.com>

> http://www.fhste.com.br/inscricoes/nbproject/mqcmi.html
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.


From 58363553 at qq.com  Fri Mar 22 16:21:00 2013
From: 58363553 at qq.com (=?ISO-8859-1?B?Y2llbA==?=)
Date: Sat, 23 Mar 2013 00:21:00 +0800
Subject: [Bioperl-l] bioperl installation problem
Message-ID: <tencent_4DDD95B145899AF5173CBF5A@qq.com>

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as :"failed 503 Service temporarily Unavailable", how can I deal with this problem? thx


Hanny



From lzwright at gmail.com  Thu Mar 21 21:08:41 2013
From: lzwright at gmail.com (liz wright)
Date: Thu, 21 Mar 2013 17:08:41 -0400
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
Message-ID: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>

Hi, I just force installed bioperl on ubuntu linux as this approach was
proposed as a viable alternative when certain tests fail, but I would like
to check that the fail errors listed below will not significantly impair
bioperl usage as I am new to all this and don't really know how to
interpret the error messages.  Thanks, Liz Wright


* WARNING: Configuration was initially created with Module::Build
  version '0.38' but we are now using version '0.4003'.
  If errors occur, you must re-run the Build.PL or Makefile.PL script.
Will try to install symlinks to /usr/local/bin
  CJFIELDS/BioPerl-1.6.1.tar.gz
  sudo ./Build install  -- OK
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
failure ignored because 'force' in effect
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
failure ignored because 'force' in effect
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
failure ignored because 'force' in effect
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
failure ignored because 'force' in effect
 MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
failure ignored because 'force' in effect
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
failure ignored because 'force' in effect


From lzwright at gmail.com  Fri Mar 22 12:44:10 2013
From: lzwright at gmail.com (liz wright)
Date: Fri, 22 Mar 2013 08:44:10 -0400
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>

As a follow up to my previous message, this gives a bit more information as
to why the make tests failed:

  make test had returned bad status, won't install without force
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test NO
 RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
'/usr/bin/perl Build.PL --installdirs site' returned status 512
 TODDR/XML-Parser-2.41.tar.gz                 : make NO
 KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness failed
 MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
not OK (XML::DOM); additionally test harness failed
 BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
not OK (XML::SAX::Expat)
 MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
not OK (XML::Parser); additionally test harness failed
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
missing
(Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)

On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:

> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect
>
>
>


From carandraug+dev at gmail.com  Mon Mar 25 06:40:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Mon, 25 Mar 2013 06:40:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
Message-ID: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>

Hi

I need something to keep a bunch of genes belonging to the same family
organized. It is more than a plain hash since the family can be
divided into multiple ways (subfamilies, types and classes) that
overlap each other, but using a database seems overkill to me. I
couldn't find a module on CPAN that does it so I might write one if no
one suggests an alternative. Basically, with it I wanna be able to do
something like this

  my $histones = Bio::Family->new(
      -classes      => ['canonical', 'variant'],
      -types        => ['H2A', 'H2B', 'H3', 'H4'],
      -subfamilies => [ ... ],
  );

  $histones->add_member ($seqob,
      -class => 'canonical',
      -type  => 'H3',
  );

  @all_members = $histones->members;
  @canonicals  = $histones->class('canonical');

I already wrote a bit of POD for it
http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
on its design before start coding, as I fear it might be too focused
for the problem I have at hand. Could someone give me some advice
about it?

I'm also thinking that maybe I should write some sort of general perl
module, outside the Bio::* namespace.

Thanks,
Carn?



From longbow0 at gmail.com  Mon Mar 25 08:42:38 2013
From: longbow0 at gmail.com (longbow leo)
Date: Mon, 25 Mar 2013 16:42:38 +0800
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAA8+_pxr2hENF_N8vDKVT_q4_qdbAB2GbpkSQOkkizP67tf88Q@mail.gmail.com>
Message-ID: <CAKPXXke637b18wS3DPPrunw1+n-q3NciSvsP=bxEeLDC5n7yVw@mail.gmail.com>

Hi Liz,

There are already "bioperl' and "bioperl-run" packages for ubuntu. It is
not necessary to install bioperl from source code.

Haizhou

On Fri, Mar 22, 2013 at 8:44 PM, liz wright <lzwright at gmail.com> wrote:

> As a follow up to my previous message, this gives a bit more information as
> to why the make tests failed:
>
>   make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test NO
>  RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
> '/usr/bin/perl Build.PL --installdirs site' returned status 512
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
> missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness
> failed
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
> not OK (XML::DOM); additionally test harness failed
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
> not OK (XML::SAX::Expat)
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
> missing
>
> (Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)
>
> On Thu, Mar 21, 2013 at 5:08 PM, liz wright <lzwright at gmail.com> wrote:
>
> > Hi, I just force installed bioperl on ubuntu linux as this approach was
> > proposed as a viable alternative when certain tests fail, but I would
> like
> > to check that the fail errors listed below will not significantly impair
> > bioperl usage as I am new to all this and don't really know how to
> > interpret the error messages.  Thanks, Liz Wright
> >
> >
> >
> > * WARNING: Configuration was initially created with Module::Build
> >   version '0.38' but we are now using version '0.4003'.
> >   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> > Will try to install symlinks to /usr/local/bin
> >   CJFIELDS/BioPerl-1.6.1.tar.gz
> >   sudo ./Build install  -- OK
> > Failed during this command:
> >  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> > failure ignored because 'force' in effect
> >  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> > failure ignored because 'force' in effect
> >  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> > failure ignored because 'force' in effect
> >  TODDR/XML-Parser-2.41.tar.gz                 : make NO
> >  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> > failure ignored because 'force' in effect
> >  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> > failure ignored because 'force' in effect
> >  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> > failure ignored because 'force' in effect
> >
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From l.m.timmermans at students.uu.nl  Mon Mar 25 11:19:36 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Mon, 25 Mar 2013 12:19:36 +0100
Subject: [Bioperl-l] Fwd: bioperl errors
In-Reply-To: <CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
Message-ID: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>

On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
> Hi, I just force installed bioperl on ubuntu linux as this approach was
> proposed as a viable alternative when certain tests fail, but I would like
> to check that the fail errors listed below will not significantly impair
> bioperl usage as I am new to all this and don't really know how to
> interpret the error messages.  Thanks, Liz Wright
>
>
> * WARNING: Configuration was initially created with Module::Build
>   version '0.38' but we are now using version '0.4003'.
>   If errors occur, you must re-run the Build.PL or Makefile.PL script.
> Will try to install symlinks to /usr/local/bin
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   sudo ./Build install  -- OK
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
> failure ignored because 'force' in effect
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
> failure ignored because 'force' in effect
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
> failure ignored because 'force' in effect
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
> failure ignored because 'force' in effect
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
> failure ignored because 'force' in effect
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect

Most of those are XML modules that need an external XML library. Force
installing won't solve that problem. Installing expat (on my ubuntu
that'd be libexpat1) should be the solution. Odds are the other
failures are dependent failures that will also disappear.

Leon


From cjfields at illinois.edu  Mon Mar 25 12:54:21 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:54:21 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>

IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:

https://metacpan.org/module/Bio::Cluster::FamilyI

My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

chris

On Mar 25, 2013, at 1:40 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I need something to keep a bunch of genes belonging to the same family
> organized. It is more than a plain hash since the family can be
> divided into multiple ways (subfamilies, types and classes) that
> overlap each other, but using a database seems overkill to me. I
> couldn't find a module on CPAN that does it so I might write one if no
> one suggests an alternative. Basically, with it I wanna be able to do
> something like this
> 
>  my $histones = Bio::Family->new(
>      -classes      => ['canonical', 'variant'],
>      -types        => ['H2A', 'H2B', 'H3', 'H4'],
>      -subfamilies => [ ... ],
>  );
> 
>  $histones->add_member ($seqob,
>      -class => 'canonical',
>      -type  => 'H3',
>  );
> 
>  @all_members = $histones->members;
>  @canonicals  = $histones->class('canonical');
> 
> I already wrote a bit of POD for it
> http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
> on its design before start coding, as I fear it might be too focused
> for the problem I have at hand. Could someone give me some advice
> about it?
> 
> I'm also thinking that maybe I should write some sort of general perl
> module, outside the Bio::* namespace.
> 
> Thanks,
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 25 12:56:37 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 12:56:37 +0000
Subject: [Bioperl-l] bioperl errors
In-Reply-To: <CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
References: <CAA8+_pwi+5=-scHtMTNgWiUaUruCoVG5anS9rFK4T_6eAsfaiQ@mail.gmail.com>
	<CAA8+_pw62wYEHVSuir72XF0sS3e9gBSgJ_e5F5q+KYjSHp05Lg@mail.gmail.com>
	<CAC1jpXDC1CqMQs8NJ2rbV9hphHjf-je=YnJzFeAZx_HJyHE5Rg@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1733@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 6:19 AM, Leon Timmermans <l.m.timmermans at students.uu.nl> wrote:

> On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
>> Hi, I just force installed bioperl on ubuntu linux as this approach was
>> proposed as a viable alternative when certain tests fail, but I would like
>> to check that the fail errors listed below will not significantly impair
>> bioperl usage as I am new to all this and don't really know how to
>> interpret the error messages.  Thanks, Liz Wright
>> 
>> 
>> * WARNING: Configuration was initially created with Module::Build
>>  version '0.38' but we are now using version '0.4003'.
>>  If errors occur, you must re-run the Build.PL or Makefile.PL script.
>> Will try to install symlinks to /usr/local/bin
>>  CJFIELDS/BioPerl-1.6.1.tar.gz
>>  sudo ./Build install  -- OK
>> Failed during this command:
>> LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
>> failure ignored because 'force' in effect
>> KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
>> failure ignored because 'force' in effect
>> BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TODDR/XML-Parser-2.41.tar.gz                 : make NO
>> MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
>> failure ignored because 'force' in effect
>> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
>> failure ignored because 'force' in effect
> 
> Most of those are XML modules that need an external XML library. Force
> installing won't solve that problem. Installing expat (on my ubuntu
> that'd be libexpat1) should be the solution. Odds are the other
> failures are dependent failures that will also disappear.
> 
> Leon

Also, the version on CPAN has been updated to handle 'optional' dependencies; AcePerl for instance is pretty much in maintenance mode (maybe deprecated) and hasn't been updated in years.

chris




From fossandonc at hotmail.com  Mon Mar 25 13:29:48 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Mon, 25 Mar 2013 10:29:48 -0300
Subject: [Bioperl-l] bioperl installation problem
In-Reply-To: <000201ce2959$17ed7830$47c86890$@qq.com>
References: <000201ce2959$17ed7830$47c86890$@qq.com>
Message-ID: <SNT133-ds57FF786B3A8DB70E8F9FACFD70@phx.gbl>

Hi,
I use Windows but I dropped ActivePerl some time ago in preference of
Strawberry Perl (http://strawberryperl.com/), which have better support for
installation directly from CPAN via command line.

I'm not sure if I understood correctly but you installed new Perl 5.16 over
the old 5.10?? In that case I would recommend to completely uninstall the
previous Perl version and then install the new clean Perl version.

On the other hand, the error message points to a problem connecting to the
Uwinnipeg server, so maybe they are down (in fact I just tried on my browser
and received the same error so they have problems with their servers), maybe
use Bribes instead; you don?t need to add ALL the repos anyway, just be sure
to add the http://bioperl.org/DIST, which contains the
"BioPerl-1.6.1-ppm.tar.gz", the last ActivePerl release that can be install
using the Perl Package Manager.

If you want to install the latest version, you will have to ditch the PPM,
type CPAN in command line and use that interface to get the
"BioPerl-1.6.901"
(http://www.bioperl.org/wiki/Installing_BioPerl_on_Windows#Installation_usin
g_CPAN_or_manual_installation). Beware that BioPerl will always give some
tests errors when installing that way, so you have to add "force" when
installing and everything will be fine.

Hope that helps,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de ciel
Enviado el: viernes, 22 de marzo de 2013 13:21
Para: bioperl-l
Asunto: [Bioperl-l] bioperl installation problem

Dear 


I couldn't install bioperl in my computer successfully, I tried the perl
version from ActivePerl-5.16.3.1603-MSWin32-x86-296746.msi to old version
ActivePerl-5.10.0.1003-MSWin32-x86-285500.rar.


when I use 5.10 version, the command repo add uwinnipeg gave me errors as
:"failed 503 Service temporarily Unavailable", how can I deal with this
problem? thx


Hanny

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hartzell at alerce.com  Mon Mar 25 16:23:32 2013
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 25 Mar 2013 09:23:32 -0700
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
Message-ID: <20816.31236.737983.55186@gargle.gargle.HOWL>

Carn? Draug writes:
 > [...]
 > So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
 > Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
 > give some feedback if it's adequate for the rest of the project.
 > 
 > https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm

Looks wonderful!

I use a "private" section that I think corresponds to what you call
"internal".  Is there a BioPerl tradition one way or the other?

You might make the SYNOPSIS just a tad less confusing if you point
some meaningful text into the text sections of the GenerateSection
parts, something like "text = Info about mailing lists goes here".  I
scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
lists" had an empty attribute and the other two had nonsense text.  It
looks like FEEDBACK is just an empty level 1 header, but
otherwise....

 > To minimize the number of files added to each distro, I also wrote
 > another plugin which the PluginBundle uses. I wrote it today so you're
 > likely to not have it installed yet.
 > 
 > https://metacpan.org/module/Pod::Weaver::Section::GenerateSection

I can see that being useful. In the name, did you mean "interpolated"
(which you use further down) where you say "interpreted"?

This is a useful contribution!

g.



From cjfields at illinois.edu  Mon Mar 25 16:46:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 25 Mar 2013 16:46:49 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <20816.31236.737983.55186@gargle.gargle.HOWL>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>

On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:

> Carn? Draug writes:
>> [...]
>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>> give some feedback if it's adequate for the rest of the project.
>> 
>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
> 
> Looks wonderful!
> 
> I use a "private" section that I think corresponds to what you call
> "internal".  Is there a BioPerl tradition one way or the other?

Not really, but there probably should be a more standard way of doing this.

> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".  I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....
> 
>> To minimize the number of files added to each distro, I also wrote
>> another plugin which the PluginBundle uses. I wrote it today so you're
>> likely to not have it installed yet.
>> 
>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
> 
> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?
> 
> This is a useful contribution!
> 
> g.

Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

chris




From carandraug+dev at gmail.com  Tue Mar 26 01:13:36 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 01:13:36 +0000
Subject: [Bioperl-l] bugtracker for Dist::Zilla::PluginBundle::BioPerl
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_18=o4rK5=THzhEh_KxnCa=ho160-O7arqYZxYR7-R-4w@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F1E9@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2xBCAYPGKfRJCdDXs+fi-34s6grC-AT4LRPpv=yPuWWQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74D9F26D@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1mwhY-Z90_nEsuyxBXHHKy+3n7r+4DADMSrE4_iXNzAA@mail.gmail.com>
	<CAPOrs_01Pb3xTFcM7h5fDOzEAu9X9DeAXA9EQzE+FAn0m3GZbw@mail.gmail.com>
	<CAPOrs_3pwONp456Aq44mODh392nYSjc=Qy8B7DLU=KFksQ4OOQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DA5B46@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_1AJ6vEGQgL_e+NWVqg44CBc200E-_7VgQnJh8qvdYt5Q@mail.gmail.com>
	<CAPOrs_14d=S__X4vfj+enavHidu3Xjt25OOjzWTQM6mDByXyVw@mail.gmail.com>
	<20816.31236.737983.55186@gargle.gargle.HOWL>
	<118F034CF4C3EF48A96F86CE585B94BF74DC1D7A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2F4yaXPR7ySHQ2jy0UjA5-FhfrWgNvkoF=0DKq5nzHeg@mail.gmail.com>

On 25 March 2013 16:23, George Hartzell <hartzell at alerce.com> wrote:
> You might make the SYNOPSIS just a tad less confusing if you point
> some meaningful text into the text sections of the GenerateSection
> parts, something like "text = Info about mailing lists goes here".

I don't understand your suggestion. Could you explain it again please?

> I
> scratched my head a bit wondering why "FEEDBACK" had nothing, "Mailing
> lists" had an empty attribute and the other two had nonsense text.  It
> looks like FEEDBACK is just an empty level 1 header, but
> otherwise....

It's not empty. Feedback is level 1, which contains three level 2
headings for mailing list, support and reporting bugs. The code being
generated should match exactly the feedback section of all current
BioPerl modules. See the feedback section of the Bio::DB::BiblioI that
I recently released with this set up:

https://metacpan.org/module/Bio::DB::BiblioI#FEEDBACK

and compare with the old release of Bio::SeqIO

https://metacpan.org/module/Bio::SeqIO#FEEDBACK

> I can see that being useful. In the name, did you mean "interpolated"
> (which you use further down) where you say "interpreted"?

Yes, that's what I meant. I have just pushed the fix, thank you.

On 25 March 2013 16:46, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Mar 25, 2013, at 11:23 AM, George Hartzell <hartzell at alerce.com> wrote:
>
>> Carn? Draug writes:
>>> [...]
>>> So I wrote Pod::Weaver::PluginBundle::BioPerl to be used with
>>> Dist::Zilla::PluginBundle::BioPerl. Would be nice if someone could
>>> give some feedback if it's adequate for the rest of the project.
>>>
>>> https://github.com/bioperl/dist-zilla-pluginbundle-bioperl/blob/master/lib/Pod/Weaver/PluginBundle/BioPerl.pm
>>
>> Looks wonderful!
>>
>> I use a "private" section that I think corresponds to what you call
>> "internal".  Is there a BioPerl tradition one way or the other?
>
> Not really, but there probably should be a more standard way of doing this.

I think the large majority of the modules have a head1 APPENDIX that
says "Internal methods are usually preceded with a _" which contained
each method and attribute by the same order they appear on the code
inside a head2. I just followed the name that was already there
"internal", but it's very easy to change. At the moment, what I set up
recognizes the following:

=attr (for attributes)
=method
=func (for functions)
=internal (internal methods)

It doesn't matter the order they appear on the source, PodWeaver will
group and reorder them. It is easy to change the keywords, and add or
remove the groups. Just let me know what the bundle should be doing.
Take a look at

https://github.com/bioperl/Bio-Biblio/blob/master/lib/Bio/DB/BiblioI.pm

which generates

https://metacpan.org/module/Bio::DB::BiblioI

>>> https://metacpan.org/module/Pod::Weaver::Section::GenerateSection
>>
>> [...]
>>
>> This is a useful contribution!
>>
>
> Yes, agreed.  The original purpose of the BioPerl Dist::Zilla bundle (set up during GSoC a few years ago by Sheena) was to make releases easier and more consistent across independent dists if need be; if configuring and using Pod::Weaver simplifies boilerplate and makes documentatio easier I'm all for it.

I wrote another plugin the day after to generate the legal section
which is mainly aimed at BioPerl and distributions with many modules,
where the authors and copyright owners are not always the same. It
takes the copyright information from a block of comments in each
source file.

https://metacpan.org/module/Pod::Weaver::Section::Legal::Complicated

And yesterday the contributors plugin was released again after also
implementing the option to find the names of contributors in the
source of individual files

https://metacpan.org/module/Pod::Weaver::Section::Contributors

I can easily make the changes on our pluginbundles, or write new ones.
And authors from other packages are usually happy to receive patches
so it's also easy to expand on the ones that already exist. The only
problem left is defining what a BioPerl POD should look like. The pod
weaver pluginbundle as it is now, is just what looked appropriate to
me. But would be great if someone could comment on it so adjustments
to it can be made.

Carn?



From amelia.ireland at gmod.org  Mon Mar 25 23:55:23 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Mon, 25 Mar 2013 16:55:23 -0700
Subject: [Bioperl-l] [Gmod-gbrowse] Last day for early registration for
	GMOD 2013
In-Reply-To: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
References: <CA+JTaowy22hea2Fj-D45T6NwhkGKHHZbhc9xWSn2+tW0Dj+ohg@mail.gmail.com>
Message-ID: <CAALsq01L4pRuOTsHh-wxmHuKBs24g3Q=DW2ngqaYq4386FAmHQ@mail.gmail.com>

GMOD is very pleased to announce the keynote speaker for the 2013 GMOD
community meeting is Dr. Kentaro Yoshida from the Sainsbury Lab (
http://tsl.ac.uk), talking about the Open Ash Dieback effort. This
pioneering bioinformatics project is employing two increasingly important
paradigms--open access to data and crowdsourcing--to gather genetic
analyses of ash and a fungal pathogen that is threatening tree populations
in the UK. Expect an interesting and inspiring talk!

Online registration: http://gmod2013.eventbrite.com

If you are interested in attending remotely, we will be using Go To Meeting
(http://gotomeeting.com) to allow people to attend virtually. Please email
me if you would like to join in.

Look forward to seeing you all in Cambridge!


On Wed, Mar 20, 2013 at 7:28 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi,
>
> With several guest speakers, including Jane Lomax from GO, Joseph
> Rossetto from the EBI, and Manuel Corpas from the Genome Analysis
> Centre, this GMOD meeting is shaping up to be a very intersting
> meeting indeed.  Today (March 21) is the last day to register with the
> early registration pricing.  To register, go to
>
>   http://gmod2013.eventbrite.com/
>
> I look forward to seeing you next month (April 5-6) in Cambridge,
> England.  For more information about GMOD 2013, go to
>
>   http://www.gmod.org/wiki/April_2013_GMOD_Meeting
>
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


From carandraug+dev at gmail.com  Tue Mar 26 03:48:49 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 26 Mar 2013 03:48:49 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2VDEt5OeKsZdNegygdTv_ZPJXcVXO6JS65sFjVCVKKZg@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI

This module mentions Bio::Cluster::Family but I can't seem to find it anywhere.

> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I think I was overcomplicating, this class might do what I want
thought in a different way. My idea of a family of genes doesn't
really match it, but I should be able to work with it by mixing it
with Set::Object.

Thank you,
Carn?



From briano at bioteam.net  Tue Mar 26 17:51:07 2013
From: briano at bioteam.net (Brian Osborne)
Date: Tue, 26 Mar 2013 13:51:07 -0400
Subject: [Bioperl-l] Wiki details
Message-ID: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>

All,

I'm looking at various module pages in the Wiki and it seems that all links are broken. For example, the "<biblio>" parser tag does not work, parser functions like #setvar aren't working and because of this the link to CPAN is broken, and so on. I'm guessing that some upgrade did not restore custom code or install extensions used in the earlier version, and Special:Version confirms this, this code is not installed.

If someone would like to contact me privately and give me credentials I can take a look at the MediaWiki directory, see if I can fix this.

Brian O.




From p.j.a.cock at googlemail.com  Tue Mar 26 18:10:10 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 26 Mar 2013 18:10:10 +0000
Subject: [Bioperl-l] Wiki details
In-Reply-To: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
References: <EF70238E-CDBE-4AE2-B54A-C8562FD7CBFB@verizon.net>
Message-ID: <CAKVJ-_5nOp8sXBhLRJ2Kvrzyf0rUGjTfs=PMd7pX_CqYAQ6djg@mail.gmail.com>

On Tue, Mar 26, 2013 at 5:51 PM, Brian Osborne <briano at bioteam.net> wrote:
> All,
>
> I'm looking at various module pages in the Wiki and it seems that all
> links are broken. For example, the "<biblio>" parser tag does not work,
> parser functions like #setvar aren't working and because of this the link to
> CPAN is broken, and so on. I'm guessing that some upgrade did not restore
> custom code or install extensions used in the earlier version, and
> Special:Version confirms this, this code is not installed.
>
> If someone would like to contact me privately and give me credentials I
> can take a look at the MediaWiki directory, see if I can fix this.
>
> Brian O.

Hi Brian,

I was aware of issues with the  "<biblio>" plugin, but not all of this.
Most likely this is from the server move at the end of 2012,
http://news.open-bio.org/news/2012/11/server-transition-to-aws/

Assuming someone senior from BioPerl (or Chris Dag?) will vouch
for you, we'd ask you to join the root-l mailing list where OBF server
admin stuff happens. We'll need a preferred username (e.g. briano
or bosborne) and your SSH public key (the new server does not
accept simple username/password logins).

Regards,

Peter
(With his OBF hat on)


From antony.vincent.1 at ulaval.ca  Tue Mar 26 23:24:20 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 16:24:20 -0700 (PDT)
Subject: [Bioperl-l]  One letter protein sequence to three letters
Message-ID: <35222270.post@talk.nabble.com>


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I
try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From Russell.Smithies at agresearch.co.nz  Tue Mar 26 23:44:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 12:44:35 +1300
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAA77@exchsth.agresearch.co.nz>

You're passing an ordinary String to Bio::SeqUtils->seq3 (that's what $hsp->query_string returns) but  I think it needs to be a Bio::PrimarySeqI compliant object.

try this:

$seqobj = Bio::PrimarySeq->new ( -seq => $hsp->query_string);
$polypeptide_3char = Bio::SeqUtils->seq3($seqobj);


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Wednesday, 27 March 2013 12:24 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] One letter protein sequence to three letters


Hi!

I wan't to parse a blastp output for have an hsp with three letters code. I try with this:

my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");  my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if
	
	$qseq = $hsp->query_string;
	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);

	print $polypeptide_3char;

	
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

And I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Not a Bio::PrimarySeqI object but [$self]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
STACK: blast_parsing.pl:36
-----------------------------------------------------------
I don't understand why my code generate this error!

Thanks :)
--
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222270.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From antony.vincent.1 at ulaval.ca  Wed Mar 27 01:32:09 2013
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Tue, 26 Mar 2013 18:32:09 -0700 (PDT)
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <35222270.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
Message-ID: <35222552.post@talk.nabble.com>


Yes! That works and I understand now, thanks for you precious help!
:handshake:

Antony03 wrote:
> 
> Hi!
> 
> I wan't to parse a blastp output for have an hsp with three letters code.
> I try with this:
> 
> my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
>   				    -format => 'fasta' );
>  my $query1 = <$query1_in>; 
>  my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
>   				      -format => 'fasta' );
>  my $query2 = <$query2_in>; 
>  
>  my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>
> "$algo");
>  my $report = $factory->bl2seq($query1, $query2);
> 
> ############################################################################################################
>  while (my $result = $report->next_result) {  # while 1
>     print "Query: ".$result->query_name."\n\n";
>     while (my $hit = $result->next_hit) {     # while 2
>  	while (my $hsp = $hit->next_hsp) {    # while 3
>  
> if ( $hsp->percent_identity >= "$identity" ) 
> 
> 	{ # start of if
> 	
> 	$qseq = $hsp->query_string;
> 	$polypeptide_3char = Bio::SeqUtils->seq3($qseq);
> 
> 	print $polypeptide_3char;
> 
> 	
> 		
> }
>  	} # end of while 3
>     print "\n";
>     }	# end of while 2
>  }	# end of while 3
> 
> And I got this error:
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Not a Bio::PrimarySeqI object but [$self]
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> STACK: Bio::SeqUtils::seq3 /usr/share/perl5/Bio/SeqUtils.pm:187
> STACK: blast_parsing.pl:36
> -----------------------------------------------------------
> I don't understand why my code generate this error!
> 
> Thanks :)
> 

-- 
View this message in context: http://old.nabble.com/One-letter-protein-sequence-to-three-letters-tp35222270p35222552.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From alexeymorozov1991 at gmail.com  Wed Mar 27 02:34:01 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Wed, 27 Mar 2013 11:34:01 +0900
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <35222552.post@talk.nabble.com>
References: <35222270.post@talk.nabble.com>
	<35222552.post@talk.nabble.com>
Message-ID: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?


From Russell.Smithies at agresearch.co.nz  Wed Mar 27 02:50:24 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 27 Mar 2013 15:50:24 +1300
Subject: [Bioperl-l] Fwd:  One letter protein sequence to three letters
In-Reply-To: <CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>

Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
Or is there a chance that $identity is going to contain a string rather than a float?

I could be completely wrong of course  ...

--Russell
-- 


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
Sent: Wednesday, 27 March 2013 3:34 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters

Well, there is one little thing I don't get. Why is

if ( $hsp->percent_identity >= "$identity" )

any better than

if ( $hsp->percent_identity >= $identity)

Ie what do quotes do?
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From cjfields at illinois.edu  Wed Mar 27 03:13:19 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 27 Mar 2013 03:13:19 +0000
Subject: [Bioperl-l] One letter protein sequence to three letters
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
References: <35222270.post@talk.nabble.com>	<35222552.post@talk.nabble.com>
	<CAK=7cMMWiS30fZUuAe15ZvUmQ8xmox+d6nB=i91VA+=_cyEy5Q@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF373657AAB7F@exchsth.agresearch.co.nz>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC4070@CHIMBX5.ad.uillinois.edu>

You are correct.   Quotes should be unnecessary in this case, percent identities are calculated I believe from the midline.

chris

On Mar 26, 2013, at 9:50 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> Not 100% sure but is the first one going to do a string compare rather than a numeric compare?
> Or is there a chance that $identity is going to contain a string rather than a float?
> 
> I could be completely wrong of course  ...
> 
> --Russell
> -- 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Alexey Morozov
> Sent: Wednesday, 27 March 2013 3:34 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Fwd: One letter protein sequence to three letters
> 
> Well, there is one little thing I don't get. Why is
> 
> if ( $hsp->percent_identity >= "$identity" )
> 
> any better than
> 
> if ( $hsp->percent_identity >= $identity)
> 
> Ie what do quotes do?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From adsj at novozymes.com  Wed Mar 27 12:19:01 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:19:01 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
Message-ID: <87li99593e.fsf@topper.koldfront.dk>

We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
with drawing panels that have tracks with split locations - an exception
is thrown in 2.24.

Here are the outputs of the test-script I've made:

  Bio::Graphics::VERSION: 1.995
  Simple location  ... ok
  Join location  ... ok

and

  Bio::Graphics::VERSION: 2.24
  Simple location  ... ok
  Join location  ... Can't locate object method "has_tag" via package "Bio::Location::Simple" at /usr/share/perl5/Bio/Graphics/Glyph.pm line 706, <DATA> line 192.

The test script looks like this:

== =
#!/usr/bin/perl

use strict;
use warnings;

use Bio::Graphics;

use Bio::SeqFeature::Generic;
use Bio::Factory::FTLocationFactory;

print "Bio::Graphics::VERSION: $Bio::Graphics::VERSION\n";

test_panel_with_location('1..12',              'Simple location');
test_panel_with_location('join(1..10,15..20)', 'Join location');

sub test_panel_with_location {
    my ($location_string, $msg)=@_;

    print "$msg  ... ";
    my $location=Bio::Factory::FTLocationFactory->from_string($location_string);
    my $seq=Bio::SeqFeature::Generic->new;
    $seq->location($location);

    my $panel=Bio::Graphics::Panel->new(-length=>500, -width=>500);
    $panel->add_track($seq);
    eval { $panel->png };
    print $@ || "ok\n";
}
== =

Am I doing something wrong in the script, or is this a regression in
Bio::Graphics somewhere?


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From adsj at novozymes.com  Wed Mar 27 12:33:53 2013
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 27 Mar 2013 13:33:53 +0100
Subject: [Bioperl-l] Bio::Graphics 2.24: fails to draw tracks with split
	locations?
In-Reply-To: <87li99593e.fsf@topper.koldfront.dk> ("Adam =?iso-8859-1?Q?Sj?=
	=?iso-8859-1?Q?=F8gren=22's?= message of
	"Wed, 27 Mar 2013 13:19:01 +0100")
References: <87li99593e.fsf@topper.koldfront.dk>
Message-ID: <87hajx58em.fsf@topper.koldfront.dk>

adsj at novozymes.com (Adam Sj?gren) writes:

> We just upgraded Bio::Graphics from 1.995 to 2.24, and noticed a problem
> with drawing panels that have tracks with split locations - an exception
> is thrown in 2.24.

[...]

Ahh, this has been fixed between 2.24 and 2.32 - (we upgraded to 2.24
because that is the version in the latest Ubuntu LTS).

2.32 works fine:

  Bio::Graphics::VERSION: 2.32
  Simple location  ... ok
  Join location  ... ok

Sorry for the noise.


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From carandraug+dev at gmail.com  Thu Mar 28 14:55:48 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 14:55:48 +0000
Subject: [Bioperl-l]  Google Summer of Code - BioPerl proposals
Message-ID: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>

On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
> Just a heads-up, if there are any students interested in the Google Summer of
> Code, the Open Bioinformatics Foundation is planning on participating again
> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
> looking for prospective projects.
>
> We're open for any project ideas this year, so let us know what you would like
> to do!

Hi

I had already mentioned that I would like to finish the split of the
project into smaller distributions. Is it acceptable to finish
projects from previous years? I noticed that the wiki page for BioPerl
projects is still empty for this year. Should I fill it? Would someone
be able to mentor that?

Carn?



From carandraug+dev at gmail.com  Thu Mar 28 16:23:18 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 28 Mar 2013 16:23:18 +0000
Subject: [Bioperl-l] organizing a gene family in memory
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2aay=8G8Gb5WKJxOz+x=8PSD=48ctvbBCPxEFVrrz1sQ@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74DC170A@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_32AU=Vc1yZofWyLM+CVQj0Xa6et+7rKHrXSHVU-TY2sA@mail.gmail.com>

On 25 March 2013 12:54, Fields, Christopher J <cjfields at illinois.edu> wrote:
> IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:
>
> https://metacpan.org/module/Bio::Cluster::FamilyI
>
> My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

I'm looking at these now and thinking of making the split from live
into a separate distribution now. But I'm unsure about two of the
files

Bio/ClusterIO/dbsnp.pm
Bio/Cluster/SequenceFamily.pm

Would you agree that these would fit better into a Bio-Variations and
Bio-Seq distribution?

Carn?



From hlapp at drycafe.net  Sat Mar 30 17:24:26 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 30 Mar 2013 12:24:26 -0500
Subject: [Bioperl-l] Google Summer of Code - BioPerl proposals
In-Reply-To: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
References: <CAPOrs_2NuGVeLV8nVdCnLbyMXYhsZT7qcWCW6-bTuXcc70kpbA@mail.gmail.com>
Message-ID: <723EBB03-97B3-4750-876C-68F55256DCB6@drycafe.net>

Hi Carn?,

Not sure I've missed a response to this. If indeed there hasn't been one, let me just chime in non-authoritatively that in principle there's nothing wrong with picking up past pieces. I would argue you'd have to make a convincing argument as to why and how you'd surmount the hurdles that brought the previous project to a premature end (or why it ran out of time and you won't), and as to how it's desirability has not diminished since then even though nobody else picked it up.

If you want to apply as a student, you don't strictly have to put it up on the wiki, but it'd be prudent to discuss your ideas on this list prior to submission. Presumably you were planning that anyway, though.

-hilmar

Sent with a tap.

On Mar 28, 2013, at 9:55 AM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> On 18 March 2013 21:26, Christopher Fields <cjfields at illinois.edu> wrote:
>> Just a heads-up, if there are any students interested in the Google Summer of
>> Code, the Open Bioinformatics Foundation is planning on participating again
>> this year!  Pjotr Prins will be organizing for OBF; all the Bio* projects are
>> looking for prospective projects.
>> 
>> We're open for any project ideas this year, so let us know what you would like
>> to do!
> 
> Hi
> 
> I had already mentioned that I would like to finish the split of the
> project into smaller distributions. Is it acceptable to finish
> projects from previous years? I noticed that the wiki page for BioPerl
> projects is still empty for this year. Should I fill it? Would someone
> be able to mentor that?
> 
> Carn?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From briano at bioteam.net  Sun Mar 31 14:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 14:11:03 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 07:11:03 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
Message-ID: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>

I've fixed a few issues related to paths, so no more server errors. I can 
also see in the debugger that data's being retrieved from the databases. 
However, it appears that links like "javascript:submitMe('Bio::Seq')" 
aren't actually submitting, though I see no errors in the browser's 
console. Taking a closer look ...

On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote:
>
> It should be just (shudder) Berkeley DB. 
>
>
>
>
> On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
> wrote: 
>
> > I think it uses mysql but I don't know if that was reconstituted on the 
> new server. 
> > 
> > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
> wrote: 
> > 
> >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
> wrote: 
> >>> Hi All, 
> >>> 
> >>> Don't know if anyone admin folk are aware, but the bioperl.orgdeobfuscator 
> >>> is generating internal server errors. I've also been having problems 
> with 
> >>> broken documentation links (cpan links producning the wrong modules, 
> and 
> >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> >>> 
> >>> I am, for now, still obfuscated... 
> >>> 
> >>> Cheers, 
> >>> James 
> >> 
> >> I would guess this is a side effect from the recent server move, 
> >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> >> 
> >> Peter 
> >> _______________________________________________ 
> >> Root-l mailing list 
> >> Roo... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > 
> > Jason Stajich 
> > jason.... at gmail.com <javascript:> 
> > ja... at bioperl.org <javascript:> 
> > 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 15:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From briano at bioteam.net  Sun Mar 31 15:05:00 2013
From: briano at bioteam.net (briano at bioteam.net)
Date: Sun, 31 Mar 2013 08:05:00 -0700 (PDT)
Subject: [Bioperl-l] [Root-l]  deobfuscator broken....
In-Reply-To: <b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
References: <50CA313B.9060904@imperial.ac.uk>
	<CAKVJ-_615d=97ngOK3_XadPsy_SrHS+jMyCj00ji3OTVB088=g@mail.gmail.com>
	<0F706FA4-68B8-4E50-BDEC-BF8632929BB6@gmail.com>
	<A6ECFFCE-8274-4B60-B681-64AA04285059@davemessina.com>
	<b37f07d7-4bb8-40bd-b4c2-a89c00f6e955@googlegroups.com>
Message-ID: <1ea8ae1f-eb55-4f05-98cb-b55a51224edc@googlegroups.com>

I've never used Deobfuscator so I don't know what the interface elements 
are supposed to do. Can someone familiar with it take a look at 
http://http://bioperl.org/cgi-bin/deob_interface.cgi?

On Sunday, March 31, 2013 10:11:03 AM UTC-4, bri... at bioteam.net wrote:
>
> I've fixed a few issues related to paths, so no more server errors. I can 
> also see in the debugger that data's being retrieved from the databases. 
> However, it appears that links like "javascript:submitMe('Bio::Seq')" 
> aren't actually submitting, though I see no errors in the browser's 
> console. Taking a closer look ... 
>
> On Thursday, December 13, 2012 6:41:35 PM UTC-5, Dave Messina wrote: 
> > 
> > It should be just (shudder) Berkeley DB. 
> > 
> > 
> > 
> > 
> > On Dec 13, 2012, at 18:18, Jason Stajich <jason.... at gmail.com<javascript:>> 
>
> > wrote: 
> > 
> > > I think it uses mysql but I don't know if that was reconstituted on 
> the 
> > new server. 
> > > 
> > > On Dec 13, 2012, at 2:52 PM, Peter Cock <p.j.a... at googlemail.com<javascript:>> 
>
> > wrote: 
> > > 
> > >> On Thu, Dec 13, 2012 at 7:49 PM, James Abbott <j.ab... at imperial.ac.uk<javascript:>> 
>
> > wrote: 
> > >>> Hi All, 
> > >>> 
> > >>> Don't know if anyone admin folk are aware, but the 
> bioperl.orgdeobfuscator 
> > >>> is generating internal server errors. I've also been having problems 
> > with 
> > >>> broken documentation links (cpan links producning the wrong modules, 
> > and 
> > >>> pdoc pages missing) but can't seem to replicate that problem now.... 
> > >>> 
> > >>> I am, for now, still obfuscated... 
> > >>> 
> > >>> Cheers, 
> > >>> James 
> > >> 
> > >> I would guess this is a side effect from the recent server move, 
> > >> CC'ing root-l in case anyone of the sys-admin team had an idea. 
> > >> 
> > >> Peter 
> > >> _______________________________________________ 
> > >> Root-l mailing list 
> > >> Roo... at lists.open-bio.org <javascript:> 
> > >> http://lists.open-bio.org/mailman/listinfo/root-l 
> > > 
> > > Jason Stajich 
> > > jason.... at gmail.com <javascript:> 
> > > ja... at bioperl.org <javascript:> 
> > > 
> > > 
> > > _______________________________________________ 
> > > Bioperl-l mailing list 
> > > Biop... at lists.open-bio.org <javascript:> 
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>