From briano at bioteam.net  Mon Sep  1 14:17:43 2014
From: briano at bioteam.net (Brian Osborne)
Date: Mon, 1 Sep 2014 08:17:43 -0600
Subject: [Bioperl-l] Converting pdb files to dssp file
In-Reply-To: <CAPdEJuXi0drHPCU_wiN2ez-GxCSkW3572kE_PbrL30snpc_r=g@mail.gmail.com>
References: <CAPdEJuXi0drHPCU_wiN2ez-GxCSkW3572kE_PbrL30snpc_r=g@mail.gmail.com>
Message-ID: <0118D4A7-9B41-4196-BBD2-ADED8DE20370@verizon.net>

Vandana,

Bio::Structure::IO::pdb reads and writes PDB format, but Bio::Structure::SecStr::DSSP::Res only reads *dssp files.

I don?t think this conversion is possible with BioPerl.

Brian O.

On Aug 30, 2014, at 11:08 PM, vandana Baranwal <lovevandu08 at gmail.com> wrote:

> Hello
> Is is possible to convert a pdb file int dssp file using bioperl. I searched a lot but didn't get a fruitful answer.
> I want to convert approximately 1000 pdb files into dssp files.
> 
> Any help will be highly appreciated
> 
> -- 
> Thanks & Regards
> Vandana Kumari
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From p.j.a.cock at googlemail.com  Wed Sep 10 08:15:52 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 10 Sep 2014 09:15:52 +0100
Subject: [Bioperl-l] Fwd: [Bosc-announce] Questionnaire about BOSC 2014 and
	2015
In-Reply-To: <D8975658-86FC-4C24-91F1-4963009B8C34@gmail.com>
References: <D8975658-86FC-4C24-91F1-4963009B8C34@gmail.com>
Message-ID: <CAKVJ-_5iBko3Mb6p348TL6vacKDsugsB4h=XqW=TckjJsPuqKw@mail.gmail.com>

Dear all,

If you attended the OBF run Bioinformatics Open Source Conference (BOSC)
this year, or might attend BOSC 2015 (or the Galaxy Community Conference,
GCC2015) please could you fill in this short survey.

Thank you,

Peter

---------- Forwarded message ----------
From: Nomi Harris <nlharris at gmail.com>
Date: Wed, Sep 10, 2014 at 2:32 AM
Subject: [Bosc-announce] Questionnaire about BOSC 2014 and 2015
To: bosc-announce at mailman.open-bio.org
Cc: BOSC 2014 <bosc at open-bio.org>


Hi all,

The BOSC organizing committee is looking into the possibility of
holding BOSC 2015 in Norwich, UK, just after GCC2015. We are seeking
feedback on that option, as well as more general feedback on BOSC 2014
(from those who didn?t attend it as well as those who did).

We've put together a short (5-minute) questionnaire to collect your
feedback--please go to http://bit.ly/BOSCsurvey to participate. The
deadline for submitting your response is Monday, September 15.

We appreciate your response, and hope to see you at BOSC 2015!

Sincerely,
       Nomi Harris and Peter Cock
       Co-Chairs, BOSC 2014 and BOSC 2015


_______________________________________________
Bosc-announce mailing list
Bosc-announce at mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/bosc-announce


From bioperl at etrumeus.com  Fri Sep 12 17:10:34 2014
From: bioperl at etrumeus.com (D. Joe)
Date: Fri, 12 Sep 2014 17:10:34 +0000
Subject: [Bioperl-l] web site?
Message-ID: <20140912171034.GY11796@quercus.etrumeus.com>


Went to look for the web site for the first time in a while, seemed down. 
Checked isitdownforeveryoneorjustme and it's down for them, too.

Tried both bioperl.org (as advertized for the project at Github,
which is still up) and www.bioperl.org.


DNS doesnt' look set to expire until December 2014, so that doesn't seem to
be it.  

www.bioperl.org resolves for me to 54.243.166.98, as does www.open-bio.org
(which is also down, so it's not, for instance, just a problem with the
bioperl-specific web server settings)

mailman.open-bio.org resolves to 54.243.246.167 and seems to be up, so I
expect this message will go through at least (since the MX for bioperl.org
points to lists.open-bio.org which resolves to the same as
mailman.open-bio.org).

Not sure if this is the best place to report it, but there it is.


Hope that helps,

-- 
D. Joe
man screen | grep -A2 weird
  A weird imagination is most useful to gain full advantage of
  all the features.

From cjfields at illinois.edu  Fri Sep 12 17:48:11 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 12 Sep 2014 17:48:11 +0000
Subject: [Bioperl-l] web site?
In-Reply-To: <20140912171034.GY11796@quercus.etrumeus.com>
References: <20140912171034.GY11796@quercus.etrumeus.com>
Message-ID: <53FDF350-CF29-4453-94BD-8F8DC138E595@illinois.edu>

There was an AWS security maintenance upgrade that took the site down for a short period.  It?s back up now.

chris

On Sep 12, 2014, at 12:10 PM, D. Joe <bioperl at etrumeus.com> wrote:

> 
> Went to look for the web site for the first time in a while, seemed down. 
> Checked isitdownforeveryoneorjustme and it's down for them, too.
> 
> Tried both bioperl.org (as advertized for the project at Github,
> which is still up) and www.bioperl.org.
> 
> 
> DNS doesnt' look set to expire until December 2014, so that doesn't seem to
> be it.  
> 
> www.bioperl.org resolves for me to 54.243.166.98, as does www.open-bio.org
> (which is also down, so it's not, for instance, just a problem with the
> bioperl-specific web server settings)
> 
> mailman.open-bio.org resolves to 54.243.246.167 and seems to be up, so I
> expect this message will go through at least (since the MX for bioperl.org
> points to lists.open-bio.org which resolves to the same as
> mailman.open-bio.org).
> 
> Not sure if this is the best place to report it, but there it is.
> 
> 
> Hope that helps,
> 
> -- 
> D. Joe
> man screen | grep -A2 weird
>  A weird imagination is most useful to gain full advantage of
>  all the features.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From dmitry at karasik.eu.org  Fri Sep 12 18:16:55 2014
From: dmitry at karasik.eu.org (Dmitry Karasik)
Date: Fri, 12 Sep 2014 20:16:55 +0200
Subject: [Bioperl-l] memory leak in Bio::Species
Message-ID: <20140912181655.GA82263@nataraj.karasik.eu.org>

Dear all,

I've hit a memory leak issue that OOMs our daemons once in a while, and what is
worse, I don't have the BioPerl expertise to fix it (I would send a patch
otherwise ). The problem is that Bio::Species and/or the modules it uses forms
cyclic references, which are never killed by perl automatically. I guess
either some internal data structure has to be reworked, or there should be some
strategic placing of Scalar::Util::weaken, but I have no idea where (or rather,
I could devise a hack that hammers weaken() instantly, but I don't think
this is the right approach).

It's very simple to reproduce, f.ex. by this:

	use Devel::Cycle;
	use Bio::Species;
	find_cycle(Bio::Species->new(-classification => ['A']));

which outputs

	Cycle (1):
           $Bio::Species::A->{'taxon'} => \%Bio::Taxon::B               
         $Bio::Taxon::B->{'_ancestor'} => \%Bio::Taxon::C               
             $Bio::Taxon::C->{'_desc'} => \%D                           
                             $D->{'1'} => \%Bio::Taxon::B               

	Cycle (2):
            $Bio::Species::A->{'tree'} => \%Bio::Tree::Tree::E          
        $Bio::Tree::Tree::E->{'_rootnode'} => \%Bio::Taxon::C               
             $Bio::Taxon::C->{'_desc'} => \%D                           
                             $D->{'1'} => \%Bio::Taxon::B               
         $Bio::Taxon::B->{'_ancestor'} => \%Bio::Taxon::C     

whereas I would expect it would print nothing.

I should really much like to ask the devs for a closer look. It's here on
github: https://github.com/bioperl/bioperl-live/issues/81

Thank you in advance!

-- 
Sincerely,
	Dmitry Karasik

From maj at fortinbras.us  Fri Sep 12 18:31:29 2014
From: maj at fortinbras.us (Mark A Jensen)
Date: Fri, 12 Sep 2014 14:31:29 -0400
Subject: [Bioperl-l] memory leak in Bio::Species
In-Reply-To: <20140912181655.GA82263@nataraj.karasik.eu.org>
References: <20140912181655.GA82263@nataraj.karasik.eu.org>
Message-ID: <99a613afcbd0ccc666decff45c0cc6@ip-10-0-3-59>

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From maj at fortinbras.us  Fri Sep 12 18:31:30 2014
From: maj at fortinbras.us (Mark A Jensen)
Date: Fri, 12 Sep 2014 14:31:30 -0400
Subject: [Bioperl-l] memory leak in Bio::Species
In-Reply-To: <20140912181655.GA82263@nataraj.karasik.eu.org>
References: <20140912181655.GA82263@nataraj.karasik.eu.org>
Message-ID: <55ba957838554c00935f24668dc97a@ip-10-0-3-59>

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From cjfields at illinois.edu  Tue Sep 16 20:41:10 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 16 Sep 2014 20:41:10 +0000
Subject: [Bioperl-l] Whither Bio::FeatureIO?
In-Reply-To: <CALRrKEMq21B0UBsO7SxikiBtAn5+Ze1OB-fz8_EOKUFSSgJVcg@mail.gmail.com>
References: <0193E1DB-1057-4974-ABEA-CF97AE9EAB1A@alerce.com>
	<36A84142-EB26-4980-B503-D20B1C8E085F@illinois.edu>
	<CA+JTaoxgv6gU5cxb1F-hQgaLwHdaOpnX3KiGqe+Xtgm2MzsRUQ@mail.gmail.com>
	<EC5050FA-995A-48E5-9167-6592A3A0BB75@illinois.edu>
	<D44B272F-3195-486E-AD80-CBD9039DE743@illinois.edu>
	<21506.41834.519236.301093@alacrity.local>
	<CALRrKEMq21B0UBsO7SxikiBtAn5+Ze1OB-fz8_EOKUFSSgJVcg@mail.gmail.com>
Message-ID: <66FA1AE3-E9A5-4869-8D50-6DFE4738D165@illinois.edu>

Cool!  I guess I could probably announce this as being released at some point now :)

chris

PS - I may have a decent test environment set up for longer-term evaluation, but it would be nice to see if we can get something working with travis-ci or a smoker setup, just so I can check whether the main branch refactoring is clobbering chado (as I suspect it is).

On Sep 16, 2014, at 1:50 PM, George Hartzell <hartzell.george at gene.com<mailto:hartzell.george at gene.com>> wrote:


Hi All,

It took a while, but I was finally able to run my little litmus test and the good news is that it appears to pass.

I modified my ansible playbook that implements the steps described in INSTALL.Chado<https://svn.code.sf.net/p/gmod/svn/schema/trunk/chado/INSTALL.Chado> so that it uses the version of Bio::FeatureIO that is now on CPAN instead of pulling the github master.

The resulting installation ran to completion and then was able to load the yeast gff3 file:

cp /vagrant/saccharomyces_cerevisiae.gff .
gmod_gff3_preprocessor.pl<http://gmod_gff3_preprocessor.pl/> --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
gmod_bulk_load_gff3.pl<http://gmod_bulk_load_gff3.pl/> --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted


and the resulting database seems to be stitched together reasonably (though I?m not a particularly informed judge of its character).

@chris thanks for the help on this!!!!

g.

?

On Sat, Aug 30, 2014 at 9:24 PM, George Hartzell <hartzell at alerce.com<mailto:hartzell at alerce.com>> wrote:
Fields, Christopher J writes:
 > Just a quick update on this: I released a separate Bio::FeatureIO
 > release to CPAN that represents the code split out from the core
 > modules:
 >
 >    https://metacpan.org/pod/Bio::FeatureIO
 >
 > I had to do some cleanup to get code to work and tests passing with
 > some sanity.  A *lot* of things were not passing tests when we
 > moved this over.
 >
 > This should represent what was last working with Chado though.
 > However, I haven?t officially announced anything yet b/c I would
 > like to shake bugs out of it. Can either of you try this out on a
 > Chado run to make sure everything is up to snuff (or at least point
 > out issues)?  Time depending, I would like to get something running
 > on (for instance) Travis-CI, maybe including some optional
 > Chado-related stuff.  This would also help so that we can work on
 > merging what has been done on master so that these pass the same
 > tests.

I can't do anything until Tuesday, but will be happy to run it through
the standard Chado build process when I get back to work.

Thanks for digging into it.

g.


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From lairdm at sfu.ca  Tue Sep 16 21:16:59 2014
From: lairdm at sfu.ca (Matthew Laird)
Date: Tue, 16 Sep 2014 14:16:59 -0700
Subject: [Bioperl-l] GenBank files CONTIG line
Message-ID: <5418A8CB.1000103@sfu.ca>

Good afternoon,

I wanted to report what I think is an issue but I'm not positive yet.  I 
found this old mailing list posting from May 
(http://lists.open-bio.org/pipermail/bioperl-l/2014-May/071583.html) 
about the changes to NCBI's genbank files, and I just grabbed the latest 
bioperl live with August's patch to hopefully solve it.  That part 
worked great, instead of spewing a few GB of warns and the whole 
sequence multiple times it read the genbank file and wrote out an embl 
file perfectly fine.

However the current bioperl live created a new issue.  I have a mirror 
of NCBI's bacterial genomes directory (yes, I know, I need to move to 
the new directory structure in the next 6 months) and this pipeline 
takes the genbank file and makes the embl, ptt, faa, and fna as needed. 
  This usually takes seconds.  Whatever changed in bioperl live compared 
to BioPerl 1.6.922 causes the script to spin doing something very 
intensely for tens of minutes, slowly writing out the ptt file.

Simply copying genbank.pm from bioperl live to my install directory 
solved both the CONTIG issue and kept the whole conversion process 
speedy.  So I'm happy for now, but I wanted to mention this in case it 
rings a bell with anyone on what could have changed to make parsing a 
gbk in to a ptt so much less efficient now.

Thanks.

-- 
Matthew Laird
Lead Software Developer, Bioinformatics
Brinkman Laboratory
Simon Fraser University, Burnaby, BC, Canada

From cjfields at illinois.edu  Tue Sep 16 22:39:15 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 16 Sep 2014 22:39:15 +0000
Subject: [Bioperl-l] Whither Bio::FeatureIO?
In-Reply-To: <CALRrKENXNp1M7bRTRjN5nx0igradxkttP9mAj3dSvKFXppLtug@mail.gmail.com>
References: <0193E1DB-1057-4974-ABEA-CF97AE9EAB1A@alerce.com>
	<36A84142-EB26-4980-B503-D20B1C8E085F@illinois.edu>
	<CA+JTaoxgv6gU5cxb1F-hQgaLwHdaOpnX3KiGqe+Xtgm2MzsRUQ@mail.gmail.com>
	<EC5050FA-995A-48E5-9167-6592A3A0BB75@illinois.edu>
	<D44B272F-3195-486E-AD80-CBD9039DE743@illinois.edu>
	<21506.41834.519236.301093@alacrity.local>
	<CALRrKEMq21B0UBsO7SxikiBtAn5+Ze1OB-fz8_EOKUFSSgJVcg@mail.gmail.com>
	<66FA1AE3-E9A5-4869-8D50-6DFE4738D165@illinois.edu>
	<CALRrKENXNp1M7bRTRjN5nx0igradxkttP9mAj3dSvKFXppLtug@mail.gmail.com>
Message-ID: <21BEF156-7A27-4673-829A-1E98B24CCBB6@illinois.edu>

It *might* be possible to set this up on Travis-CI independently on Bio::FeatureIO, which would be beneficial from a testing viewpoint (as we need to track what works w/ refactored FeatureIO vs what doesn?t).

I suppose what we need to check with a refactor (master branch) is:

1) Maintaining a sane amount of compat. with Chado.  ?Sane' meaning Bio::SF::Annotated will need to be chucked or completely reimplemented from scratch, as it is much less than sane now
2) If needed having a concurrently developed version of Chado to make it work.

It may not require much on #2 if Chado isn?t reliant on some of the less API-friendly parts of Bio::SF::Annotated (namely the heavy annotation associated with it).

chris

On Sep 16, 2014, at 4:53 PM, George Hartzell <hartzell.george at gene.com<mailto:hartzell.george at gene.com>> wrote:


@scott, do you have test setup for the GMOD stuff?

g.

?

On Tue, Sep 16, 2014 at 1:41 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
Cool!  I guess I could probably announce this as being released at some point now :)

chris

PS - I may have a decent test environment set up for longer-term evaluation, but it would be nice to see if we can get something working with travis-ci or a smoker setup, just so I can check whether the main branch refactoring is clobbering chado (as I suspect it is).

On Sep 16, 2014, at 1:50 PM, George Hartzell <hartzell.george at gene.com<mailto:hartzell.george at gene.com>> wrote:


Hi All,

It took a while, but I was finally able to run my little litmus test and the good news is that it appears to pass.

I modified my ansible playbook that implements the steps described in INSTALL.Chado<https://svn.code.sf.net/p/gmod/svn/schema/trunk/chado/INSTALL.Chado> so that it uses the version of Bio::FeatureIO that is now on CPAN instead of pulling the github master.

The resulting installation ran to completion and then was able to load the yeast gff3 file:

cp /vagrant/saccharomyces_cerevisiae.gff .
gmod_gff3_preprocessor.pl<http://gmod_gff3_preprocessor.pl/> --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
gmod_bulk_load_gff3.pl<http://gmod_bulk_load_gff3.pl/> --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted


and the resulting database seems to be stitched together reasonably (though I?m not a particularly informed judge of its character).

@chris thanks for the help on this!!!!

g.

?

On Sat, Aug 30, 2014 at 9:24 PM, George Hartzell <hartzell at alerce.com<mailto:hartzell at alerce.com>> wrote:
Fields, Christopher J writes:
 > Just a quick update on this: I released a separate Bio::FeatureIO
 > release to CPAN that represents the code split out from the core
 > modules:
 >
 >    https://metacpan.org/pod/Bio::FeatureIO
 >
 > I had to do some cleanup to get code to work and tests passing with
 > some sanity.  A *lot* of things were not passing tests when we
 > moved this over.
 >
 > This should represent what was last working with Chado though.
 > However, I haven?t officially announced anything yet b/c I would
 > like to shake bugs out of it. Can either of you try this out on a
 > Chado run to make sure everything is up to snuff (or at least point
 > out issues)?  Time depending, I would like to get something running
 > on (for instance) Travis-CI, maybe including some optional
 > Chado-related stuff.  This would also help so that we can work on
 > merging what has been done on master so that these pass the same
 > tests.

I can't do anything until Tuesday, but will be happy to run it through
the standard Chado build process when I get back to work.

Thanks for digging into it.

g.




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From cjfields at illinois.edu  Wed Sep 17 13:59:36 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 17 Sep 2014 13:59:36 +0000
Subject: [Bioperl-l] GenBank files CONTIG line
In-Reply-To: <5418A8CB.1000103@sfu.ca>
References: <5418A8CB.1000103@sfu.ca>
Message-ID: <0B13F23A-425A-4C44-9D9E-095EDF3E7D05@illinois.edu>

Mathew,

That?s particularly odd; the problem pops up after that commit was added?  

Would it be possible for you to post a bug report on GitHub issues about this?

    https://github.com/bioperl/bioperl-live/issues

If this is involving anything other that a simple next_seq/write_seq loop (e.g. if you are doing any additional data manipulation) it would also help to see example code so we can replicate this; once that is in place we can work on bisecting down the problematic commit.

chris

On Sep 16, 2014, at 4:16 PM, Matthew Laird <lairdm at sfu.ca> wrote:

> Good afternoon,
> 
> I wanted to report what I think is an issue but I'm not positive yet.  I found this old mailing list posting from May (http://lists.open-bio.org/pipermail/bioperl-l/2014-May/071583.html) about the changes to NCBI's genbank files, and I just grabbed the latest bioperl live with August's patch to hopefully solve it.  That part worked great, instead of spewing a few GB of warns and the whole sequence multiple times it read the genbank file and wrote out an embl file perfectly fine.
> 
> However the current bioperl live created a new issue.  I have a mirror of NCBI's bacterial genomes directory (yes, I know, I need to move to the new directory structure in the next 6 months) and this pipeline takes the genbank file and makes the embl, ptt, faa, and fna as needed.  This usually takes seconds.  Whatever changed in bioperl live compared to BioPerl 1.6.922 causes the script to spin doing something very intensely for tens of minutes, slowly writing out the ptt file.
> 
> Simply copying genbank.pm from bioperl live to my install directory solved both the CONTIG issue and kept the whole conversion process speedy.  So I'm happy for now, but I wanted to mention this in case it rings a bell with anyone on what could have changed to make parsing a gbk in to a ptt so much less efficient now.
> 
> Thanks.
> 
> -- 
> Matthew Laird
> Lead Software Developer, Bioinformatics
> Brinkman Laboratory
> Simon Fraser University, Burnaby, BC, Canada
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From bosborne11 at verizon.net  Wed Sep 17 14:24:48 2014
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 17 Sep 2014 10:24:48 -0400
Subject: [Bioperl-l] GenBank files CONTIG line
In-Reply-To: <5418A8CB.1000103@sfu.ca>
References: <5418A8CB.1000103@sfu.ca>
Message-ID: <FE14170E-75B9-431F-A89F-4FBC9206D350@verizon.net>

Matthew,

What's an easy way for me to reproduce this performance problem, making the *ptt file?

Brian O.

On Sep 16, 2014, at 5:16 PM, Matthew Laird <lairdm at sfu.ca> wrote:

> Good afternoon,
> 
> I wanted to report what I think is an issue but I'm not positive yet.  I found this old mailing list posting from May (http://lists.open-bio.org/pipermail/bioperl-l/2014-May/071583.html) about the changes to NCBI's genbank files, and I just grabbed the latest bioperl live with August's patch to hopefully solve it.  That part worked great, instead of spewing a few GB of warns and the whole sequence multiple times it read the genbank file and wrote out an embl file perfectly fine.
> 
> However the current bioperl live created a new issue.  I have a mirror of NCBI's bacterial genomes directory (yes, I know, I need to move to the new directory structure in the next 6 months) and this pipeline takes the genbank file and makes the embl, ptt, faa, and fna as needed.  This usually takes seconds.  Whatever changed in bioperl live compared to BioPerl 1.6.922 causes the script to spin doing something very intensely for tens of minutes, slowly writing out the ptt file.
> 
> Simply copying genbank.pm from bioperl live to my install directory solved both the CONTIG issue and kept the whole conversion process speedy.  So I'm happy for now, but I wanted to mention this in case it rings a bell with anyone on what could have changed to make parsing a gbk in to a ptt so much less efficient now.
> 
> Thanks.
> 
> -- 
> Matthew Laird
> Lead Software Developer, Bioinformatics
> Brinkman Laboratory
> Simon Fraser University, Burnaby, BC, Canada
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From Daniel.Lang at biologie.uni-freiburg.de  Mon Sep 22 18:13:57 2014
From: Daniel.Lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Mon, 22 Sep 2014 20:13:57 +0200
Subject: [Bioperl-l] Parent/parent_id attribute
Message-ID: <542066E5.5060401@biologie.uni-freiburg.de>

Hi,

I'm using bioperl 1.6.923-1 (Ubuntu Trusty package) and
Bio::DB::SeqFeature to store and manipulate GFF3 files.

I'm wondering why the "Parent" GFF3 attributes are stored as parent_id
values in the feature objects, but not returned as such in the gff3_string?

GFF3:
Chr01   transdecoder    mRNA    5216    5627    .       +       .
ID=T1.Chr01.mRNA.1;Parent=T1.Chr01.gene.1;Alias=T1.asmbl_1|m.6484,T1.ORF;Name=T1.Chr01.mRNA.1

Example debugger trace after fetching stored feature:

x $f
0  Bio::DB::SeqFeature=HASH(0x3e3a798)
   'attributes' => HASH(0x3e3a858)
      'Alias' => ARRAY(0x3e3a8b8)
         0  'T1.asmbl_1|m.6484'
         1  'T1.ORF'
      'load_id' => ARRAY(0x3e3aca8)
         0  'T1.Chr01.mRNA.1'
      'parent_id' => ARRAY(0x3e3acf0)
         0  'T1.Chr01.gene.1'
   'is_circular' => 0
   'name' => 'T1.Chr01.mRNA.1'
   'phase' => undef
   'primary_id' => 2428
   'ref' => 'Chr01'
   'score' => undef
   'source' => 'transdecoder'
   'start' => 5216
   'stop' => 5627
   'store' => Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x39b95d0)
      'class_loaded' => HASH(0x3e3a2b8)
         'Bio::DB::SeqFeature' => 1
      'dbh' => DBI::db=HASH(0x3dc1e40)
           empty hash
      'dumpdir' => '/tmp'
      'is_temp' => undef
      'namespace' => undef
      'seqfeatureclass' => 'Bio::DB::SeqFeature'
      'settings_cache' => HASH(0x3dc1d98)
         'autoindex' => 1
         'compress' => 0
         'index_subfeatures' => 1
         'serializer' => 'Storable'
      'writeable' => undef
   'strand' => 1
   'type' => 'mRNA'

x $f->gff3_string
0
"Chr01\cItransdecoder\cImRNA\cI5216\cI5627\cI.\cI+\cI.\cIName=T1.Chr01.mRNA.1;ID=2428;Alias=T1.asmbl_1%7Cm.6484,T1.ORF"

What is the best practice to store parentage? I'm currently adding an
additional "Parent" value using add_tag_value.

Or is this a bug in the version I'm using?

Best,
Daniel
-- 

Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        +49 761 203 6945
phone:      +49 761 203 6989
homepage:   http://www.plant-biotech.net/
            http://www.cosmoss.org/
e-mail:     daniel.lang at biologie.uni-freiburg.de

#################################################
My software never has bugs.
It just develops random features.
#################################################




From cjfields at illinois.edu  Sun Sep 28 03:26:43 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 28 Sep 2014 03:26:43 +0000
Subject: [Bioperl-l] Parent/parent_id attribute
In-Reply-To: <542066E5.5060401@biologie.uni-freiburg.de>
References: <542066E5.5060401@biologie.uni-freiburg.de>
Message-ID: <892AC2D6-99CA-42EB-9EF8-7496C7D6F670@illinois.edu>

Hi Daniel,

Not sure if you got an answer to this one yet.  I?m cc?ing the gmod-gbrowse group just in case this was missed here.  

chris

On Sep 22, 2014, at 1:13 PM, Daniel Lang <Daniel.Lang at biologie.uni-freiburg.de> wrote:

> Hi,
> 
> I'm using bioperl 1.6.923-1 (Ubuntu Trusty package) and
> Bio::DB::SeqFeature to store and manipulate GFF3 files.
> 
> I'm wondering why the "Parent" GFF3 attributes are stored as parent_id
> values in the feature objects, but not returned as such in the gff3_string?
> 
> GFF3:
> Chr01   transdecoder    mRNA    5216    5627    .       +       .
> ID=T1.Chr01.mRNA.1;Parent=T1.Chr01.gene.1;Alias=T1.asmbl_1|m.6484,T1.ORF;Name=T1.Chr01.mRNA.1
> 
> Example debugger trace after fetching stored feature:
> 
> x $f
> 0  Bio::DB::SeqFeature=HASH(0x3e3a798)
>   'attributes' => HASH(0x3e3a858)
>      'Alias' => ARRAY(0x3e3a8b8)
>         0  'T1.asmbl_1|m.6484'
>         1  'T1.ORF'
>      'load_id' => ARRAY(0x3e3aca8)
>         0  'T1.Chr01.mRNA.1'
>      'parent_id' => ARRAY(0x3e3acf0)
>         0  'T1.Chr01.gene.1'
>   'is_circular' => 0
>   'name' => 'T1.Chr01.mRNA.1'
>   'phase' => undef
>   'primary_id' => 2428
>   'ref' => 'Chr01'
>   'score' => undef
>   'source' => 'transdecoder'
>   'start' => 5216
>   'stop' => 5627
>   'store' => Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x39b95d0)
>      'class_loaded' => HASH(0x3e3a2b8)
>         'Bio::DB::SeqFeature' => 1
>      'dbh' => DBI::db=HASH(0x3dc1e40)
>           empty hash
>      'dumpdir' => '/tmp'
>      'is_temp' => undef
>      'namespace' => undef
>      'seqfeatureclass' => 'Bio::DB::SeqFeature'
>      'settings_cache' => HASH(0x3dc1d98)
>         'autoindex' => 1
>         'compress' => 0
>         'index_subfeatures' => 1
>         'serializer' => 'Storable'
>      'writeable' => undef
>   'strand' => 1
>   'type' => 'mRNA'
> 
> x $f->gff3_string
> 0
> "Chr01\cItransdecoder\cImRNA\cI5216\cI5627\cI.\cI+\cI.\cIName=T1.Chr01.mRNA.1;ID=2428;Alias=T1.asmbl_1%7Cm.6484,T1.ORF"
> 
> What is the best practice to store parentage? I'm currently adding an
> additional "Parent" value using add_tag_value.
> 
> Or is this a bug in the version I'm using?
> 
> Best,
> Daniel
> -- 
> 
> Dr. Daniel Lang
> University of Freiburg, Plant Biotechnology
> Schaenzlestr. 1, D-79104 Freiburg
> fax:        +49 761 203 6945
> phone:      +49 761 203 6989
> homepage:   http://www.plant-biotech.net/
>            http://www.cosmoss.org/
> e-mail:     daniel.lang at biologie.uni-freiburg.de
> 
> #################################################
> My software never has bugs.
> It just develops random features.
> #################################################
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From adsj at novozymes.com  Mon Sep 29 15:17:31 2014
From: adsj at novozymes.com (Adam =?utf-8?Q?Sj=C3=B8gren?=)
Date: Mon, 29 Sep 2014 17:17:31 +0200
Subject: [Bioperl-l] Invalid EMBL files generated in rare circumstances;
	line wrapping
Message-ID: <877g0msbg4.fsf@topper.koldfront.dk>

  Hi.

If you craft a tag on a feature sneakily (or if you are unlucky)
Bio::SeqIO will create invalid EMBL, separating the "/" from the
qualifier name:

    ID   unknown; SV 1; linear; unassigned DNA; STD; UNC; 4 BP.
    XX
    AC   unknown;
    XX
    XX
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   CDS             1..4
    FT                   /
    FT                   note="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
    FT                   X"
    XX
    SQ   Sequence 4 BP; 1 A; 1 C; 1 G; 1 T; 0 other;
         actg                                                                      4
    //

In this example "/" and "note" are on separate lines, which is wrong; at
least BioPerl does not accept it itself.

Here is a script to create the above output (BioPerl 1.6.901 used):

    #!/usr/bin/perl

    use strict;
    use warnings;

    use Bio::Seq::RichSeq;
    use Bio::SeqFeature::Generic;
    use IO::String;
    use Bio::SeqIO;

    my $seq=Bio::Seq::RichSeq->new(-display_id=>'TEST', -seq=>'actg');
    my $cds=Bio::SeqFeature::Generic->new(-primary_tag=>'CDS', -start=>1, -end=>4);
    $cds->add_tag_value(note=>'XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX X');
    $seq->add_SeqFeature($cds);

    my $string;
    my $str=IO::String->new($string);
    my $io=Bio::SeqIO->new(-fh=>$str, -format=>'embl');
    $io->write_seq($seq);
    print $string;

Changing the position of the space in the note makes a/the difference.

Maybe there is a bug lurking in the line wrapping/formatting code
somewhere...

Does this sound like a bug to anyone else?

  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com


From cjfields at illinois.edu  Mon Sep 29 15:41:10 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 29 Sep 2014 15:41:10 +0000
Subject: [Bioperl-l] Invalid EMBL files generated in rare circumstances;
	line wrapping
In-Reply-To: <877g0msbg4.fsf@topper.koldfront.dk>
References: <877g0msbg4.fsf@topper.koldfront.dk>
Message-ID: <8C956BCF-72C8-45C6-BE07-1AA5B14BFDAE@illinois.edu>

I can reproduce that on master branch.  It?s a weird consequence/side-effect of the text wrapping I think; if you remove the space at the end of the string of X?s and allow the module to text wrap the line it works fine.  I don?t think we?ve ever run into it frankly.  

If possible can you file it as a bug on GitHub?

chris

On Sep 29, 2014, at 10:17 AM, Adam Sj?gren <adsj at novozymes.com> wrote:

>  Hi.
> 
> If you craft a tag on a feature sneakily (or if you are unlucky)
> Bio::SeqIO will create invalid EMBL, separating the "/" from the
> qualifier name:
> 
>    ID   unknown; SV 1; linear; unassigned DNA; STD; UNC; 4 BP.
>    XX
>    AC   unknown;
>    XX
>    XX
>    XX
>    FH   Key             Location/Qualifiers
>    FH
>    FT   CDS             1..4
>    FT                   /
>    FT                   note="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>    FT                   X"
>    XX
>    SQ   Sequence 4 BP; 1 A; 1 C; 1 G; 1 T; 0 other;
>         actg                                                                      4
>    //
> 
> In this example "/" and "note" are on separate lines, which is wrong; at
> least BioPerl does not accept it itself.
> 
> Here is a script to create the above output (BioPerl 1.6.901 used):
> 
>    #!/usr/bin/perl
> 
>    use strict;
>    use warnings;
> 
>    use Bio::Seq::RichSeq;
>    use Bio::SeqFeature::Generic;
>    use IO::String;
>    use Bio::SeqIO;
> 
>    my $seq=Bio::Seq::RichSeq->new(-display_id=>'TEST', -seq=>'actg');
>    my $cds=Bio::SeqFeature::Generic->new(-primary_tag=>'CDS', -start=>1, -end=>4);
>    $cds->add_tag_value(note=>'XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX X');
>    $seq->add_SeqFeature($cds);
> 
>    my $string;
>    my $str=IO::String->new($string);
>    my $io=Bio::SeqIO->new(-fh=>$str, -format=>'embl');
>    $io->write_seq($seq);
>    print $string;
> 
> Changing the position of the space in the note makes a/the difference.
> 
> Maybe there is a bug lurking in the line wrapping/formatting code
> somewhere...
> 
> Does this sound like a bug to anyone else?
> 
>  Best regards,
> 
>    Adam
> 
> -- 
>                                                          Adam Sj?gren
>                                                    adsj at novozymes.com
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From asjo at koldfront.dk  Mon Sep 29 18:55:30 2014
From: asjo at koldfront.dk (Adam =?utf-8?Q?Sj=C3=B8gren?=)
Date: Mon, 29 Sep 2014 20:55:30 +0200
Subject: [Bioperl-l] Invalid EMBL files generated in rare circumstances;
	line wrapping
In-Reply-To: <8C956BCF-72C8-45C6-BE07-1AA5B14BFDAE@illinois.edu> (Christopher
	J. Fields's message of "Mon, 29 Sep 2014 15:41:10 +0000")
References: <877g0msbg4.fsf@topper.koldfront.dk>
	<8C956BCF-72C8-45C6-BE07-1AA5B14BFDAE@illinois.edu>
Message-ID: <87d2ae5k9p.fsf@topper.koldfront.dk>

"Fields, Christopher J" <cjfields at illinois.edu> writes:

> I can reproduce that on master branch. It?s a weird
> consequence/side-effect of the text wrapping I think; if you remove
> the space at the end of the string of X?s and allow the module to text
> wrap the line it works fine. I don?t think we?ve ever run into it
> frankly.

Yes, it looks like a corner case that I was "unlucky" enough to hit.

> If possible can you file it as a bug on GitHub?

Certainly: https://github.com/bioperl/bioperl-live/issues/84


  Best regards,

    Adam

-- 
 "The key to performance is elegance, not battalions          Adam Sj?gren
  of special cases."                                     asjo at koldfront.dk


From maj at fortinbras.us  Tue Sep 30 03:41:33 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 29 Sep 2014 23:41:33 -0400
Subject: [Bioperl-l] Spankin' new (alpha) build system for Bioperl-Run
Message-ID: <a772a0ca8d7937306676a0128c1b3573@mail.fortinbras.us>

All (esp. George)-

My work on Issue #11 (https://github.com/bioperl/bioperl-run/issues/11) 
has metastasized.

The proximate problem was tests that fail because of once-local 
prerequisites. The ultimate
problems are

- Why should I have to install every single wrapper when I only want X?
- Why should I care about any test that doesn't deal with X?
- Why doesn't X bring along its own prereq metadata (including Bio 
prereqs),
   rather than tag along with the distro and hope for the best?

(And I think these are the ultimate problems across BioPerl in terms of 
decentralized
distribution.)

My solution was

- Add to the distro real, manually prepared metadata on prerequisites 
for all
   the tools
- Add an interactive selector that allows a user to pick their desired 
tools at
   perl Build.PL-time
- Have Module::Build check only (and ALL) the prereqs of the desired 
tools, and
   inform user of missing ones at perl Build.PL-time
- Make use of the persistence of the config information to skip/run .t 
files as
   appropriate
- Update ALL the tests to check whether to skip based on user selection
- Make M::B install only the relevant distro modules and documentation, 
not everything,
   at ./Build install-time

This is ready for brave alpha-testers at 
https://github.com/bioperl/bioperl-run/tree/topic/issue11.
Just do 'perl Build.PL'.

Pod below has some more details-- comments very welcome

MAJ

NAME
     Bio::Tools::Run::Build - Instrument the build for features

SYNOPSIS

...

DESCRIPTION
     Bio::Tools::Run::Build is a subclass of Module::Build that allows 
an
     author to offer users the ability to select and install 
pre-configured
     subsets of modules that are packaged in a single large M::B-based
     distribution.

     Grouping and selection of distro modules is driven by the optional
     features concept as defined in CPAN::Meta::Spec and used by
     Module::Build.

     The subclass provides the following:

     *   Author specification of features and their prereqs

         The build author develops metadata files in json that follow
         "optional_features" in CPAN::Meta::Spec to group distribution
         modules and dependencies as selectable features.

     *   Interactive user selection of features

         The user can be presented with an interactive selector during
         Build.PL runs.

     *   Prereq checking of user selected features only

         M::B only checks for the presence of selected feature 
dependencies.

     *   Build-persistent recording of user selections

         The build object records the selection of features in the
         $build->feature field. This can be used in test files to 
determine
         whether tests should be skipped (and not failed). See
         Bio::Tools::Run::Build::Test.

     *   Installation only of selected feature modules

         Bio::Tools::Run::Build adds a build action, "deselect", which 
runs
         after the "code" and "docs" actions. "deselect" removes 
unselected
         modules from the blib/lib directory and unneeded documentation 
from
         the blib/libdoc directory. This keeps the "install" action from
         installing unwanted files.

MOTIVATION
     The BioPerl-Run distribution contains a large variety of wrappers 
and
     parsers that handle the execution and output of many different
     bioinformatics tools. It has been provided as a large distro that
     installs and attempts to test all of its modules. Many users need 
only a
     small fraction of the functionality BioPerl-Run provides, relevant 
only
     to the tools they have installed. On the other hand, managing many
     different packages is unwieldy and uninviting for volunteer 
maintainers.

     The system described here is a compromise that enables a user to 
select,
     test and install only those modules that meet the need, yet reduces 
the
     maintenance effort to the management of a set of metadata files in 
a
     single distribution.

...

From maj at fortinbras.us  Tue Sep 30 04:30:37 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Tue, 30 Sep 2014 00:30:37 -0400
Subject: [Bioperl-l] Spankin' new (alpha) build system for Bioperl-Run
In-Reply-To: <a772a0ca8d7937306676a0128c1b3573@mail.fortinbras.us>
References: <a772a0ca8d7937306676a0128c1b3573@mail.fortinbras.us>
Message-ID: <ab2553b16169a84d12e1cac3dabdd178@mail.fortinbras.us>

 

(minus damn linebreaks)

All (esp. George)-

My work on Issue #11
(https://github.com/bioperl/bioperl-run/issues/11) has
metastasized.

The proximate problem was tests that fail because of
once-local prerequisites. The ultimate problems are

- Why should I have
to install every single wrapper when I only want X?

- Why should I care
about any test that doesn't deal with X?

- Why doesn't X bring along
its own prereq metadata (including Bio prereqs), rather than tag along
with the distro and hope for the best?

(And I think these are the
ultimate problems across BioPerl in terms of decentralized
distribution.)

My solution was

- Add to the distro real, manually
prepared metadata on prerequisites for all the tools

- Add an
interactive selector that allows a user to pick their desired tools at
perl Build.PL-time

- Have Module::Build check only (and ALL) the
prereqs of the desired tools, and inform user of missing ones at perl
Build.PL-time

- Make use of the persistence of the config information
to skip/run .t files as appropriate

- Update ALL the tests to check
whether to skip based on user selection

- Make M::B install only the
relevant distro modules and documentation, not everything, at ./Build
install-time

This is ready for brave alpha-testers at
https://github.com/bioperl/bioperl-run/tree/topic/issue11. Just do 'perl
Build.PL'.

Pod below has some more details-- comments very
welcome

MAJ

NAME
 Bio::Tools::Run::Build - Instrument the build for
features

SYNOPSIS

...

DESCRIPTION

Bio::Tools::Run::Build is a
subclass of Module::Build that allows an author to offer users the
ability to select and install pre-configured subsets of modules that are
packaged in a single large M::B-based distribution.

Grouping and
selection of distro modules is driven by the optional features concept
as defined in CPAN::Meta::Spec and used by Module::Build.

The subclass
provides the following:

* Author specification of features and their
prereqs

The build author develops metadata files in json that follow
"optional_features" in CPAN::Meta::Spec to group distribution modules
and dependencies as selectable features.

* Interactive user selection
of features

The user can be presented with an interactive selector
during Build.PL runs.

* Prereq checking of user selected features
only

M::B only checks for the presence of selected feature
dependencies.

* Build-persistent recording of user selections

The
build object records the selection of features in the $build->feature
field. This can be used in test files to determine whether tests should
be skipped (and not failed). See Bio::Tools::Run::Build::Test.

*
Installation only of selected feature modules

Bio::Tools::Run::Build
adds a build action, "deselect", which runs after the "code" and "docs"
actions. "deselect" removes unselected modules from the blib/lib
directory and unneeded documentation from the blib/libdoc directory.
This keeps the "install" action from installing unwanted
files.

MOTIVATION

The BioPerl-Run distribution contains a large
variety of wrappers and parsers that handle the execution and output of
many different bioinformatics tools. It has been provided as a large
distro that installs and attempts to test all of its modules. Many users
need only a small fraction of the functionality BioPerl-Run provides,
relevant only to the tools they have installed. On the other hand,
managing many different packages is unwieldy and uninviting for
volunteer maintainers.

The system described here is a compromise that
enables a user to select, test and install only those modules that meet
the need, yet reduces the maintenance effort to the management of a set
of metadata files in a single distribution.

On 2014-09-29 23:41, Mark
A. Jensen wrote:
> All (esp. George)-
> 

All (esp. George)-

My work on
Issue #11 (https://github.com/bioperl/bioperl-run/issues/11) has
metastasized.

The proximate problem was tests that fail because of
once-local prerequisites. The ultimate
problems are

- Why should I have
to install every single wrapper when I only want X?
- Why should I care
about any test that doesn't deal with X?
- Why doesn't X bring along its
own prereq metadata (including Bio prereqs),
 rather than tag along with
the distro and hope for the best?

(And I think these are the ultimate
problems across BioPerl in terms of decentralized
distribution.)

My
solution was

- Add to the distro real, manually prepared metadata on
prerequisites for all
 the tools
- Add an interactive selector that
allows a user to pick their desired tools at
 perl Build.PL-time
- Have
Module::Build check only (and ALL) the prereqs of the desired tools,
and
 inform user of missing ones at perl Build.PL-time
- Make use of the
persistence of the config information to skip/run .t files as

appropriate
- Update ALL the tests to check whether to skip based on
user selection
- Make M::B install only the relevant distro modules and
documentation, not everything,
 at ./Build install-time

This is ready
for brave alpha-testers at
https://github.com/bioperl/bioperl-run/tree/topic/issue11.
Just do 'perl
Build.PL'.

Pod below has some more details-- comments very
welcome

MAJ

NAME
 Bio::Tools::Run::Build - Instrument the build for
features

SYNOPSIS

...

DESCRIPTION
 Bio::Tools::Run::Build is a
subclass of Module::Build that allows an
 author to offer users the
ability to select and install pre-configured
 subsets of modules that
are packaged in a single large M::B-based
 distribution.

 Grouping and
selection of distro modules is driven by the optional
 features concept
as defined in CPAN::Meta::Spec and used by
 Module::Build.

 The
subclass provides the following:

 * Author specification of features
and their prereqs

 The build author develops metadata files in json
that follow
 "optional_features" in CPAN::Meta::Spec to group
distribution
 modules and dependencies as selectable features.

 *
Interactive user selection of features

 The user can be presented with
an interactive selector during
 Build.PL runs.

 * Prereq checking of
user selected features only

 M::B only checks for the presence of
selected feature dependencies.

 * Build-persistent recording of user
selections

 The build object records the selection of features in the

$build->feature field. This can be used in test files to determine

whether tests should be skipped (and not failed). See

Bio::Tools::Run::Build::Test.

 * Installation only of selected feature
modules

 Bio::Tools::Run::Build adds a build action, "deselect", which
runs
 after the "code" and "docs" actions. "deselect" removes
unselected
 modules from the blib/lib directory and unneeded
documentation from
 the blib/libdoc directory. This keeps the "install"
action from
 installing unwanted files.

MOTIVATION
 The BioPerl-Run
distribution contains a large variety of wrappers and
 parsers that
handle the execution and output of many different
 bioinformatics tools.
It has been provided as a large distro that
 installs and attempts to
test all of its modules. Many users need only a
 small fraction of the
functionality BioPerl-Run provides, relevant only
 to the tools they
have installed. On the other hand, managing many
 different packages is
unwieldy and uninviting for volunteer maintainers.

 The system
described here is a compromise that enables a user to select,
 test and
install only those modules that meet the need, yet reduces the

maintenance effort to the management of a set of metadata files in a

single distribution.

...

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From online at davemessina.com  Tue Sep 30 06:07:36 2014
From: online at davemessina.com (Dave Messina)
Date: Tue, 30 Sep 2014 01:07:36 -0500
Subject: [Bioperl-l] Spankin' new (alpha) build system for Bioperl-Run
In-Reply-To: <ab2553b16169a84d12e1cac3dabdd178@mail.fortinbras.us>
References: <a772a0ca8d7937306676a0128c1b3573@mail.fortinbras.us>
	<ab2553b16169a84d12e1cac3dabdd178@mail.fortinbras.us>
Message-ID: <CAM3TQQWrFtfmAzz+DwjU_TmfDTgWd4yEdRw_sAcnhTTQ7=8JFw@mail.gmail.com>

Very cool! Nice work Mark!!




On Mon, Sep 29, 2014 at 11:30 PM, Mark A. Jensen <maj at fortinbras.us> wrote:

>  (minus damn linebreaks)
>
>
> All (esp. George)-
>
> My work on Issue #11 (https://github.com/bioperl/bioperl-run/issues/11) has metastasized.
>
> The proximate problem was tests that fail because of once-local prerequisites. The ultimate problems are
>
> - Why should I have to install every single wrapper when I only want X?
>
> - Why should I care about any test that doesn't deal with X?
>
> - Why doesn't X bring along its own prereq metadata (including Bio prereqs), rather than tag along with the distro and hope for the best?
>
> (And I think these are the ultimate problems across BioPerl in terms of decentralized distribution.)
>
> My solution was
>
> - Add to the distro real, manually prepared metadata on prerequisites for all the tools
>
> - Add an interactive selector that allows a user to pick their desired tools at perl Build.PL-time
>
> - Have Module::Build check only (and ALL) the prereqs of the desired tools, and inform user of missing ones at perl Build.PL-time
>
> - Make use of the persistence of the config information to skip/run .t files as appropriate
>
> - Update ALL the tests to check whether to skip based on user selection
>
> - Make M::B install only the relevant distro modules and documentation, not everything, at ./Build install-time
>
> This is ready for brave alpha-testers at https://github.com/bioperl/bioperl-run/tree/topic/issue11. Just do 'perl Build.PL'.
>
> Pod below has some more details-- comments very welcome
>
> MAJ
>
> NAME
>     Bio::Tools::Run::Build - Instrument the build for features
>
> SYNOPSIS
>
> ...
>
> DESCRIPTION
>
> Bio::Tools::Run::Build is a subclass of Module::Build that allows an author to offer users the ability to select and install pre-configured subsets of modules that are packaged in a single large M::B-based distribution.
>
> Grouping and selection of distro modules is driven by the optional features concept as defined in CPAN::Meta::Spec and used by Module::Build.
>
> The subclass provides the following:
>
> *   Author specification of features and their prereqs
>
> The build author develops metadata files in json that follow "optional_features" in CPAN::Meta::Spec to group distribution modules and dependencies as selectable features.
>
> *   Interactive user selection of features
>
> The user can be presented with an interactive selector during Build.PL runs.
>
> *   Prereq checking of user selected features only
>
> M::B only checks for the presence of selected feature dependencies.
>
> *   Build-persistent recording of user selections
>
> The build object records the selection of features in the $build->feature field. This can be used in test files to determine whether tests should be skipped (and not failed). See Bio::Tools::Run::Build::Test.
>
> *   Installation only of selected feature modules
>
> Bio::Tools::Run::Build adds a build action, "deselect", which runs after the "code" and "docs" actions. "deselect" removes unselected modules from the blib/lib directory and unneeded documentation from the blib/libdoc directory. This keeps the "install" action from installing unwanted files.
>
> MOTIVATION
>
> The BioPerl-Run distribution contains a large variety of wrappers and parsers that handle the execution and output of many different bioinformatics tools. It has been provided as a large distro that installs and attempts to test all of its modules. Many users need only a small fraction of the functionality BioPerl-Run provides, relevant only to the tools they have installed. On the other hand, managing many different packages is unwieldy and uninviting for volunteer maintainers.
>
> The system described here is a compromise that enables a user to select, test and install only those modules that meet the need, yet reduces the maintenance effort to the management of a set of metadata files in a single distribution.
>
> On 2014-09-29 23:41, Mark A. Jensen wrote:
> > All (esp. George)-
> >
>
>  All (esp. George)-
>
> My work on Issue #11 (https://github.com/bioperl/bioperl-run/issues/11) has metastasized.
>
> The proximate problem was tests that fail because of once-local prerequisites. The ultimate
> problems are
>
> - Why should I have to install every single wrapper when I only want X?
> - Why should I care about any test that doesn't deal with X?
> - Why doesn't X bring along its own prereq metadata (including Bio prereqs),
>   rather than tag along with the distro and hope for the best?
>
> (And I think these are the ultimate problems across BioPerl in terms of decentralized
> distribution.)
>
> My solution was
>
> - Add to the distro real, manually prepared metadata on prerequisites for all
>   the tools
> - Add an interactive selector that allows a user to pick their desired tools at
>   perl Build.PL-time
> - Have Module::Build check only (and ALL) the prereqs of the desired tools, and
>   inform user of missing ones at perl Build.PL-time
> - Make use of the persistence of the config information to skip/run .t files as
>   appropriate
> - Update ALL the tests to check whether to skip based on user selection
> - Make M::B install only the relevant distro modules and documentation, not everything,
>   at ./Build install-time
>
> This is ready for brave alpha-testers at https://github.com/bioperl/bioperl-run/tree/topic/issue11.
> Just do 'perl Build.PL'.
>
> Pod below has some more details-- comments very welcome
>
> MAJ
>
> NAME
>     Bio::Tools::Run::Build - Instrument the build for features
>
> SYNOPSIS
>
> ...
>
> DESCRIPTION
>     Bio::Tools::Run::Build is a subclass of Module::Build that allows an
>     author to offer users the ability to select and install pre-configured
>     subsets of modules that are packaged in a single large M::B-based
>     distribution.
>
>     Grouping and selection of distro modules is driven by the optional
>     features concept as defined in CPAN::Meta::Spec and used by
>     Module::Build.
>
>     The subclass provides the following:
>
>     *   Author specification of features and their prereqs
>
>         The build author develops metadata files in json that follow
>         "optional_features" in CPAN::Meta::Spec to group distribution
>         modules and dependencies as selectable features.
>
>     *   Interactive user selection of features
>
>         The user can be presented with an interactive selector during
>         Build.PL runs.
>
>     *   Prereq checking of user selected features only
>
>         M::B only checks for the presence of selected feature dependencies.
>
>     *   Build-persistent recording of user selections
>
>         The build object records the selection of features in the
>         $build->feature field. This can be used in test files to determine
>         whether tests should be skipped (and not failed). See
>         Bio::Tools::Run::Build::Test.
>
>     *   Installation only of selected feature modules
>
>         Bio::Tools::Run::Build adds a build action, "deselect", which runs
>         after the "code" and "docs" actions. "deselect" removes unselected
>         modules from the blib/lib directory and unneeded documentation from
>         the blib/libdoc directory. This keeps the "install" action from
>         installing unwanted files.
>
> MOTIVATION
>     The BioPerl-Run distribution contains a large variety of wrappers and
>     parsers that handle the execution and output of many different
>     bioinformatics tools. It has been provided as a large distro that
>     installs and attempts to test all of its modules. Many users need only a
>     small fraction of the functionality BioPerl-Run provides, relevant only
>     to the tools they have installed. On the other hand, managing many
>     different packages is unwieldy and uninviting for volunteer maintainers.
>
>     The system described here is a compromise that enables a user to select,
>     test and install only those modules that meet the need, yet reduces the
>     maintenance effort to the management of a set of metadata files in a
>     single distribution.
>
> ...
>
>   Message 1 of 152
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
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From alexeymorozov1991 at gmail.com  Tue Sep 30 06:20:16 2014
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Tue, 30 Sep 2014 15:20:16 +0900
Subject: [Bioperl-l] Getting pairwise alignment scores for existing multiple
	alignment
Message-ID: <CAK=7cMOkPqofM6j12X77kBFhUb6ZPNFXNeN3YEHsQZU1r+yeDg@mail.gmail.com>

Dear colleagues,
Is there a method in bioperl that will calculate pairwise alignment scores
for any given pair of genes in MSA (according to a given matrix and gap
opening/extension cost)? It seems that Bio::SimpleAlign methods only work
with score if it has been described in MSA file and can only hold a general
multiple sequence alignment score.

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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From cjfields at illinois.edu  Tue Sep 30 16:54:33 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 30 Sep 2014 16:54:33 +0000
Subject: [Bioperl-l] Getting pairwise alignment scores for existing
 multiple	alignment
In-Reply-To: <CAK=7cMOkPqofM6j12X77kBFhUb6ZPNFXNeN3YEHsQZU1r+yeDg@mail.gmail.com>
References: <CAK=7cMOkPqofM6j12X77kBFhUb6ZPNFXNeN3YEHsQZU1r+yeDg@mail.gmail.com>
Message-ID: <C9F90635-0BC1-4F41-93FD-13A2897AE023@illinois.edu>

On Sep 30, 2014, at 1:20 AM, Alexey Morozov <alexeymorozov1991 at gmail.com<mailto:alexeymorozov1991 at gmail.com>> wrote:

Dear colleagues,
Is there a method in bioperl that will calculate pairwise alignment scores for any given pair of genes in MSA (according to a given matrix and gap opening/extension cost)? It seems that Bio::SimpleAlign methods only work with score if it has been described in MSA file and can only hold a general multiple sequence alignment score.

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

Bio::Align::PairwiseStatistics appears to deal with this, see if it fits your needs.  You may need to extract the pairwise alignment of the two genes if they are in a multiple sequence alignment.

chris

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