From johncumbers at gmail.com  Tue Dec  1 02:10:16 2009
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 30 Nov 2009 23:10:16 -0800
Subject: [Biopython] MuscleCommandline and phyiout
Message-ID: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>

Hello,

I'm using the MuscleCommandline wrapper and I'm having trouble getting the
Phylip interleaved output format.  For the Muscle command line I would type
"muscle -in myinputfile -phyiout myoutputfile" and this command in python:
cline = MuscleCommandline (input=output_file_name_FASTA,
out=output_file_name_aligned)

But for phyiout, this doesn't work:
cline = MuscleCommandline (input=output_file_name_FASTA,
phyiout=output_file_name_aligned)
returning: ValueError: Option name phyiout was not found.

I tried to lookup the possibilities here:
http://www.biopython.org/DIST/docs/api/Bio.Align.Applications._Muscle.MuscleCommandline-class.html

but couldn't find them, any help appreciated,
cheers,
John


John Cumbers, Ph.D Candidate
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.
cell +1 (401) 523 8190, office +1 (650) 604-1914, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA

From biopython at maubp.freeserve.co.uk  Tue Dec  1 04:23:54 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 09:23:54 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
Message-ID: <320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>

On Tue, Dec 1, 2009 at 7:10 AM, John Cumbers <johncumbers at gmail.com> wrote:
> Hello,
>
> I'm using the MuscleCommandline wrapper and I'm having trouble getting the
> Phylip interleaved output format. ?For the Muscle command line I would type
> "muscle -in myinputfile -phyiout myoutputfile"

What version of MUSCLE do you have? v3.7 doesn't mention this
option in the command line help, nor does the current manual:
http://www.drive5.com/muscle/muscle.html

Peter


From biopython at maubp.freeserve.co.uk  Tue Dec  1 04:52:19 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 09:52:19 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
Message-ID: <320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>

On Tue, Dec 1, 2009 at 9:23 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Dec 1, 2009 at 7:10 AM, John Cumbers <johncumbers at gmail.com> wrote:
>> Hello,
>>
>> I'm using the MuscleCommandline wrapper and I'm having trouble getting the
>> Phylip interleaved output format. ?For the Muscle command line I would type
>> "muscle -in myinputfile -phyiout myoutputfile"
>
> What version of MUSCLE do you have? v3.7 doesn't mention this
> option in the command line help, nor does the current manual:
> http://www.drive5.com/muscle/muscle.html

It looks like an undocumented option, much like -phyi (which I guessed)
for PHYLIP interlaced and -phys for PHYLIP sequential. These match
the documented format options (e.g. -msf, -html, -clw and -clwstrict).
i.e. You can use this:

"muscle -in myinputfile -phyi -out myoutputfile"

I think we should ask the MUSCLE author which of these
undocumented arguments are actually supported rather than
adding them all.

Peter


From bartomas at gmail.com  Tue Dec  1 11:25:36 2009
From: bartomas at gmail.com (bar tomas)
Date: Tue, 1 Dec 2009 16:25:36 +0000
Subject: [Biopython] Host_organism field in SwissProt
Message-ID: <fdcd75820912010825w76a8aa55q4385cae0c8e0b49@mail.gmail.com>

Hi,
I'm using BioPython for processing protein sequences from SwissProt database.
I'm following the excellent tutorial documentation on SwissProt querying (p.107)
I'm just wondering about the meaning of the field 'host_organism' in a
swissprot record, as I haven't yet found a record where the value of
this field is supplied.
If the record concerns the protein sequence of a bacteria, for
instance, does the host_organism field contain a list of taxonomic ids
of possible host organisms where the bacteria can be found?
Many thanks

From biopython at maubp.freeserve.co.uk  Tue Dec  1 14:19:23 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 19:19:23 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
	<320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
Message-ID: <320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>

On Tue, Dec 1, 2009 at 9:52 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> It looks like an undocumented option, much like -phyi (which I guessed)
> for PHYLIP interlaced and -phys for PHYLIP sequential. These match
> the documented format options (e.g. -msf, -html, -clw and -clwstrict).
> i.e. You can use this:
>
> "muscle -in myinputfile -phyi -out myoutputfile"
>
> I think we should ask the MUSCLE author which of these
> undocumented arguments are actually supported rather than
> adding them all.

Robert Edgar agreed the documentation was out of sync, and has
confirmed these are safe arguments to include in our wrapper.

Peter

From biopython at maubp.freeserve.co.uk  Tue Dec  1 14:21:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 19:21:35 +0000
Subject: [Biopython] Host_organism field in SwissProt
In-Reply-To: <fdcd75820912010825w76a8aa55q4385cae0c8e0b49@mail.gmail.com>
References: <fdcd75820912010825w76a8aa55q4385cae0c8e0b49@mail.gmail.com>
Message-ID: <320fb6e00912011121o41237344v61d1570a919d54b4@mail.gmail.com>

On Tue, Dec 1, 2009 at 4:25 PM, bar tomas <bartomas at gmail.com> wrote:
> Hi,
> I'm using BioPython for processing protein sequences from SwissProt database.
> I'm following the excellent tutorial documentation on SwissProt querying (p.107)
> I'm just wondering about the meaning of the field 'host_organism' in a
> swissprot record, as I haven't yet found a record where the value of
> this field is supplied.
> If the record concerns the protein sequence of a bacteria, for
> instance, does the host_organism field contain a list of taxonomic ids
> of possible host organisms where the bacteria can be found?
> Many thanks

I suspect (without checking) that this field only applies to viruses
(or perhaps pathogens) and so will usually be empty.

Peter

P.S. Page numbers (and even section numbers) in the tutorial do
change from release to release - the section names are usually
stable.

From biopython at maubp.freeserve.co.uk  Tue Dec  1 14:34:19 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 19:34:19 +0000
Subject: [Biopython] Fwd: [Utilities-announce] NCBI E-Utility Policy Change
In-Reply-To: <320fb6e00912011129j68dda3b2p6df9a232f0462458@mail.gmail.com>
References: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov>
	<320fb6e00912011129j68dda3b2p6df9a232f0462458@mail.gmail.com>
Message-ID: <320fb6e00912011134u2481644aw5dfdfe9f9a3049f0@mail.gmail.com>

Hi all,

Attention NCBI Entrez users - the NCBI really do want you to include
your email address, and it will be mandatory in future! See below...

If using Bio.Entrez, the tool parameter will by default be set to
Biopython, but the email is omitted. We already encourage the email
to be included in our documentation but given the new NCBI guidance
I'd suggest we make omitting the email issue a warning in the next
release (and an error in the subsequent release of Biopython?).

Peter


---------- Forwarded message ----------
From: ?<utilities-announce at ncbi.nlm.nih.gov>
Date: Tue, Dec 1, 2009 at 6:59 PM
Subject: [Utilities-announce] NCBI E-Utility Policy Change
To: utilities-announce at ncbi.nlm.nih.gov


As part of an ongoing effort to ensure efficient access to the Entrez
Utilities (E-utilities) by all users, NCBI has decided to change the
usage policy for the E-utilities effective June 1, 2010. Effective on
June 1, 2010, all E-utility requests, either using standard URLs or
SOAP, must contain non-null values for both the &tool and &email
parameters. Any E-utility request made after June 1, 2010 that does
not contain values for both parameters will return an error explaining
that these parameters must be included in E-utility requests.



The value of the &tool parameter should be a URI-safe string that is
the name of the software package, script or web page producing the
E-utility request.



The value of the &email parameter should be a valid e-mail address for
the appropriate contact person or group responsible for maintaining
the tool producing the E-utility request.



NCBI uses these parameters to contact users whose use of the
E-utilities violates the standard usage policies described at
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements.
These usage policies are designed to prevent excessive requests from a
small group of users from reducing or eliminating the wider
community's access to the E-utilities. NCBI will attempt to contact a
user at the e-mail address provided in the &email parameter prior to
blocking access to the E-utilities.



NCBI realizes that this policy change will require many of our users
to change their code. Based on past experience, we anticipate that
most of our users should be able to make the necessary changes before
the June 1, 2010 deadline. If you have any concerns about making these
changes by that date, or if you have any questions about these
policies, please contact eutilities at ncbi.nlm.nih.gov.



Thank you for your understanding and cooperation in helping us
continue to deliver a reliable and efficient web service.



_______________________________________________
Utilities-announce mailing list
http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce
-------------- next part --------------
_______________________________________________
Utilities-announce mailing list
http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce

From cjfields at illinois.edu  Tue Dec  1 14:54:48 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 1 Dec 2009 13:54:48 -0600
Subject: [Biopython] Fwd: [Utilities-announce] NCBI E-Utility Policy
	Change
In-Reply-To: <320fb6e00912011134u2481644aw5dfdfe9f9a3049f0@mail.gmail.com>
References: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov>
	<320fb6e00912011129j68dda3b2p6df9a232f0462458@mail.gmail.com>
	<320fb6e00912011134u2481644aw5dfdfe9f9a3049f0@mail.gmail.com>
Message-ID: <1EE2400D-D3F7-49DC-82D7-001EE18F2030@illinois.edu>

I'll be following the same (exclusion of the email a warning in next bioperl release in Jan, and an error for the spring release).

chris

On Dec 1, 2009, at 1:34 PM, Peter wrote:

> Hi all,
> 
> Attention NCBI Entrez users - the NCBI really do want you to include
> your email address, and it will be mandatory in future! See below...
> 
> If using Bio.Entrez, the tool parameter will by default be set to
> Biopython, but the email is omitted. We already encourage the email
> to be included in our documentation but given the new NCBI guidance
> I'd suggest we make omitting the email issue a warning in the next
> release (and an error in the subsequent release of Biopython?).
> 
> Peter
> 
> 
> ---------- Forwarded message ----------
> From:  <utilities-announce at ncbi.nlm.nih.gov>
> Date: Tue, Dec 1, 2009 at 6:59 PM
> Subject: [Utilities-announce] NCBI E-Utility Policy Change
> To: utilities-announce at ncbi.nlm.nih.gov
> 
> 
> As part of an ongoing effort to ensure efficient access to the Entrez
> Utilities (E-utilities) by all users, NCBI has decided to change the
> usage policy for the E-utilities effective June 1, 2010. Effective on
> June 1, 2010, all E-utility requests, either using standard URLs or
> SOAP, must contain non-null values for both the &tool and &email
> parameters. Any E-utility request made after June 1, 2010 that does
> not contain values for both parameters will return an error explaining
> that these parameters must be included in E-utility requests.
> 
> 
> 
> The value of the &tool parameter should be a URI-safe string that is
> the name of the software package, script or web page producing the
> E-utility request.
> 
> 
> 
> The value of the &email parameter should be a valid e-mail address for
> the appropriate contact person or group responsible for maintaining
> the tool producing the E-utility request.
> 
> 
> 
> NCBI uses these parameters to contact users whose use of the
> E-utilities violates the standard usage policies described at
> http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements.
> These usage policies are designed to prevent excessive requests from a
> small group of users from reducing or eliminating the wider
> community's access to the E-utilities. NCBI will attempt to contact a
> user at the e-mail address provided in the &email parameter prior to
> blocking access to the E-utilities.
> 
> 
> 
> NCBI realizes that this policy change will require many of our users
> to change their code. Based on past experience, we anticipate that
> most of our users should be able to make the necessary changes before
> the June 1, 2010 deadline. If you have any concerns about making these
> changes by that date, or if you have any questions about these
> policies, please contact eutilities at ncbi.nlm.nih.gov.
> 
> 
> 
> Thank you for your understanding and cooperation in helping us
> continue to deliver a reliable and efficient web service.
> 
> 
> 
> _______________________________________________
> Utilities-announce mailing list
> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce
> <ATT00001.txt>_______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython



From mike.thon at gmail.com  Wed Dec  2 07:31:45 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Wed, 2 Dec 2009 13:31:45 +0100
Subject: [Biopython] Getting the sequence for a SeqFeature
In-Reply-To: <320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
References: <320fb6e00911060422u2d2742d5r7b5b1db98c991df5@mail.gmail.com>
	<320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
Message-ID: <0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>

I was wondering if you have implemented this method yet and if so, is it in a repository somewhere where I can try it?  I was about to post a message on this and I searched the archives first (!) and found this thread.  I have genbank genomic sequences and I need to get the transcript sequences for the CDS features.  

thanks
Mike

On Nov 6, 2009, at 1:47 PM, Peter wrote:

> On Fri, Nov 6, 2009 at 12:22 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> Hi all,
>> 
>> I am planing to add a new method to the SeqFeature object, but
>> would like a little feedback first. This email is really just the
>> background - I'll write up a few examples later to try and make
>> this a bit clearer...
> 
> OK, here is a non-trivial example - the first CDS feature in the
> GenBank file NC_000932.gb (included as a Biopython unit test),
> which is a three part join on the reverse strand. In this case, the
> GenBank file includes the protein translation for the CDS features
> so we can use it to check our results.
> 
> We can parse this GenBank file into a SeqRecord with:
> 
> from Bio import SeqIO
> record = SeqIO.read(open("../biopython/Tests/GenBank/NC_000932.gb"), "gb")
> 
> Let's have a look at the first CDS feature (index 2):
> 
> f = record.features[2]
> print f.type, f.location, f.strand, f.location_operator
> for sub_f in f.sub_features :
>    print " - ", sub_f.location, sub_f.strand
> table = f.qualifiers.get("transl_table",[1])[0] # List of one int
> print "Table", table
> 
> Giving:
> 
> CDS [97998:69724] -1 join
> -  [97998:98024] -1
> -  [98561:98793] -1
> -  [69610:69724] -1
> Table 11
> 
> Looking at the raw GenBank file, this feature has location string:
> 
> complement(join(97999..98024,98562..98793,69611..69724))
> 
> i.e. To get the sequence you need to do this (note zero based
> Python counting as in the output above):
> 
> print (record.seq[97998:98024] + record.seq[98561:98793] +
> record.seq[69610:69724]).reverse_complement()
> 
> And then translate it using NCBI genetic code table 11,
> 
> print "Manual translation:"
> print (record.seq[97998:98024] + record.seq[98561:98793] +
> record.seq[69610:69724]).reverse_complement().translate(table=11,
> cds=True)
> print "Given translation:"
> print f.qualifiers["translation"][0] # List of one string
> print "Biopython translation (with proposed code):"
> print f.extract(record.seq).translate(table, cds=True)
> 
> And the output, together with the provided translation in the
> feature annotation, and the shortcut with the new code I am
> proposing to include in Biopython:
> 
> Manual translation:
> MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK
> Given translation:
> MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK
> Biopython translation:
> MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK
> 
> The point of all this was with the proposed new extract method,
> you just need:
> 
> feature_seq = f.extract(record.seq)
> 
> instead of:
> 
> feature_seq = (record.seq[97998:98024] + record.seq[98561:98793] +
> record.seq[69610:69724]).reverse_complement()
> 
> which is in itself a slight simplification since you'd need to get the
> those coordinates from the sub features, worry about strands, etc.
> 
> Peter
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython



From kellrott at gmail.com  Wed Dec  2 10:12:53 2009
From: kellrott at gmail.com (Kyle Ellrott)
Date: Wed, 2 Dec 2009 07:12:53 -0800
Subject: [Biopython] Getting the sequence for a SeqFeature
In-Reply-To: <0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>
References: <320fb6e00911060422u2d2742d5r7b5b1db98c991df5@mail.gmail.com>
	<320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
	<0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>
Message-ID: <bb02be080912020712w51d3515bk85d0e66d9d9b195f@mail.gmail.com>

On Wed, Dec 2, 2009 at 4:31 AM, Michael Thon <mike.thon at gmail.com> wrote:

> I was wondering if you have implemented this method yet and if so, is it in
> a repository somewhere where I can try it?  I was about to post a message on
> this and I searched the archives first (!) and found this thread.  I have
> genbank genomic sequences and I need to get the transcript sequences for the
> CDS features.
>
>
It should be in the main GIT repository at
http://github.com/biopython/biopython/
It's to new to have made an official release version yet.

Kyle

From biopython at maubp.freeserve.co.uk  Wed Dec  2 17:44:11 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 2 Dec 2009 22:44:11 +0000
Subject: [Biopython] Getting the sequence for a SeqFeature
In-Reply-To: <bb02be080912020712w51d3515bk85d0e66d9d9b195f@mail.gmail.com>
References: <320fb6e00911060422u2d2742d5r7b5b1db98c991df5@mail.gmail.com>
	<320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
	<0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>
	<bb02be080912020712w51d3515bk85d0e66d9d9b195f@mail.gmail.com>
Message-ID: <320fb6e00912021444g11b27f81k8a3c8675ddc25169@mail.gmail.com>

On Wed, Dec 2, 2009 at 3:12 PM, Kyle Ellrott <kellrott at gmail.com> wrote:
> On Wed, Dec 2, 2009 at 4:31 AM, Michael Thon <mike.thon at gmail.com> wrote:
>
>> I was wondering if you have implemented this method yet and if so, is it in
>> a repository somewhere where I can try it? ?I was about to post a message on
>> this and I searched the archives first (!) and found this thread. ?I have
>> genbank genomic sequences and I need to get the transcript sequences for the
>> CDS features.
>>
>
> It should be in the main GIT repository at
> http://github.com/biopython/biopython/
> It's to new to have made an official release version yet.
>
> Kyle

Kyle has also been following the dicussion on the dev mailing
list, where it was mentioned this was now "on the trunk". See
also: http://www.biopython.org/wiki/SourceCode

Getting people using and testing the code now would be nice,
especially if we hope to get a release out before too long.

Peter


From richard_w_g_price at academia.edu  Wed Dec  2 20:21:26 2009
From: richard_w_g_price at academia.edu (Richard Price)
Date: Wed, 2 Dec 2009 17:21:26 -0800
Subject: [Biopython] New Academia.edu feature for Biopython
Message-ID: <cc0d7cc0912021721g660b39a2ga13c8213ec701454@mail.gmail.com>

Dear Biopython members,


I wanted to tell the list about a new feature on Academia.edu.
Academia.edu launched 12 months ago and now helps 300,000 academics a
month answer the question 'who's researching what?'


We have built a dedicated page on Academia.edu for the Biopython mailing list:


http://lists.academia.edu/See-members-of-Biopython


This page will show you fellow members already on Academia.edu.  You
can see their papers, research interests, and other information.


Visit the link below, sign up with Academia.edu, and see who else from
Biopython is on Academia.edu.



http://lists.academia.edu/See-members-of-Biopython


Richard


Dr. Richard Price, post-doc, Philosophy Dept, Oxford University.
Founder of Academia.edu

From mike.thon at gmail.com  Thu Dec  3 00:20:12 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 3 Dec 2009 06:20:12 +0100
Subject: [Biopython] can't compile version from github
Message-ID: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>

Don't know if this belongs on the dev mailing list or here...

I just checked out a copy of biopython from the github repo and I tried to install it in an non-root directory to try out a new feature.  

here is the command I ran on the command line:
python setup.py install --prefix=/Users/mike/biopython_dev

Here is the offending part of the compile:

gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype

The installer did not find the numpy that I installed using easy_install so I continued without it and without Reportlab.  (Mac OS 10.6)

Mike






From biopython at maubp.freeserve.co.uk  Thu Dec  3 05:19:32 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 3 Dec 2009 10:19:32 +0000
Subject: [Biopython] can't compile version from github
In-Reply-To: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
Message-ID: <320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>

On Thu, Dec 3, 2009 at 5:20 AM, Michael Thon <mike.thon at gmail.com> wrote:
> Don't know if this belongs on the dev mailing list or here...

Tricky - I might have picked the dev list, but this is fine.

> I just checked out a copy of biopython from the github repo and I
> tried to install it in an non-root directory to try out a new feature.
>
> here is the command I ran on the command line:
> python setup.py install --prefix=/Users/mike/biopython_dev
>
> Here is the offending part of the compile:
>
> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
> In file included from Bio/triemodule.c:3:
> Bio/trie.h:12: warning: function declaration isn?t a prototype
>
> The installer did not find the numpy that I installed using easy_install
> so I continued without it and without Reportlab. ?(Mac OS 10.6)
>
> Mike

Ah - Snow Leopard. Are you using the Apple provided Python with Mac OS 10.6?
Apple have as usual done odd things with Python, but people have
reported getting
it to work.

Looking at the compiler flags I am puzzled about the inclusion of
"-arch ppc" since
Snow Leopard is x86 only. Could you give us the whole of the compile log? What
you have shown just has a warning - no actual error. Also, doing it in
stages would
be wiser:

#First remove old build files:
python setup clean

#Do the compile:
python setup build

#Run the unit tests:
python setup test

#To install under your home directory I'd use:
python steup install --prefix=/Users/mike/

Peter


From mike.thon at gmail.com  Thu Dec  3 07:17:17 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 3 Dec 2009 13:17:17 +0100
Subject: [Biopython] can't compile version from github
In-Reply-To: <320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
	<320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
Message-ID: <EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>


On Dec 3, 2009, at 11:19 AM, Peter wrote:

> On Thu, Dec 3, 2009 at 5:20 AM, Michael Thon <mike.thon at gmail.com> wrote:
>> Don't know if this belongs on the dev mailing list or here...
> 
> Tricky - I might have picked the dev list, but this is fine.
> 
>> I just checked out a copy of biopython from the github repo and I
>> tried to install it in an non-root directory to try out a new feature.
>> 
>> here is the command I ran on the command line:
>> python setup.py install --prefix=/Users/mike/biopython_dev
>> 
>> Here is the offending part of the compile:
>> 
>> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
>> In file included from Bio/triemodule.c:3:
>> Bio/trie.h:12: warning: function declaration isn?t a prototype
>> 
>> The installer did not find the numpy that I installed using easy_install
>> so I continued without it and without Reportlab.  (Mac OS 10.6)
>> 
>> Mike
> 
> Ah - Snow Leopard. Are you using the Apple provided Python with Mac OS 10.6?
> Apple have as usual done odd things with Python, but people have
> reported getting
> it to work.

 
Yup, I'm using the Apple-provided python.  Below is the full output of the build phase.  

...so, as usual, I am off on a tangent instead of working on the stuff that actually needs to get done.  I don't really need to get this installed.  I just wanted to try the SeqFeature.extract method that you mentioned in a previous thread.  I realized that I probably don't need to compile all the C extensions to get that to work so I opened up SeqFeature.py to see what this method looks like.  I couldn't find it so I suppose this method has not made its way into the main git repo on github.  In the end, I wrote one myself but it would still be good to compare its output to what you have in biopython.

...but I still have this biopython from github that won't compile and it probably should.  So, if you have any ideas what might be wrong and how to fix it I can try it and report back.
-Mike

python setup.py build
running build
running build_py
*** Numerical Python *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Numerical Python at http://numpy.sourceforge.net/.

Do you want to continue this installation? (Y/n)  Y
*** Reportlab *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Reportlab at http://www.reportlab.org/downloads.html.

Do you want to continue this installation? (Y/n)  Y
running build_ext
building 'Bio.trie' extension
creating build/temp.macosx-10.6-universal-2.6
creating build/temp.macosx-10.6-universal-2.6/Bio
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ?_write_value_to_handle?:
Bio/triemodule.c:480: error: too few arguments to function ?PyMarshal_WriteObjectToString?
Bio/triemodule.c:482: warning: passing argument 3 of ?PyString_AsStringAndSize? from incompatible pointer type
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ?_write_value_to_handle?:
Bio/triemodule.c:480: error: too few arguments to function ?PyMarshal_WriteObjectToString?
Bio/triemodule.c:482: warning: passing argument 3 of ?PyString_AsStringAndSize? from incompatible pointer type
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ?_write_value_to_handle?:
Bio/triemodule.c:480: error: too few arguments to function ?PyMarshal_WriteObjectToString?
Bio/triemodule.c:482: warning: passing argument 3 of ?PyString_AsStringAndSize? from incompatible pointer type
lipo: can't open input file: /var/folders/wI/wIckOkhJHe0hxBDeAEI1VE+++TI/-Tmp-//ccemhRHR.out (No such file or directory)
error: command 'gcc-4.2' failed with exit status 1



From biopython at maubp.freeserve.co.uk  Thu Dec  3 07:26:12 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 3 Dec 2009 12:26:12 +0000
Subject: [Biopython] can't compile version from github
In-Reply-To: <EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
	<320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
	<EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>
Message-ID: <320fb6e00912030426gc84e3f5w6e238638e9b40b2e@mail.gmail.com>

On Thu, Dec 3, 2009 at 12:17 PM, Michael Thon <mike.thon at gmail.com> wrote:
>
> Yup, I'm using the Apple-provided python. ?Below is the full output of the build phase.

I'll take a look at it, but until I have a machine with Snow Leopard,
solving this will be tricky. Any other Snow Leopard users please
speak up.

> ...so, as usual, I am off on a tangent instead of working on the stuff that
> actually needs to get done. ?I don't really need to get this installed. ?I just
> wanted to try the SeqFeature.extract method that you mentioned in a
> previous thread. ?I realized that I probably don't need to compile all the
> C extensions to get that to work so I opened up SeqFeature.py to see
> what this method looks like. ?I couldn't find it so I suppose this method
> has not made its way into the main git repo on github. ?In the end, I
> wrote one myself but it would still be good to compare its output to
> what you have in biopython.

I'm not sure why you couldn't find this in the latest code from git.
The method is in Bio/SeqFeature.py, search for "def extract":
http://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py

You can probably take a working Biopython 1.52 install, and manually
update just the Bio/SeqFeature.py file if you really need to.

You could also try installing just the "pure Python" part of Biopython
by hacking setup.py to set EXTENSIONS = [], as done for Jython.

> ...but I still have this biopython from github that won't compile and it
> probably should. ?So, if you have any ideas what might be wrong and
> how to fix it I can try it and report back.

I'll try to get back to you on this shortly.

Peter


From johncumbers at gmail.com  Fri Dec  4 02:50:43 2009
From: johncumbers at gmail.com (John Cumbers)
Date: Thu, 3 Dec 2009 23:50:43 -0800
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
	<320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
	<320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>
Message-ID: <cfd758050912032350w61e2fc82v6c674834765e3c32@mail.gmail.com>

Many thanks Peter,
Sorry for delayed reply, I filter this list and forgot to check the folder
:)
Best wishes,
John

John Cumbers, Ph.D Candidate
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.
cell +1 (401) 523 8190, office +1 (650) 604-1914, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA


On Tue, Dec 1, 2009 at 11:19 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Tue, Dec 1, 2009 at 9:52 AM, Peter <biopython at maubp.freeserve.co.uk>
> wrote:
> >
> > It looks like an undocumented option, much like -phyi (which I guessed)
> > for PHYLIP interlaced and -phys for PHYLIP sequential. These match
> > the documented format options (e.g. -msf, -html, -clw and -clwstrict).
> > i.e. You can use this:
> >
> > "muscle -in myinputfile -phyi -out myoutputfile"
> >
> > I think we should ask the MUSCLE author which of these
> > undocumented arguments are actually supported rather than
> > adding them all.
>
> Robert Edgar agreed the documentation was out of sync, and has
> confirmed these are safe arguments to include in our wrapper.
>
> Peter
>

From biopython at maubp.freeserve.co.uk  Fri Dec  4 07:32:23 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 4 Dec 2009 12:32:23 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <cfd758050912032350w61e2fc82v6c674834765e3c32@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
	<320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
	<320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>
	<cfd758050912032350w61e2fc82v6c674834765e3c32@mail.gmail.com>
Message-ID: <320fb6e00912040432k628392c5n57fc79a3b68a88eb@mail.gmail.com>

On Fri, Dec 4, 2009 at 7:50 AM, John Cumbers <johncumbers at gmail.com> wrote:
> Many thanks Peter,
> Sorry for delayed reply, I filter this list and forgot to check the folder
> :)
> Best wishes,
> John

Bug filed,
http://bugzilla.open-bio.org/show_bug.cgi?id=2961

From brynedal at gmail.com  Fri Dec  4 14:01:49 2009
From: brynedal at gmail.com (Boel Brynedal)
Date: Fri, 4 Dec 2009 14:01:49 -0500
Subject: [Biopython] Problems installing Biopython
Message-ID: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>

Dear List,

I am trying to install Biopython from source on my Mac OS X v.10.6.1. I ran
into some problems when building Biopython, thought that it might be due to
the fact that I am missing xcore tools (gcc-4.0 was missing) so I installed
version 2.5 of xcore. This is however the output as I try to build biopython
after installing xcore:

$ python setup.py install
running install
running build
running build_py
creating build
a lot of creating, copying etc etc...
running build_ext
building 'Bio.clistfns' extension
creating build/temp.macosx-10.3-fat-2.6
creating build/temp.macosx-10.3-fat-2.
6/Bio
gcc-4.0 -arch ppc -arch i386 -fno-strict-aliasing -fno-common -dynamic
-DNDEBUG -g -O3
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
Bio/clistfnsmodule.c -o build/temp.macosx-10.3-fat-2.6/Bio/clistfnsmodule.o
In file included from /usr/include/architecture/i386/math.h:626,
                 from /usr/include/math.h:28,
                 from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/pyport.h:235,
                 from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:58,
                 from Bio/clistfnsmodule.c:10:
/usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
Intel with Mac OS X Deployment Target < 10.4 is invalid.
Compiling with an SDK that doesn't seem to exist:
/Developer/SDKs/MacOSX10.4u.sdk
Please check your Xcode installation
gcc-4.0 -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g
-bundle -undefined dynamic_lookup
build/temp.macosx-10.3-fat-2.6/Bio/clistfnsmodule.o -o
build/lib.macosx-10.3-fat-2.6/Bio/clistfns.so
ld: library not found for -lbundle1.o
collect2: ld returned 1 exit status
ld: library not found for -lbundle1.o
collect2: ld returned 1 exit status
lipo: can't open input file:
/var/folders/fy/fySdohlPEBSVFU-YIflSGk+++TI/-Tmp-//cc1Cm89x.out (No such
file or directory)
error: command 'gcc-4.0' failed with exit status 1


I am new to using Mac, and not the most talented computer nerd, but it seems
like we have two problems here:
the systems seems to be looking for MacOSX10.4u.sdk, when the xcore tools
I've installed contain MacOSX10.5.sdk and MacOSX10.6.sdk. Why does it look
for the earlier version, and what can I do about it?
#warning Building for Intel with Mac OS X Deployment Target < 10.4 is
invalid - this I do not understand at all.

I'm using Python 2.6.4 and I'm trying to install biopython-1.52.

Any tips, comments or ideas would be greatly appreciated!
Thank you,
Boel

From mike.thon at gmail.com  Fri Dec  4 15:27:41 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Fri, 4 Dec 2009 21:27:41 +0100
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
Message-ID: <6D780E44-39B7-4CFF-975B-D72722A5E5B2@gmail.com>

Hi Boel - I installed biopython using easy_install on Mac OS 10.6.2 and didn't have any problems.  I don't know what xcore is.  Do you mean Xcode?  the version I have is 3.2.1 and I downloaded it from developer.apple.com

-Mike



From p.j.a.cock at googlemail.com  Fri Dec  4 15:52:46 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Dec 2009 20:52:46 +0000
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
Message-ID: <320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>

On Fri, Dec 4, 2009 at 7:01 PM, Boel Brynedal wrote:
> Dear List,
>
> I am new to using Mac, and not the most talented computer
> nerd, but it seems like we have two problems here:
> the systems seems to be looking for MacOSX10.4u.sdk,
> when the xcore tools I've installed contain MacOSX10.5.sdk
> and MacOSX10.6.sdk. Why does it look
> for the earlier version, and what can I do about it?
> #warning Building for Intel with Mac OS X Deployment Target < 10.4 is
> invalid - this I do not understand at all.

Sadly there are some general issues with Python on
Snow Leopard (this isn't just a Biopython issue). Right
now as far as I know none of our core developers have
Snow Leopard (10.6) so it is hard to help.

However, with Leopard (10.4), when installing XCode I
had the option of installing the 10.3 headers too. Could
you re-install XCode and check this time for an option
to include the headers for 10.4 (and/or 10.3)?

Peter

From mjldehoon at yahoo.com  Sat Dec  5 10:59:41 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 5 Dec 2009 07:59:41 -0800 (PST)
Subject: [Biopython] CompareAce parser
Message-ID: <613008.1949.qm@web62407.mail.re1.yahoo.com>

Hi everybody,

In Bio.Motif, there is a nominal parser for CompareAce files. However, this parser has almost no functionality. Would anybody mind if we deprecate this module for the next release? Whereas we usually might declare the module obsolete before deprecating it, in this case I think we can deprecate it straightaway since currently this parser does very little.

--Michiel.


      

From bartek at rezolwenta.eu.org  Sat Dec  5 19:58:41 2009
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Sun, 6 Dec 2009 01:58:41 +0100
Subject: [Biopython] CompareAce parser
In-Reply-To: <613008.1949.qm@web62407.mail.re1.yahoo.com>
References: <613008.1949.qm@web62407.mail.re1.yahoo.com>
Message-ID: <8b34ec180912051658s2acb9da1na03a8b0577fa6a8d@mail.gmail.com>

Hi,

I don't have anything against deprecating, even though I don't the
advantages of doing so. (the module is trivial, but so is the output
of compareACE: a number giving a score between motifs. The score,
however is not trivial and I wouldn't want to reimplement it.)

cheers
  Bartek

On Sat, Dec 5, 2009 at 4:59 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi everybody,
>
> In Bio.Motif, there is a nominal parser for CompareAce files. However, this parser has almost no functionality. Would anybody mind if we deprecate this module for the next release? Whereas we usually might declare the module obsolete before deprecating it, in this case I think we can deprecate it straightaway since currently this parser does very little.
>
> --Michiel.
>
>
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>



-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433


From biopython at maubp.freeserve.co.uk  Sun Dec  6 09:10:22 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 6 Dec 2009 14:10:22 +0000
Subject: [Biopython] CompareAce parser
In-Reply-To: <8b34ec180912051658s2acb9da1na03a8b0577fa6a8d@mail.gmail.com>
References: <613008.1949.qm@web62407.mail.re1.yahoo.com>
	<8b34ec180912051658s2acb9da1na03a8b0577fa6a8d@mail.gmail.com>
Message-ID: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>

On Sun, Dec 6, 2009 at 12:58 AM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> Hi,
>
> I don't have anything against deprecating, even though I don't the
> advantages of doing so. (the module is trivial, but so is the output
> of compareACE: a number giving a score between motifs. The score,
> however is not trivial and I wouldn't want to reimplement it.)
>
> cheers
> ?Bartek

So the reason this parser is so simple and has almost no functionality
is just a reflection of the simplicity of the CompareAce files? If so, I'd
say leave the parser in.

Peter


From mjldehoon at yahoo.com  Sun Dec  6 09:31:47 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sun, 6 Dec 2009 06:31:47 -0800 (PST)
Subject: [Biopython] CompareAce parser
In-Reply-To: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
Message-ID: <889087.95522.qm@web62406.mail.re1.yahoo.com>

> So the reason this parser is so simple and has almost no
> functionality is just a reflection of the simplicity of
> the CompareAce files?

Not exactly. CompareAce files can have different outputs, depending on the query given to CompareAce. The simplest query returns only one number. The current CompareAce parser can only parse this output. In other words,

>>> input = open("test.out")
>>> from Bio.Motif.Parsers import AlignAce
>>> AlignAce.CompareAceParser().parse(input)
0.92130000000000001

is equivalent to

>>> input = open("test.out")
>>> float(input.read())
0.92130000000000001

I am not against having a CompareAce parser in Biopython, but if we have such a parser it should be able to handle more output formats than just the trivial output format.

With this in mind, I think we should either extend the CompareAce parser to handle cases that cannot be trivially handled by a simple Python command, or remove it altogether. If we do keep it in Biopython, there should also be some documentation to cover it, and perhaps a unit test.

--Michiel

--- On Sun, 12/6/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] CompareAce parser
> To: "Bartek Wilczynski" <bartek at rezolwenta.eu.org>
> Cc: "Michiel de Hoon" <mjldehoon at yahoo.com>, biopython at biopython.org
> Date: Sunday, December 6, 2009, 9:10 AM
> On Sun, Dec 6, 2009 at 12:58 AM,
> Bartek Wilczynski
> <bartek at rezolwenta.eu.org>
> wrote:
> > Hi,
> >
> > I don't have anything against deprecating, even though
> I don't the
> > advantages of doing so. (the module is trivial, but so
> is the output
> > of compareACE: a number giving a score between motifs.
> The score,
> > however is not trivial and I wouldn't want to
> reimplement it.)
> >
> > cheers
> > ?Bartek
> 
> So the reason this parser is so simple and has almost no
> functionality
> is just a reflection of the simplicity of the CompareAce
> files? If so, I'd
> say leave the parser in.
> 
> Peter
> 


      


From brynedal at gmail.com  Sun Dec  6 16:38:55 2009
From: brynedal at gmail.com (Boel Brynedal)
Date: Sun, 6 Dec 2009 16:38:55 -0500
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
	<320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>
Message-ID: <2167c9200912061338g164a8f61x25df698cab5c0548@mail.gmail.com>

Hi Peter,

I downloaded XCode again and included the 10.4 support - this seem to have
fixed it.
Thank you very much!

Boel

2009/12/4 Peter Cock <p.j.a.cock at googlemail.com>

> On Fri, Dec 4, 2009 at 7:01 PM, Boel Brynedal wrote:
> > Dear List,
> >
> > I am new to using Mac, and not the most talented computer
> > nerd, but it seems like we have two problems here:
> > the systems seems to be looking for MacOSX10.4u.sdk,
> > when the xcore tools I've installed contain MacOSX10.5.sdk
> > and MacOSX10.6.sdk. Why does it look
> > for the earlier version, and what can I do about it?
> > #warning Building for Intel with Mac OS X Deployment Target < 10.4 is
> > invalid - this I do not understand at all.
>
> Sadly there are some general issues with Python on
> Snow Leopard (this isn't just a Biopython issue). Right
> now as far as I know none of our core developers have
> Snow Leopard (10.6) so it is hard to help.
>
> However, with Leopard (10.4), when installing XCode I
> had the option of installing the 10.3 headers too. Could
> you re-install XCode and check this time for an option
> to include the headers for 10.4 (and/or 10.3)?
>
> Peter
>

From biopython at maubp.freeserve.co.uk  Sun Dec  6 16:49:28 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 6 Dec 2009 21:49:28 +0000
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <2167c9200912061338g164a8f61x25df698cab5c0548@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
	<320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>
	<2167c9200912061338g164a8f61x25df698cab5c0548@mail.gmail.com>
Message-ID: <320fb6e00912061349v2dbc3586g185701894e8e7c05@mail.gmail.com>

> 2009/12/4 Peter Cock <p.j.a.cock at googlemail.com>
>> However, with Leopard (10.4), when installing XCode I
>> had the option of installing the 10.3 headers too. Could
>> you re-install XCode and check this time for an option
>> to include the headers for 10.4 (and/or 10.3)?

Minor typo - Leopard is Mac OS 10.5 of course ;)

On Sun, Dec 6, 2009 at 9:38 PM, Boel Brynedal wrote:
> Hi Peter,
>
> I downloaded XCode again and included the 10.4 support - this
> seem to have fixed it.
> Thank you very much!
>
> Boel

Excellent - thanks for letting us know.

Peter

From biopython at maubp.freeserve.co.uk  Mon Dec  7 07:14:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Dec 2009 12:14:35 +0000
Subject: [Biopython] Deprecating old Bio.GFF module in preparation for new
	code?
Message-ID: <320fb6e00912070414i3e4503dt311953b99d2efeb5@mail.gmail.com>

Dear all,

Is anyone using the "old" Bio.GFF module in Biopython?

This was written by Michael Hoffman back 2002, and allowed
access to a General Feature Format (GFF) MySQL database
created with BioPerl's Bio::DB:GFF.  It may need updating to
work with the latest BioPerl, or GFF3 files (I don't know). This
old code did not include any GFF parser of its own.

As those on the dev mailing list will know, Brad Chapman
has been working on a GFF parser (covering GFF3, and
the older GFF2 and GTF files). The obvious place to put
this is under Bio.GFF.

I would therefore like to propose deprecating the current
Bio.GFF code in the next release of Biopython (hopefully
this month), which will allow us to replace it with Brad's
new parser in the subsequent release.

If anyone is using the old module, please let us know now.

Thank you,

Peter

From biopython at maubp.freeserve.co.uk  Mon Dec  7 09:02:51 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Dec 2009 14:02:51 +0000
Subject: [Biopython] can't compile version from github
In-Reply-To: <320fb6e00912030426gc84e3f5w6e238638e9b40b2e@mail.gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
	<320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
	<EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>
	<320fb6e00912030426gc84e3f5w6e238638e9b40b2e@mail.gmail.com>
Message-ID: <320fb6e00912070602i3a881fd7nd758d71ce0d1a3f4@mail.gmail.com>

On Thu, Dec 3, 2009 at 12:26 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Dec 3, 2009 at 12:17 PM, Michael Thon <mike.thon at gmail.com> wrote:
>
>> ...but I still have this biopython from github that won't compile and it
>> probably should. ?So, if you have any ideas what might be wrong and
>> how to fix it I can try it and report back.
>
> I'll try to get back to you on this shortly.
>

Hi Michael,

As discussed on the other thread, could you try reinstalling XCode on
Snow Leopard (Mac OS X 10.6), but this time tick the option to include
the older headers (Tiger 10.4 SDK - not sure exactly what it is called).

http://lists.open-bio.org/pipermail/biopython/2009-December/005906.html

Peter


From iwan.grin at googlemail.com  Tue Dec  8 13:52:13 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Tue, 8 Dec 2009 19:52:13 +0100
Subject: [Biopython] Parsing problem
Message-ID: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>

Hi all,

I am having a little problem while trying to parse a GenBank (or rather
GenProt) file using BioPython. I am trying to extract the position on the
genome from the "coded_by" qualifier of the CDS feature of a protein.

The "coded_by" string in this specific case looks like this:

'complement(NC_012967.1:
3622110..3624728)'

Now, when I run

Bio.GFF.easy.LocationFromString('complement(NC_012967.1:3622110..3624728)' )

I get

File "/usr/lib/pymodules/python2.6/Bio/GFF/easy.py", line 419, in __init__
   list.__init__(self, [int(location_str)-1]) # zero based, nip it in the
bud
ValueError: invalid literal for int() with base 10:
'NC_012967.1:3622110..3624728'

Is there another way to parse this location string or do I have to cook up
some kind of custom RegExp?

Iwan

P.S.: Code snippet:

from Bio import Entrez
from Bio import SeqIO
from Bio import GFF
gi = 254163455
handle = Entrez.efetch(db="protein", id=gi, rettype="gb")
record= SeqIO.read(handle,"genbank")
handle.close()
for feature in record.features:
   if(feature.type=="CDS" and feature.qualifiers.has_key("coded_by")):
       print feature.qualifiers["coded_by"][0],
       loc=GFF.easy.LocationFromString(feature.qualifiers["coded_by"][0])
       print loc.start(),loc.end(), loc.complement

From biopython at maubp.freeserve.co.uk  Tue Dec  8 17:43:29 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 8 Dec 2009 22:43:29 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
Message-ID: <320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>

On Tue, Dec 8, 2009 at 6:52 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
> Hi all,
>
> I am having a little problem while trying to parse a GenBank (or rather
> GenProt) file using BioPython. I am trying to extract the position on the
> genome from the "coded_by" qualifier of the CDS feature of a protein.
>
> The "coded_by" string in this specific case looks like this:
>
> 'complement(NC_012967.1:
> 3622110..3624728)'

Oh, one of those tricky cross references to another file :(

> Now, when I run
>
> Bio.GFF.easy.LocationFromString('complement(NC_012967.1:3622110..3624728)' )
>

This is interesting timing - Bio.GFF.easy has a lot of
code which duplicated the EMBL/GenBank parsing,
and I'm actually suggesting we deprecate it in the
next release (!). What made you use Bio.GFF in the
first place? It has never been documented. That said,
it does look like you found a bug in Bio.GFF.easy ...

In the long term, I think Bio.GenBank would be a
better place to put this functionality (and reworking
the location parsing is on the todo list, partly as it
is currently a speed bottleneck).

Peter

From biopython at maubp.freeserve.co.uk  Tue Dec  8 18:53:29 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 8 Dec 2009 23:53:29 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
Message-ID: <320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>

On Tue, Dec 8, 2009 at 10:43 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Dec 8, 2009 at 6:52 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
>> Hi all,
>>
>> I am having a little problem while trying to parse a GenBank (or rather
>> GenProt) file using BioPython. I am trying to extract the position on the
>> genome from the "coded_by" qualifier of the CDS feature of a protein.
>>
>> The "coded_by" string in this specific case looks like this:
>>
>> 'complement(NC_012967.1:
>> 3622110..3624728)'
>
> Oh, one of those tricky cross references to another file :(

It looks like the Bio.GFF.easy code expects that to be formatted
as NC_012967.1:complement(3622110..3624728) and not as
complement(NC_012967.1:3622110..3624728)

Peter

From iwan.grin at googlemail.com  Wed Dec  9 07:33:09 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Wed, 9 Dec 2009 13:33:09 +0100
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
Message-ID: <b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>

Hi Peter, Thank you for your reply.

I am new to BioPython and stumbled upon GFF.easy while searching through the
API docs. Actually, What I wanted was a way to parse that location string
into an SeqFeature-like thing from which I could get start, end and
strand.Unfortunately I could not find the correct parser in Bio.Genbank -
any suggestions are welcome.

I agree with you that Bio.GFF.easy expects the Accession number before the
complement. (Actually for my purpose I do not need the accession number at
all.)

Iwan

2009/12/9 Peter <biopython at maubp.freeserve.co.uk>

> On Tue, Dec 8, 2009 at 10:43 PM, Peter <biopython at maubp.freeserve.co.uk>
> wrote:
> > On Tue, Dec 8, 2009 at 6:52 PM, Iwan Grin <iwan.grin at googlemail.com>
> wrote:
> >> Hi all,
> >>
> >> I am having a little problem while trying to parse a GenBank (or rather
> >> GenProt) file using BioPython. I am trying to extract the position on
> the
> >> genome from the "coded_by" qualifier of the CDS feature of a protein.
> >>
> >> The "coded_by" string in this specific case looks like this:
> >>
> >> 'complement(NC_012967.1:
> >> 3622110..3624728)'
> >
> > Oh, one of those tricky cross references to another file :(
>
> It looks like the Bio.GFF.easy code expects that to be formatted
> as NC_012967.1:complement(3622110..3624728) and not as
> complement(NC_012967.1:3622110..3624728)
>
> Peter
>

From biopython at maubp.freeserve.co.uk  Wed Dec  9 08:25:44 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Dec 2009 13:25:44 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
Message-ID: <320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>

On Wed, Dec 9, 2009 at 12:33 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
> Hi Peter, Thank you for your reply.
>
> I am new to BioPython and stumbled upon GFF.easy while searching through the
> API docs. Actually, What I wanted was a way to parse that location string
> into an SeqFeature-like thing from which I could get start, end and
> strand.Unfortunately I could not find the correct parser in Bio.Genbank -
> any suggestions are welcome.

Right now Bio.GenBank doesn't really expose the location parsing in an
easy to use way like Bio.GFF.easy does.

> I agree with you that Bio.GFF.easy expects the Accession number before the
> complement. (Actually for my purpose I do not need the accession number at
> all.)

The pragmatic solution is to write your own quick parser to pull out the
coordinates (if that is all you need).

We'll have to look at this as part of the discussion of what to do with the
old Bio.GFF (as part of planning for Brad's new GFF parsing code).

Peter

From chapmanb at 50mail.com  Wed Dec  9 08:38:02 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Wed, 9 Dec 2009 08:38:02 -0500
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
Message-ID: <20091209133802.GB79820@sobchak.mgh.harvard.edu>

Iwan and Peter;

> > I am new to BioPython and stumbled upon GFF.easy while searching through the
> > API docs. Actually, What I wanted was a way to parse that location string
> > into an SeqFeature-like thing from which I could get start, end and
> > strand.Unfortunately I could not find the correct parser in Bio.Genbank -
> > any suggestions are welcome.
> 
> Right now Bio.GenBank doesn't really expose the location parsing in an
> easy to use way like Bio.GFF.easy does.

If you don't like ugly code, please avert your eyes now. This will
work with the standard GenBank parsing and is definitely not future
proof since it involves using private members. However, it'll work
for something quick n' dirty:

from Bio.GenBank import _FeatureConsumer
from Bio.SeqFeature import SeqFeature

def gb_string_to_feature(content, use_fuzziness=True):
    """Convert a GenBank location string into a SeqFeature.
    """
    consumer = _FeatureConsumer(use_fuzziness)
    consumer._cur_feature = SeqFeature()
    consumer.location(content)
    return consumer._cur_feature

print gb_string_to_feature('complement(NC_012967.1:3622110..3624728)')

Hope this helps,
Brad

From bartek at rezolwenta.eu.org  Wed Dec  9 09:43:23 2009
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Wed, 9 Dec 2009 15:43:23 +0100
Subject: [Biopython] CompareAce parser
In-Reply-To: <889087.95522.qm@web62406.mail.re1.yahoo.com>
References: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
	<889087.95522.qm@web62406.mail.re1.yahoo.com>
Message-ID: <8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>

Hi Michiel,

I haven't given enough consideration to the maintenance costs of
having parsers like this one in biopython. I think you are right that
it's not  useful in its current state, and I don't think it's worth
putting efforts into improving it. There are already other methods of
motif comparison implemented in bio.Motif and if I was to choose an
external motif comparison software to support in biopython, I would
vote for the STAMP tool from Benos lab. So, in conclusion, I think it
would make sense to deprecate the CompareAce parser.


cheers
Bartek


On Sun, Dec 6, 2009 at 3:31 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> So the reason this parser is so simple and has almost no
>> functionality is just a reflection of the simplicity of
>> the CompareAce files?
>
> Not exactly. CompareAce files can have different outputs, depending on the query given to CompareAce. The simplest query returns only one number. The current CompareAce parser can only parse this output. In other words,
>
>>>> input = open("test.out")
>>>> from Bio.Motif.Parsers import AlignAce
>>>> AlignAce.CompareAceParser().parse(input)
> 0.92130000000000001
>
> is equivalent to
>
>>>> input = open("test.out")
>>>> float(input.read())
> 0.92130000000000001
>
> I am not against having a CompareAce parser in Biopython, but if we have such a parser it should be able to handle more output formats than just the trivial output format.
>
> With this in mind, I think we should either extend the CompareAce parser to handle cases that cannot be trivially handled by a simple Python command, or remove it altogether. If we do keep it in Biopython, there should also be some documentation to cover it, and perhaps a unit test.
>
> --Michiel
>
> --- On Sun, 12/6/09, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
>> From: Peter <biopython at maubp.freeserve.co.uk>
>> Subject: Re: [Biopython] CompareAce parser
>> To: "Bartek Wilczynski" <bartek at rezolwenta.eu.org>
>> Cc: "Michiel de Hoon" <mjldehoon at yahoo.com>, biopython at biopython.org
>> Date: Sunday, December 6, 2009, 9:10 AM
>> On Sun, Dec 6, 2009 at 12:58 AM,
>> Bartek Wilczynski
>> <bartek at rezolwenta.eu.org>
>> wrote:
>> > Hi,
>> >
>> > I don't have anything against deprecating, even though
>> I don't the
>> > advantages of doing so. (the module is trivial, but so
>> is the output
>> > of compareACE: a number giving a score between motifs.
>> The score,
>> > however is not trivial and I wouldn't want to
>> reimplement it.)
>> >
>> > cheers
>> > ?Bartek
>>
>> So the reason this parser is so simple and has almost no
>> functionality
>> is just a reflection of the simplicity of the CompareAce
>> files? If so, I'd
>> say leave the parser in.
>>
>> Peter
>>
>
>
>
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>



-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433


From iwan.grin at googlemail.com  Wed Dec  9 09:51:20 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Wed, 9 Dec 2009 15:51:20 +0100
Subject: [Biopython] Parsing problem
In-Reply-To: <20091209133802.GB79820@sobchak.mgh.harvard.edu>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
	<20091209133802.GB79820@sobchak.mgh.harvard.edu>
Message-ID: <b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>

2009/12/9 Brad Chapman <chapmanb at 50mail.com>

> Iwan and Peter;
>
> > > I am new to BioPython and stumbled upon GFF.easy while searching
> through the
> > > API docs. Actually, What I wanted was a way to parse that location
> string
> > > into an SeqFeature-like thing from which I could get start, end and
> > > strand.Unfortunately I could not find the correct parser in Bio.Genbank
> -
> > > any suggestions are welcome.
> >
> > Right now Bio.GenBank doesn't really expose the location parsing in an
> > easy to use way like Bio.GFF.easy does.
>
> If you don't like ugly code, please avert your eyes now. This will
> work with the standard GenBank parsing and is definitely not future
> proof since it involves using private members. However, it'll work
> for something quick n' dirty:
>
> from Bio.GenBank import _FeatureConsumer
> from Bio.SeqFeature import SeqFeature
>
> def gb_string_to_feature(content, use_fuzziness=True):
>    """Convert a GenBank location string into a SeqFeature.
>    """
>    consumer = _FeatureConsumer(use_fuzziness)
>    consumer._cur_feature = SeqFeature()
>    consumer.location(content)
>    return consumer._cur_feature
>
> print gb_string_to_feature('complement(NC_012967.1:3622110..3624728)')
>
> Hope this helps,
> Brad
>

Brad, Thank you very much!

as much as this is a hack, it works for what I want to have. I guess for
future proofness, either the parsers from Bio.GenBank should be exposed, or
the coded_by qualifier should be parsed as location by default, although I
am not sure how well the latter idea fits into the present data structure.

Iwan

From biopython at maubp.freeserve.co.uk  Wed Dec  9 10:05:39 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Dec 2009 15:05:39 +0000
Subject: [Biopython] CompareAce parser
In-Reply-To: <8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>
References: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
	<889087.95522.qm@web62406.mail.re1.yahoo.com>
	<8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>
Message-ID: <320fb6e00912090705h691dd0a3u32b6e8760570d3e1@mail.gmail.com>

On Wed, Dec 9, 2009 at 2:43 PM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> Hi Michiel,
>
> I haven't given enough consideration to the maintenance costs of
> having parsers like this one in biopython. I think you are right that
> it's not ?useful in its current state, and I don't think it's worth
> putting efforts into improving it. There are already other methods of
> motif comparison implemented in bio.Motif and if I was to choose an
> external motif comparison software to support in biopython, I would
> vote for the STAMP tool from Benos lab. So, in conclusion, I think it
> would make sense to deprecate the CompareAce parser.
>
> cheers
> Bartek

I hadn't looked to see just how simple the files and parser were ;)

Do you want to go ahead and make the deprecation Bartek?

Thanks,

Peter


From biopython at maubp.freeserve.co.uk  Wed Dec  9 10:26:18 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Dec 2009 15:26:18 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
	<20091209133802.GB79820@sobchak.mgh.harvard.edu>
	<b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>
Message-ID: <320fb6e00912090726w95cfa8bi542f6227f84c888b@mail.gmail.com>

On Wed, Dec 9, 2009 at 2:51 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
> Brad, Thank you very much!
>
> as much as this is a hack, it works for what I want to have. I guess for
> future proofness, either the parsers from Bio.GenBank should be exposed, or
> the coded_by qualifier should be parsed as location by default, although I
> am not sure how well the latter idea fits into the present data structure.

Brad's trick still work in Biopython 1.53 at the very least. I think we'll
try and make the location parser more accessible in future, but
changing the parsing of "coded_by" qualifiers would risk breaking
existing user scripts.

Peter

From iwan.grin at googlemail.com  Wed Dec  9 10:55:21 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Wed, 9 Dec 2009 16:55:21 +0100
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912090726w95cfa8bi542f6227f84c888b@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
	<20091209133802.GB79820@sobchak.mgh.harvard.edu>
	<b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>
	<320fb6e00912090726w95cfa8bi542f6227f84c888b@mail.gmail.com>
Message-ID: <b3475c600912090755l49ea6035ja0c34d40a7bfa9b4@mail.gmail.com>

2009/12/9 Peter <biopython at maubp.freeserve.co.uk>

> On Wed, Dec 9, 2009 at 2:51 PM, Iwan Grin <iwan.grin at googlemail.com>
> wrote:
> > Brad, Thank you very much!
> >
> > as much as this is a hack, it works for what I want to have. I guess for
> > future proofness, either the parsers from Bio.GenBank should be exposed,
> or
> > the coded_by qualifier should be parsed as location by default, although
> I
> > am not sure how well the latter idea fits into the present data
> structure.
>
> Brad's trick still work in Biopython 1.53 at the very least. I think we'll
> try and make the location parser more accessible in future, but
> changing the parsing of "coded_by" qualifiers would risk breaking
> existing user scripts.
>
> Peter
>

I would suggest to add a new "coded_by" feature and leave the qualifier as
it is.
This should minimize the risk of breaking stuff. On the other hand, This
feature would be pretty specific for CDS in Genbank Protein files.

Iwan

From bartek at rezolwenta.eu.org  Wed Dec  9 11:33:58 2009
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Wed, 9 Dec 2009 17:33:58 +0100
Subject: [Biopython] CompareAce parser
In-Reply-To: <320fb6e00912090705h691dd0a3u32b6e8760570d3e1@mail.gmail.com>
References: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
	<889087.95522.qm@web62406.mail.re1.yahoo.com>
	<8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>
	<320fb6e00912090705h691dd0a3u32b6e8760570d3e1@mail.gmail.com>
Message-ID: <8b34ec180912090833uf9ace0x8f0b76335dbd8143@mail.gmail.com>

On Wed, Dec 9, 2009 at 4:05 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> I hadn't looked to see just how simple the files and parser were ;)
>
> Do you want to go ahead and make the deprecation Bartek?

Yes. It's done and pushed to github now.

cheers
Bartek
-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433

From villahozbale at wisc.edu  Fri Dec 11 13:32:53 2009
From: villahozbale at wisc.edu (ANGEL VILLAHOZ-BALETA)
Date: Fri, 11 Dec 2009 12:32:53 -0600
Subject: [Biopython] A potential printing error in the Biopython Tutorial
	and Cookbook?
Message-ID: <70d0d6f9673f4.4b223bf5@wiscmail.wisc.edu>

Hi to all,

I believe that there is a printing error in the Biopython Tutorial and Cookbook...

Go there:

http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc102

Then check the following source code:

>>> for record in records:
...     print "title:", record["TI"]
...     if "AU" in records:
...         print "authors:", record["AU"]
...     print "source:", record["CO"]
...     print

I believe that the if sentence would have the record instead of the records because it would never print such an information about the authors since the data structure of records does not have this key but always integers as its indices.

Let me know if I am right or not.

Thanks very much,

Angel Villahoz-Baleta
Bioinformatics Programmer
University of Wisconsin-Madison

From biopython at maubp.freeserve.co.uk  Fri Dec 11 14:45:31 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 11 Dec 2009 19:45:31 +0000
Subject: [Biopython] A potential printing error in the Biopython
	Tutorial and Cookbook?
In-Reply-To: <70d0d6f9673f4.4b223bf5@wiscmail.wisc.edu>
References: <70d0d6f9673f4.4b223bf5@wiscmail.wisc.edu>
Message-ID: <320fb6e00912111145w68330b80l8b1091db48fac3fb@mail.gmail.com>

On Fri, Dec 11, 2009 at 6:32 PM, ANGEL VILLAHOZ-BALETA
<villahozbale at wisc.edu> wrote:
> Hi to all,
>
> I believe that there is a printing error in the Biopython Tutorial and Cookbook...
>
> Go there:
>
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc102
>
> Then check the following source code:
>
>>>> for record in records:
> ... ? ? print "title:", record["TI"]
> ... ? ? if "AU" in records:
> ... ? ? ? ? print "authors:", record["AU"]
> ... ? ? print "source:", record["CO"]
> ... ? ? print
>
> I believe that the if sentence would have the record
> instead of the records because it would never print
> such an information about the authors since the data
> structure of records does not have this key but always
> integers as its indices.

What version of Biopython do you have?
Could you show us the actual error message?

I've just been playing with the example, and for some
records certain fields are missing (you get a KeyError),
so this works better:

for record in records:
    print "title:", record.get("TI","?")
    print "author:", record.get("AU","?")
    print "source:", record.get("CO","?")
    print

Does that help?

Peter


From mjldehoon at yahoo.com  Fri Dec 11 20:52:08 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 11 Dec 2009 17:52:08 -0800 (PST)
Subject: [Biopython] A potential printing error in the Biopython
	Tutorial and Cookbook?
In-Reply-To: <320fb6e00912111145w68330b80l8b1091db48fac3fb@mail.gmail.com>
Message-ID: <138660.52957.qm@web62406.mail.re1.yahoo.com>

Dear Angel,

This was indeed a typing error in the tutorial.
It is fixed now as Peter suggested.
Thanks for noticing!

--Michiel.

--- On Fri, 12/11/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] A potential printing error in the Biopython Tutorial and Cookbook?
> To: "ANGEL VILLAHOZ-BALETA" <villahozbale at wisc.edu>
> Cc: biopython at lists.open-bio.org
> Date: Friday, December 11, 2009, 2:45 PM
> On Fri, Dec 11, 2009 at 6:32 PM,
> ANGEL VILLAHOZ-BALETA
> <villahozbale at wisc.edu>
> wrote:
> > Hi to all,
> >
> > I believe that there is a printing error in the
> Biopython Tutorial and Cookbook...
> >
> > Go there:
> >
> > http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc102
> >
> > Then check the following source code:
> >
> >>>> for record in records:
> > ... ? ? print "title:", record["TI"]
> > ... ? ? if "AU" in records:
> > ... ? ? ? ? print "authors:", record["AU"]
> > ... ? ? print "source:", record["CO"]
> > ... ? ? print
> >
> > I believe that the if sentence would have the record
> > instead of the records because it would never print
> > such an information about the authors since the data
> > structure of records does not have this key but
> always
> > integers as its indices.
> 
> What version of Biopython do you have?
> Could you show us the actual error message?
> 
> I've just been playing with the example, and for some
> records certain fields are missing (you get a KeyError),
> so this works better:
> 
> for record in records:
> ? ? print "title:", record.get("TI","?")
> ? ? print "author:", record.get("AU","?")
> ? ? print "source:", record.get("CO","?")
> ? ? print
> 
> Does that help?
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list? -? Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 


      


From aboulia at gmail.com  Tue Dec 15 01:01:47 2009
From: aboulia at gmail.com (Kevin Lam)
Date: Tue, 15 Dec 2009 14:01:47 +0800
Subject: [Biopython] rsync download of biopython problems
Message-ID: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>

Hi
I just tried downloading biopython via rsync

 rsync -av code.open-bio.org::cvsbiopython .

But all the files were appended with a ",v" why did that happen? (i.e. see
below)
Attic  Bio  BioSQL  CONTRIB,v  DEPRECATED,v  Doc  Experimental  LICENSE,v
MANIFEST.in,v  Martel  NEWS,v  README,v  Scripts  setup.py,v  Tests

From biopython at maubp.freeserve.co.uk  Tue Dec 15 05:37:55 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 10:37:55 +0000
Subject: [Biopython] rsync download of biopython problems
In-Reply-To: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>
References: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>
Message-ID: <320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>

On Tue, Dec 15, 2009 at 6:01 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi
> I just tried downloading biopython via rsync
>
> ?rsync -av code.open-bio.org::cvsbiopython .
>
> But all the files were appended with a ",v" why did that happen? (i.e. see
> below)
> Attic ?Bio ?BioSQL ?CONTRIB,v ?DEPRECATED,v ?Doc ?Experimental ?LICENSE,v
> MANIFEST.in,v ?Martel ?NEWS,v ?README,v ?Scripts ?setup.py,v ?Tests

CVS likes to add ",v" to files - if you wanted to download them
from the public CVS server (code.open-bio.org) you would have
had to use the CVS command line tool.

However, we don't use CVS anymore, we use git. See:
http://www.biopython.org/wiki/SourceCode

If you really want to use rsync you *might* be able to point it
at http://biopython.org/SRC/biopython/

Peter

P.S. Why did you try downloading with rsync from the code.open-bio.org?
Is there something confusing in our documentation we can fix? Thanks!


From aboulia at gmail.com  Tue Dec 15 06:39:35 2009
From: aboulia at gmail.com (Kevin Lam)
Date: Tue, 15 Dec 2009 19:39:35 +0800
Subject: [Biopython] rsync download of biopython problems
In-Reply-To: <320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>
References: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com> 
	<320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>
Message-ID: <5b6410e0912150339y296aee41xf2277c8ff582015e@mail.gmail.com>

Hi Peter,
git works fine for me!
ok lemme explain how i got there..

from http://www.biopython.org/wiki/CVS
i followed this link http://cvs.biopython.org/
which redirected me to http://www.open-bio.org/wiki/SourceCode

i was on a fresh install system of CentOS so rsync was avail so i used that.

Cheers
Kevin

On Tue, Dec 15, 2009 at 6:37 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Tue, Dec 15, 2009 at 6:01 AM, Kevin Lam <aboulia at gmail.com> wrote:
> > Hi
> > I just tried downloading biopython via rsync
> >
> >  rsync -av code.open-bio.org::cvsbiopython .
> >
> > But all the files were appended with a ",v" why did that happen? (i.e.
> see
> > below)
> > Attic  Bio  BioSQL  CONTRIB,v  DEPRECATED,v  Doc  Experimental  LICENSE,v
> > MANIFEST.in,v  Martel  NEWS,v  README,v  Scripts  setup.py,v  Tests
>
> CVS likes to add ",v" to files - if you wanted to download them
> from the public CVS server (code.open-bio.org) you would have
> had to use the CVS command line tool.
>
> However, we don't use CVS anymore, we use git. See:
> http://www.biopython.org/wiki/SourceCode
>
> If you really want to use rsync you *might* be able to point it
> at http://biopython.org/SRC/biopython/
>
> Peter
>
> P.S. Why did you try downloading with rsync from the code.open-bio.org?
> Is there something confusing in our documentation we can fix? Thanks!
>

From biopython at maubp.freeserve.co.uk  Tue Dec 15 06:48:22 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 11:48:22 +0000
Subject: [Biopython] rsync download of biopython problems
In-Reply-To: <5b6410e0912150339y296aee41xf2277c8ff582015e@mail.gmail.com>
References: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>
	<320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>
	<5b6410e0912150339y296aee41xf2277c8ff582015e@mail.gmail.com>
Message-ID: <320fb6e00912150348y7f074d94u74b3b14cc31d4c6@mail.gmail.com>

On Tue, Dec 15, 2009 at 11:39 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi Peter,
> git works fine for me!
> ok lemme explain how i got there..
>
> from http://www.biopython.org/wiki/CVS

I just the "this page is obsolete" bit at the top needs to be more prominent...

> i followed this link http://cvs.biopython.org/

I can ask the sys admins to redirect that to:
http://www.biopython.org/wiki/SourceCode

> which redirected me to http://www.open-bio.org/wiki/SourceCode

Ah - that does need updating. Thanks!

> i was on a fresh install system of CentOS so rsync was avail so i used that.

Well it "worked" (you got a copy of the CVS repository rather than a
snapshot of the code), but the CVS repository is now out of date.

Peter

From biopython at maubp.freeserve.co.uk  Tue Dec 15 12:01:38 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 17:01:38 +0000
Subject: [Biopython] Biopython 1.53 released
Message-ID: <320fb6e00912150901k138ae04bmc5d5af9c867340ec@mail.gmail.com>

Dear Biopythoneers,

We are pleased to announce the availability of Biopython 1.53, a new
stable release of the Biopython library, three months after the
release of Biopython 1.52. This is our first release since migrating
from CVS to git for source code control.

There have been some additions to our core objects ? the Seq (and
related UnknownSeq) objects gained upper and lower methods (like the
string methods of the same name but alphabet aware) plus a new ungap
method. The SeqFeature object now has an extract method to get the
region of sequence it describes (useful for getting CDS nucleotide
sequences from GenBank files). Also SeqRecord objects now support
addition, giving a new SeqRecord with the combined sequence, all the
SeqFeatures, and any common annotation.

SQLite support (built into Python 2.5+) was added to our BioSQL
interface. This is still a little experimental as we are using a draft
BioSQL SQLite schema, but this should be merged into the next
BioSQL release.

Biopython now includes wrappers for the new NCBI BLAST C++ tools,
which will be replacing the old NCBI ?legacy? BLAST tools written in
C. The plain text BLAST parser has been updated to cope as well.
Nevertheless, we (and the NCBI) still recommend using the XML output
for parsing.

Bio.Entrez includes the new (Jan 2010) DTD files from the NCBI for
parsing MedLine/PubMed data.

The NCBI codon tables have been updated from version 3.4 to 3.9, which
adds a few extra start codons, and a few new tables (Tables 16, 21, 22
and 23).

The restriction enzyme list in Bio.Restriction has been updated to the
Nov 2009 release of REBASE.

The Bio.PDB parser and output code has been updated to understand the
element column in ATOM and HETATM lines, and Bio.PDB.PDBList has been
updated for recent changes to the PDB FTP site.

Finally, support for running Biopython under Jython (using the Java
Virtual Machine) has been much improved. Note that Jython does not
support C code, and currently Jython does not parse DTD files (needed
for the Bio.Entrez XML parser). However, most of the Biopython modules
seem fine from testing Jython 2.5.0 and 2.5.1.

Sources and Windows Installers are available from our downloads page.

Thanks to the Biopython development team and to everyone who has
reported bugs or contributed patches since our last release.

--Peter, on behalf of the Biopython developers

P.S. This news post is online at
http://news.open-bio.org/news/2009/12/biopython-release-153/

You may wish to subscribe to our news feed.  For RSS links etc, see:
http://biopython.org/wiki/News

Biopython news is also on twitter:
http://twitter.com/biopython


From cgohlke at uci.edu  Tue Dec 15 12:17:53 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 09:17:53 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
Message-ID: <4B27C4C1.3090206@uci.edu>

Hello,

I have built biopython 1.53 for 64-bit Python 2.6 for Windows using 
Visual Studio 2008. The test output is attached. The installer is at 
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>

Best,

Christoph Gohlke
Laboratory for Fluorescence Dynamics
University of California, Irvine
http://www.lfd.uci.edu/~gohlke/
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: biopython-1.53.win-amd64-py2.6-test.txt
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091215/ce4a9376/attachment.txt>

From biopython at maubp.freeserve.co.uk  Tue Dec 15 12:49:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 17:49:35 +0000
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <4B27C4C1.3090206@uci.edu>
References: <4B27C4C1.3090206@uci.edu>
Message-ID: <320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>

On Tue, Dec 15, 2009 at 5:17 PM, Christoph Gohlke <cgohlke at uci.edu> wrote:
> Hello,
>
> I have built biopython 1.53 for 64-bit Python 2.6 for Windows using Visual
> Studio 2008. The test output is attached. The installer is at
> <http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>

Nice :)

Was this with NumPy 1.4.0rc2?

The fact that test_GraphicsBitmaps.py failed with a font problem
is indicative of something not quite right in ReportLab and/or PIL.
This is almost certainly not a Biopython problem.

A couple of SCOP tested failed - could you run unix2dos (or
similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
and retest? That "fixes" it on win32.

Also what does this do on your Windows 64bit python?

>>> import sys
>>> sys.platform
'win32'

I've seen threads discussing if it should return "win64" or
"win32", but the simplest way to check is try it and see.

Thanks,

Peter

From cgohlke at uci.edu  Tue Dec 15 13:22:23 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 10:22:23 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
References: <4B27C4C1.3090206@uci.edu>
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
Message-ID: <4B27D3DF.4070006@uci.edu>



On 12/15/2009 9:49 AM, Peter wrote:
> On Tue, Dec 15, 2009 at 5:17 PM, Christoph Gohlke<cgohlke at uci.edu>  wrote:
>> Hello,
>>
>> I have built biopython 1.53 for 64-bit Python 2.6 for Windows using Visual
>> Studio 2008. The test output is attached. The installer is at
>> <http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>
>
> Nice :)
>
> Was this with NumPy 1.4.0rc2?
Yes, numpy-1.4.0rc2.dev7996, also available on the same download page.

>
> The fact that test_GraphicsBitmaps.py failed with a font problem
> is indicative of something not quite right in ReportLab and/or PIL.
> This is almost certainly not a Biopython problem.
>
OK, I will check Reportlab and PIL. I now remember seeing some font 
loading issues with PIL 1.1.7 in other packages even though all internal 
tests pass.

> A couple of SCOP tested failed - could you run unix2dos (or
> similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
> and retest? That "fixes" it on win32.
>
That worked. The font error is now the only failing test.

> Also what does this do on your Windows 64bit python?
>
>>>> import sys
>>>> sys.platform
> 'win32'
'win32' is correct.
I use "'64 bit' in sys.version" to check for a 64 bit version at runtime.

>
> I've seen threads discussing if it should return "win64" or
> "win32", but the simplest way to check is try it and see.
>

Thank you. Feel free to redistribute the installer if you think it is 
good enough.

Christoph


From cgohlke at uci.edu  Tue Dec 15 13:20:07 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 10:20:07 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
References: <4B27C4C1.3090206@uci.edu>
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
Message-ID: <4B27D357.30705@uci.edu>



On 12/15/2009 9:49 AM, Peter wrote:
> On Tue, Dec 15, 2009 at 5:17 PM, Christoph Gohlke<cgohlke at uci.edu>  wrote:
>> Hello,
>>
>> I have built biopython 1.53 for 64-bit Python 2.6 for Windows using Visual
>> Studio 2008. The test output is attached. The installer is at
>> <http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>
>
> Nice :)
>
> Was this with NumPy 1.4.0rc2?
>
> The fact that test_GraphicsBitmaps.py failed with a font problem
> is indicative of something not quite right in ReportLab and/or PIL.
> This is almost certainly not a Biopython problem.
>
> A couple of SCOP tested failed - could you run unix2dos (or
> similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
> and retest? That "fixes" it on win32.
>
> Also what does this do on your Windows 64bit python?
>
>>>> import sys
>>>> sys.platform
> 'win32'
>
> I've seen threads discussing if it should return "win64" or
> "win32", but the simplest way to check is try it and see.
>
> Thanks,
>
> Peter
>
>

From biopython at maubp.freeserve.co.uk  Tue Dec 15 13:57:09 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 18:57:09 +0000
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <4B27D3DF.4070006@uci.edu>
References: <4B27C4C1.3090206@uci.edu>
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
	<4B27D3DF.4070006@uci.edu>
Message-ID: <320fb6e00912151057t41a6e889k1df389cbccf1a8cd@mail.gmail.com>

On Tue, Dec 15, 2009 at 6:22 PM, Christoph Gohlke <cgohlke at uci.edu> wrote:
>
>> The fact that test_GraphicsBitmaps.py failed with a font problem
>> is indicative of something not quite right in ReportLab and/or PIL.
>> This is almost certainly not a Biopython problem.
>>
> OK, I will check Reportlab and PIL. I now remember seeing some
> font loading issues with PIL 1.1.7 in other packages even though
> all internal tests pass.

If you are happy to investigate further, that would be great.

>> A couple of SCOP tested failed - could you run unix2dos (or
>> similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
>> and retest? That "fixes" it on win32.
>
> That worked. The font error is now the only failing test.

Good.

>> Also what does this do on your Windows 64bit python?
>>
>>>>> import sys
>>>>> sys.platform
>>
>> 'win32'
>
> 'win32' is correct.
> I use "'64 bit' in sys.version" to check for a 64 bit version at runtime.

Thanks - I just wanted to be sure.

>
> Thank you. Feel free to redistribute the installer if you think it is
> good enough.
>

Given NumPy don't offer their own 64bit installers, and the
possible need for Microsoft Visual C++ 2008 redistributable
package, perhaps linking to your page makes most sense
for now. I'll update our download page if that sounds sensible.

Thank you,

Peter

From cgohlke at uci.edu  Tue Dec 15 14:29:28 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 11:29:28 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <320fb6e00912151057t41a6e889k1df389cbccf1a8cd@mail.gmail.com>
References: <4B27C4C1.3090206@uci.edu>	
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>	
	<4B27D3DF.4070006@uci.edu>
	<320fb6e00912151057t41a6e889k1df389cbccf1a8cd@mail.gmail.com>
Message-ID: <4B27E398.3090600@uci.edu>



On 12/15/2009 10:57 AM, Peter wrote:
> On Tue, Dec 15, 2009 at 6:22 PM, Christoph Gohlke<cgohlke at uci.edu>  wrote:
>>
>>> The fact that test_GraphicsBitmaps.py failed with a font problem
>>> is indicative of something not quite right in ReportLab and/or PIL.
>>> This is almost certainly not a Biopython problem.
>>>
>> OK, I will check Reportlab and PIL. I now remember seeing some
>> font loading issues with PIL 1.1.7 in other packages even though
>> all internal tests pass.
>
> If you are happy to investigate further, that would be great.
>

Turned out that the Times-Roman font is simply missing from the 
reportlab 2.3 source distribution, which I used. The missing fonts can 
be downloaded at <http://www.reportlab.org/ftp/pfbfer.zip> and put in 
the reportlab/fonts directory. I also included these fonts in the 
updated reportlab-2.3.win-amd64-py2.6.exe installer.

All tests pass now. Some tests were skipped due to missing third party 
packages on my computer.

>>
>> Thank you. Feel free to redistribute the installer if you think it is
>> good enough.
>>
>
> Given NumPy don't offer their own 64bit installers, and the
> possible need for Microsoft Visual C++ 2008 redistributable
> package, perhaps linking to your page makes most sense
> for now. I'll update our download page if that sounds sensible.
>
Makes sense. The VC.CRT redistributable is usually installed with Python 
and I compiled with the http://bugs.python.org/issue4120 patch.

Best,

Christoph


From aboulia at gmail.com  Tue Dec 15 22:52:36 2009
From: aboulia at gmail.com (Kevin Lam)
Date: Wed, 16 Dec 2009 11:52:36 +0800
Subject: [Biopython] Entrez.efetch Service unavailable!
Message-ID: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>

Hi I have been trying to use
Entrez.efetch
to download ~1000 bacteria genomes
I read in the docs that biopython will auto take care of the delay and fetch
via the preferred site for download scripts
but I have been getting service unavailable  errors at GMT +8 1100am
is this normal? Or should i edit the source to give a larger delay buffer?
So far I have only managed to get 3 fasta sequences out

Or should I bring this up to NCBI instead?

Traceback (most recent call last):
  File "../retr-fasta.py", line 15, in ?
    handle = Entrez.efetch(db="genome", id=uid, rettype="fasta")
  File
"/home/k/lib/biopython-biopython-9a41381/build/lib.linux-x86_64-2.4/Bio/Entrez/__init__.py",
line 105, in efetch
    return _open(cgi, variables)
  File
"/home/k/lib/biopython-biopython-9a41381/build/lib.linux-x86_64-2.4/Bio/Entrez/__init__.py",
line 343, in _open
    raise IOError("Service unavailable!")
IOError: Service unavailable!


Cheers
Kevin

From biopython at maubp.freeserve.co.uk  Wed Dec 16 03:58:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 08:58:35 +0000
Subject: [Biopython] Entrez.efetch Service unavailable!
In-Reply-To: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>
References: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>
Message-ID: <320fb6e00912160058i57acc020nba7c61c53a4ec64b@mail.gmail.com>

On Wed, Dec 16, 2009 at 3:52 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi I have been trying to use
> Entrez.efetch
> to download ~1000 bacteria genomes

Why not use their FTP site? They even make bundles available, e.g.
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.gbk.tar.gz
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.faa.tar.gz
etc. Note the folder is called Bacteria for historical reasons,
it is really Prokaryotes as there are plenty of Archaea in there.

> I read in the docs that biopython will auto take care of the delay and fetch
> via the preferred site for download scripts
> but I have been getting service unavailable ?errors at GMT +8 1100am
> is this normal? Or should i edit the source to give a larger delay buffer?
> So far I have only managed to get 3 fasta sequences out

The NCBI were planning some Entrez work about now (updating
DTD files), so the downtime might be expected. I'd wait a day,
and then if it is still down email them.

Regards,

Peter


From iua1 at psu.edu  Wed Dec 16 11:49:11 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 11:49:11 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
Message-ID: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>

Hello Everyone,

I applaud the move to Github, I think it was a great decision that
will allow more people to contribute to the project.

Yet at the same time a community is built on communication and the
current mailing list feels extremely antiquated. The way of
interaction is tedious: sending emails to an address, then one reads
one message at a time, messages are not displayed in a threaded form
where multiple messages are shown at the same time. There is no of
search,  etc. and it all feels like a throwback to the 90s. Personally
I think a choice of mailman is a choice of deliberately of limiting
access to all but the most hardcore - and for example that's why the
main Python-dev uses it, it is a more of  a mechanism to keep people
away. Of course  python has comp.lang.python and it is a nice and
thriving group.

The alternative such as Google groups would be far superior in
attracting and building a community of developers and users as well.
Is this an idea that  the owners of the list would entertain?

best regards,

Istvan Albert


-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From hlapp at drycafe.net  Wed Dec 16 11:56:57 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 11:56:57 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>

Istvan,

what is your solution to Google all of a sudden deciding to take  
Google Groups down, or to make it a paid subscription service, or if  
Google goes out of business?

All of these things have happened over and over before with commercial  
vendors. Economies do go through cycles. Would it be OK to lose the  
entire archive of the mailing list in such an event?

BTW if you use a threaded email client (such as GMail, or in fact most  
modern email readers), you *will* see threaded messages. Also, the  
Biopython list is indexed in GMane I believe, so you can search there  
pretty conveniently. Finally, have you tried using Google to search  
the Biopython archive? It's not so bad, actually.

Just my $0.02 (and I'm a big fan of Google Groups).

	-hilmar

On Dec 16, 2009, at 11:49 AM, Istvan Albert wrote:

> Hello Everyone,
>
> I applaud the move to Github, I think it was a great decision that
> will allow more people to contribute to the project.
>
> Yet at the same time a community is built on communication and the
> current mailing list feels extremely antiquated. The way of
> interaction is tedious: sending emails to an address, then one reads
> one message at a time, messages are not displayed in a threaded form
> where multiple messages are shown at the same time. There is no of
> search,  etc. and it all feels like a throwback to the 90s. Personally
> I think a choice of mailman is a choice of deliberately of limiting
> access to all but the most hardcore - and for example that's why the
> main Python-dev uses it, it is a more of  a mechanism to keep people
> away. Of course  python has comp.lang.python and it is a nice and
> thriving group.
>
> The alternative such as Google groups would be far superior in
> attracting and building a community of developers and users as well.
> Is this an idea that  the owners of the list would entertain?
>
> best regards,
>
> Istvan Albert
>
>
> -- 
> Istvan Albert
> http://www.personal.psu.edu/iua1
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

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





From carlos.borroto at gmail.com  Wed Dec 16 11:57:05 2009
From: carlos.borroto at gmail.com (Carlos Javier Borroto)
Date: Wed, 16 Dec 2009 11:57:05 -0500
Subject: [Biopython] Is there any in silico PCR tool on biopython?
Message-ID: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>

Hi there,

I'm looking for a way to show some information on the specificity of
sets of primers I'm designing, I'll love to have a way to run an in
silico PCR reaction and parse the results with biopython.

Is there something to use with one of the available PCR simulation tools?

regards,
-- 
Carlos Javier Borroto
Baltimore, MD
Google Voice: (410) 929 4020

From biopython at maubp.freeserve.co.uk  Wed Dec 16 12:07:05 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:07:05 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <320fb6e00912160907m4f201a90xb85851ef9ba43271@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
> Hello Everyone,
>
> I applaud the move to Github, I think it was a great decision that
> will allow more people to contribute to the project.
>
> Yet at the same time a community is built on communication and the
> current mailing list feels extremely antiquated. The way of
> interaction is tedious: sending emails to an address, then one reads
> one message at a time, messages are not displayed in a threaded form
> where multiple messages are shown at the same time. There is no of
> search, ?etc. and it all feels like a throwback to the 90s.

A lot of that is down to your email program - I find none of
those issue apply to how I use the list (in GoogleMail).

You are specifically talking about browsing the mailing list
archive? There yes, things are a bit rudimentary, and search
isn't as good as in GoogleMail. But on the other hand it is
clearly a read only archive.

> Personally I think a choice of mailman is a choice of deliberately of
> limiting access to all but the most hardcore - and for example that's
> why the main Python-dev uses it, it is a more of ?a mechanism to
> keep people away. Of course?python has comp.lang.python and it
> is a nice and thriving group.
>
> The alternative such as Google groups would be far superior in
> attracting and building a community of developers and users as
> well. Is this an idea that ?the owners of the list would entertain?

It is something that the OBF may consider - but there are a
lot of concerns about reliance on third parties, advertising, loss
of brand control etc (see also Hilmar's email).

Peter


From biopython at maubp.freeserve.co.uk  Wed Dec 16 12:08:00 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:08:00 +0000
Subject: [Biopython] Is there any in silico PCR tool on biopython?
In-Reply-To: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
References: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
Message-ID: <320fb6e00912160908r152bbc49o38ea32a33cf6ff89@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:57 PM, Carlos Javier Borroto
<carlos.borroto at gmail.com> wrote:
> Hi there,
>
> I'm looking for a way to show some information on the specificity of
> sets of primers I'm designing, I'll love to have a way to run an in
> silico PCR reaction and parse the results with biopython.
>
> Is there something to use with one of the available PCR simulation tools?
>

I know people use Biopython with primer3 (usually the EMBOSS
wrapped version, eprimer3).

Peter

From biopython at maubp.freeserve.co.uk  Wed Dec 16 12:11:40 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:11:40 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
Message-ID: <320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:56 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>
> Also, the Biopython list is indexed in GMane I believe, so you can
> search there pretty conveniently.

Good point - should we add links to these on the mailing list wiki page?

Main mailing list:
http://dir.gmane.org/gmane.comp.python.bio.general

Dev mailing list:
http://dir.gmane.org/gmane.comp.python.bio.general

Announcement list:
http://dir.gmane.org/gmane.comp.python.bio.general

Peter

From biopython at maubp.freeserve.co.uk  Wed Dec 16 12:14:31 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:14:31 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>
Message-ID: <320fb6e00912160914w12e8ff2eiaa42b7924226eca8@mail.gmail.com>

On Wed, Dec 16, 2009 at 5:11 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Dec 16, 2009 at 4:56 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>
>> Also, the Biopython list is indexed in GMane I believe, so you can
>> search there pretty conveniently.
>
> Good point - should we add links to these on the mailing list wiki page?

Sorry, same link three times, should be:

Main mailing list:
http://dir.gmane.org/gmane.comp.python.bio.general
http://news.gmane.org/gmane.comp.python.bio.general

Dev mailing list:
http://dir.gmane.org/gmane.comp.python.bio.devel
http://news.gmane.org/gmane.comp.python.bio.devel

Announcement list:
http://dir.gmane.org/gmane.comp.python.bio.announce
http://news.gmane.org/gmane.comp.python.bio.announce

Peter

From biopython at maubp.freeserve.co.uk  Wed Dec 16 12:26:01 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:26:01 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
>
> The alternative such as Google groups would be far superior in
> attracting and building a community of developers and users as well.
> Is this an idea that ?the owners of the list would entertain?
>

As far as I can tell from the limited documentation I found on
Google Groups (maybe I was looking in the wrong place?) there
is no way to import our existing decade long mail archives.
That would be a major downside.

Also, using Google Groups would *require* all posters to have
a Google Account - a potential sticking point for some.

Peter


From cjfields at illinois.edu  Wed Dec 16 12:19:52 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 11:19:52 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160907m4f201a90xb85851ef9ba43271@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160907m4f201a90xb85851ef9ba43271@mail.gmail.com>
Message-ID: <52405282-5654-47D8-885F-4733F9A40873@illinois.edu>

On Dec 16, 2009, at 11:07 AM, Peter wrote:

> On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
>> Hello Everyone,
>> 
>> I applaud the move to Github, I think it was a great decision that
>> will allow more people to contribute to the project.
>> 
>> Yet at the same time a community is built on communication and the
>> current mailing list feels extremely antiquated. The way of
>> interaction is tedious: sending emails to an address, then one reads
>> one message at a time, messages are not displayed in a threaded form
>> where multiple messages are shown at the same time. There is no of
>> search,  etc. and it all feels like a throwback to the 90s.
> 
> A lot of that is down to your email program - I find none of
> those issue apply to how I use the list (in GoogleMail).
> 
> You are specifically talking about browsing the mailing list
> archive? There yes, things are a bit rudimentary, and search
> isn't as good as in GoogleMail. But on the other hand it is
> clearly a read only archive.
> 
>> Personally I think a choice of mailman is a choice of deliberately of
>> limiting access to all but the most hardcore - and for example that's
>> why the main Python-dev uses it, it is a more of  a mechanism to
>> keep people away. Of course python has comp.lang.python and it
>> is a nice and thriving group.
>> 
>> The alternative such as Google groups would be far superior in
>> attracting and building a community of developers and users as
>> well. Is this an idea that  the owners of the list would entertain?
> 
> It is something that the OBF may consider - but there are a
> lot of concerns about reliance on third parties, advertising, loss
> of brand control etc (see also Hilmar's email).
> 
> Peter

I agree with peter and hilmar.  Nabble and Gmane both archive the open-bio lists, at least for bioperl, but I would assume biopython as well.  For a painful example of how bad third party mail lists can be (painful at least to me), see the gmod lists at Sourceforge.

chris



From iua1 at psu.edu  Wed Dec 16 12:36:45 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 12:36:45 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
Message-ID: <c878cd560912160936p8224e55yc765ab73ba1999b7@mail.gmail.com>

On Wed, Dec 16, 2009 at 11:56 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Groups down, or to make it a paid subscription service, or if Google goes
> out of business?

>  Economies do go through cycles. Would it be OK to lose the entire
> archive of the mailing list in such an event?

Every choice has two sides. Has a positive and has negative dimension
to it. I am sure one can come up with  unlikely yet equally
pessimistic scenarios for the existing setup as well.

One thing is seems clear to me and I do not think that you are aware
of it. This mailman setup is a throttle - it imposes a negative
feedback on the amount of messages that it can handle.

This system of messages cannot grow over a certain limit. Just imagine
regularly getting a dozen new emails a day plus their followups, yet
you are just a casual user.

This would be unbearable for many people whose inboxes are already
overflowing. So they either don't participate or once they get even a
few of these messages they turn off email delivery at which point you
are left with a rudimentary site where it is hard to contribute so it
drops off their radar.

I can't even imagine what it would look like to have a popular
newsgroup being delivered to my mailbox. In a nutshell you are saying
it already works - but that is only because you get so few messages
... and getting more becomes actually inconvenient to the point at
which it has to decay again to the manageable level

Istvan

-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From hlapp at drycafe.net  Wed Dec 16 12:40:45 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 12:40:45 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
Message-ID: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>


On Dec 16, 2009, at 12:18 PM, Istvan Albert wrote:

> I am sure one can come up with  unlikely yet equally pessimistic  
> scenarios for the existing setup as well.

My point was that this is not unlikely at all. It happened with some  
of Yahoo's services, and it happened with others rather popular ones.

If you own and operate your own brand, your equipment can still go out  
of order. But at least it's under your own control. Do you see that  
difference? Would you argue that that is unimportant?

> This mailman setup is a throttle - it imposes a negative feedback on  
> the amount of messages that it can handle.

I really don't know what you mean by this. I get 200 messages a day  
from various lists. I'd be dead if I had an email client that can't  
thread and can't filter, but I do have one that can (and it's free).  
GMail can do both too, and is free. Have you tried a threading email  
reader? Can you explain how reading newsgroups through a threaded and  
filtering news reader is different and more efficient than reading  
emails through a threaded and filtering email reader?

That all being said, if what's at issue here is to have a Google Group  
interface to the Biopython mailing list, then that's actually easy to  
achieve. Someone (ideally one of the current list or project admins/ 
owners) creates a (presumably identically named) Google Group, and  
sets it to mirror the mailman mailing list.

Guys - I'm happy to help with that if you don't know how to do that.  
Create the group, subscribe drycafe at gmail.com, and make me an admin.  
I'll configure the mirroring.

	-hilmar

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





From sdavis2 at mail.nih.gov  Wed Dec 16 12:48:30 2009
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Wed, 16 Dec 2009 12:48:30 -0500
Subject: [Biopython] Is there any in silico PCR tool on biopython?
In-Reply-To: <320fb6e00912160908r152bbc49o38ea32a33cf6ff89@mail.gmail.com>
References: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
	<320fb6e00912160908r152bbc49o38ea32a33cf6ff89@mail.gmail.com>
Message-ID: <264855a00912160948q538bed21q6dc0d410d468c5c7@mail.gmail.com>

On Wed, Dec 16, 2009 at 12:08 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Dec 16, 2009 at 4:57 PM, Carlos Javier Borroto
> <carlos.borroto at gmail.com> wrote:
>> Hi there,
>>
>> I'm looking for a way to show some information on the specificity of
>> sets of primers I'm designing, I'll love to have a way to run an in
>> silico PCR reaction and parse the results with biopython.
>>
>> Is there something to use with one of the available PCR simulation tools?
>>
>
> I know people use Biopython with primer3 (usually the EMBOSS
> wrapped version, eprimer3).

Carlos,

If it is something like the UCSC genome browser in-silico PCR (for
mapping the putative amplimers from a set of primers), they (UCSC)
have an executable of the software.  I always have trouble finding
their software tools, but they are very responsive to email if you
have problems.  I don't have an example output file, but I bet it is
just tab-delimited text, so parsing is probably not too difficult.

Sean

From lueck at ipk-gatersleben.de  Wed Dec 16 12:31:18 2009
From: lueck at ipk-gatersleben.de (lueck at ipk-gatersleben.de)
Date: Wed, 16 Dec 2009 18:31:18 +0100
Subject: [Biopython] suggestion: moving to the discussion list to	Google
	groups
In-Reply-To: <320fb6e00912160914w12e8ff2eiaa42b7924226eca8@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>
	<320fb6e00912160914w12e8ff2eiaa42b7924226eca8@mail.gmail.com>
Message-ID: <20091216183118.zy9yvhd0hdcs4ggs@webmail.ipk-gatersleben.de>

What about a free forum e.g. smf (http://www.simplemachines.org/) on 
the biopython homepage?

I'm using this too and I'm quite happy. Easy building, maintaining...
Just an idea...

Zitat von Peter <biopython at maubp.freeserve.co.uk>:

> On Wed, Dec 16, 2009 at 5:11 PM, Peter 
> <biopython at maubp.freeserve.co.uk> wrote:
>> On Wed, Dec 16, 2009 at 4:56 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>>
>>> Also, the Biopython list is indexed in GMane I believe, so you can
>>> search there pretty conveniently.
>>
>> Good point - should we add links to these on the mailing list wiki page?
>
> Sorry, same link three times, should be:
>
> Main mailing list:
> http://dir.gmane.org/gmane.comp.python.bio.general
> http://news.gmane.org/gmane.comp.python.bio.general
>
> Dev mailing list:
> http://dir.gmane.org/gmane.comp.python.bio.devel
> http://news.gmane.org/gmane.comp.python.bio.devel
>
> Announcement list:
> http://dir.gmane.org/gmane.comp.python.bio.announce
> http://news.gmane.org/gmane.comp.python.bio.announce
>
> Peter
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>




From iua1 at psu.edu  Wed Dec 16 13:02:26 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:02:26 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
Message-ID: <c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>

Hi Everyone,

> Also, using Google Groups would *require* all posters to have
> a Google Account - a potential sticking point for some.

Right, but even currently one has to make an account on your  site
with email and password. Aren't you  less comfortable signing up with
various third parties than Google?

A response mentioned that Gmail's email threading works just as well
...  well it doesn't help anyone who has not already been subscribed
to the messages to begin with.  If you come to a discussion later you
cannot get that.

My goal is not to argue with each point, I only picked these two
because  both seemed to me like obvious responses yet  they are only
superficially addressing  the issues that  I brought up.

But to step back a second, and maybe I wasn't specific enough. It is
less about me, I can filter and thread my own email, I could download
the email entire archive and search it etc..
I teach an introductory level class that uses Biopython, can I
recommend my class that all go and sign up with you? I cannot really.
Many people are just learning about computing, they will be
overwhelmed with the everything interface, lack of search etc.

All of you who responded - frankly I think you are too close to this
issue to be able judge it correctly. It is like advising a newbie to
use VI, one in a hundred will love it ninety nine will hate it, but
hey who could argue that it is not super awesome? Once you do
something for a bunch of  years, you develop strategies and
everything seems to work just fine, and everything makes sense. Get
someone who is 20 and has never heard of sending emails to an address
then see what they say about it...

You all obviously care about the a community around biopython  so all
I am saying here is this:  when you look around and wish that you
could get a lot more people in - I think the answer is right there.
Make it really easy to ask question,  participate but also easy to
just not participate and just be able to catch up really quickly of
what is going on.

I wish you all the best,

Istvan Albert

-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From lueck at ipk-gatersleben.de  Wed Dec 16 13:04:17 2009
From: lueck at ipk-gatersleben.de (lueck at ipk-gatersleben.de)
Date: Wed, 16 Dec 2009 19:04:17 +0100
Subject: [Biopython] suggestion: moving to the discussion list to	Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <20091216190417.1z9yrs6mn4f4gcsw@webmail.ipk-gatersleben.de>

What about a free forum e.g. smf (http://www.simplemachines.org/) on 
the biopython homepage?

I'm using this too and I'm quite happy. Easy building, maintaining...
Just an idea...

Zitat von Hilmar Lapp <hlapp at drycafe.net>:

>
> On Dec 16, 2009, at 12:18 PM, Istvan Albert wrote:
>
>> I am sure one can come up with  unlikely yet equally pessimistic  
>> scenarios for the existing setup as well.
>
> My point was that this is not unlikely at all. It happened with some  
> of Yahoo's services, and it happened with others rather popular ones.
>
> If you own and operate your own brand, your equipment can still go 
> out  of order. But at least it's under your own control. Do you see 
> that  difference? Would you argue that that is unimportant?
>
>> This mailman setup is a throttle - it imposes a negative feedback on 
>>  the amount of messages that it can handle.
>
> I really don't know what you mean by this. I get 200 messages a day  
> from various lists. I'd be dead if I had an email client that can't  
> thread and can't filter, but I do have one that can (and it's free).  
> GMail can do both too, and is free. Have you tried a threading email  
> reader? Can you explain how reading newsgroups through a threaded and 
>  filtering news reader is different and more efficient than reading  
> emails through a threaded and filtering email reader?
>
> That all being said, if what's at issue here is to have a Google 
> Group  interface to the Biopython mailing list, then that's actually 
> easy to  achieve. Someone (ideally one of the current list or project 
> admins/ owners) creates a (presumably identically named) Google 
> Group, and  sets it to mirror the mailman mailing list.
>
> Guys - I'm happy to help with that if you don't know how to do that.  
> Create the group, subscribe drycafe at gmail.com, and make me an admin.  
> I'll configure the mirroring.
>
> 	-hilmar
>
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>




From iua1 at psu.edu  Wed Dec 16 13:13:45 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:13:45 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>

On Wed, Dec 16, 2009 at 12:40 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> If you own and operate your own brand, your equipment can still go out of
> order. But at least it's under your own control. Do you see that difference?
> Would you argue that that is unimportant?

It is a valid argument. No question about that.

I do have a comeback though, what percent of the past decade's
archive's content do you think is still actually useful? Isn't the
archive's purpose more of a historical one. And type of archiving you
could do for yourself.

But as for useful content that other people want to use - I am
guessing the half life of any particular advice is no more than about
one two two years.

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From hlapp at drycafe.net  Wed Dec 16 13:23:18 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 13:23:18 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
Message-ID: <9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>


On Dec 16, 2009, at 1:13 PM, Istvan Albert wrote:

> what percent of the past decade's archive's content do you think is  
> still actually useful?


Actually I find it very useful. We frequently cite past posts as  
references for explanations, or problems previously reported. It's one  
of the main differences between an archived mailing list and a simple  
alias for a group of people.

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





From cjfields at illinois.edu  Wed Dec 16 13:28:37 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 12:28:37 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
Message-ID: <F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>


On Dec 16, 2009, at 12:23 PM, Hilmar Lapp wrote:

> 
> On Dec 16, 2009, at 1:13 PM, Istvan Albert wrote:
> 
>> what percent of the past decade's archive's content do you think is still actually useful?
> 
> 
> Actually I find it very useful. We frequently cite past posts as references for explanations, or problems previously reported. It's one of the main differences between an archived mailing list and a simple alias for a group of people.
> 
> 	-hilmar

Agreed.  With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.

chris

From iua1 at psu.edu  Wed Dec 16 13:40:27 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:40:27 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
Message-ID: <c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>

On Wed, Dec 16, 2009 at 1:28 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
> Agreed. ?With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.

My fault for being insufficiently clear. I am not saying that having
archives is useless.

It all needs to be framed in the mindset of an unexpected event
causing an archive to be  lost. Is that irreparable harm? For example
would having a hundred more active participants be worth the small
risk of losing the archives?

I am just putting the 100 as a number out there, just to get you to
think. I think you all agree that at some level of extra participation
the risks would be well worth it.

Now I am convinced that a Google group would get more participation.
But is that 10 more people, one hundred, one thousand? That I do not
dare to guesstimate.

(definitely more than 10, ;-) )

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From cjfields at illinois.edu  Wed Dec 16 13:34:42 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 12:34:42 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <61CD9E3F-3F1A-4AC0-B863-9A24E7A373EF@illinois.edu>


On Dec 16, 2009, at 11:40 AM, Hilmar Lapp wrote:

> 
> On Dec 16, 2009, at 12:18 PM, Istvan Albert wrote:
> 
>> I am sure one can come up with  unlikely yet equally pessimistic scenarios for the existing setup as well.
> 
> My point was that this is not unlikely at all. It happened with some of Yahoo's services, and it happened with others rather popular ones.
> 
> If you own and operate your own brand, your equipment can still go out of order. But at least it's under your own control. Do you see that difference? Would you argue that that is unimportant?
> 
>> This mailman setup is a throttle - it imposes a negative feedback on the amount of messages that it can handle.
> 
> I really don't know what you mean by this. I get 200 messages a day from various lists. I'd be dead if I had an email client that can't thread and can't filter, but I do have one that can (and it's free). GMail can do both too, and is free. Have you tried a threading email reader? Can you explain how reading newsgroups through a threaded and filtering news reader is different and more efficient than reading emails through a threaded and filtering email reader?
> 
> That all being said, if what's at issue here is to have a Google Group interface to the Biopython mailing list, then that's actually easy to achieve. Someone (ideally one of the current list or project admins/owners) creates a (presumably identically named) Google Group, and sets it to mirror the mailman mailing list.
> 
> Guys - I'm happy to help with that if you don't know how to do that. Create the group, subscribe drycafe at gmail.com, and make me an admin. I'll configure the mirroring.
> 
> 	-hilmar

That would probably be a good idea for all the (most trafficked) open-bio groups.  I'll work on it from the bioperl end.

chris



From tiagoantao at gmail.com  Wed Dec 16 13:52:55 2009
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Wed, 16 Dec 2009 18:52:55 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>

On Wed, Dec 16, 2009 at 5:40 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> If you own and operate your own brand, your equipment can still go out of
> order. But at least it's under your own control. Do you see that difference?
> Would you argue that that is unimportant?

+1 .

Just to say I fully subscribe to this point of view.

github is _different_ by the very nature of being a distributed
system. If tomorrow github.com disappears, it will be very easy to
recover from it. If google turns bad, we loose a lot of history as
google groups is not inherently distributed and thus neither resilient
nor fail-safe.

I prefer the status quo to the google groups change. From my point of
view the technological autonomy provided by the OBF is a good thing.

My ?0.02,
Tiago


From biopython at maubp.freeserve.co.uk  Wed Dec 16 13:55:16 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 18:55:16 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
	<c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>
Message-ID: <320fb6e00912161055l38b8e27dpbb4c19be7c23b18b@mail.gmail.com>

On Wed, Dec 16, 2009 at 6:02 PM, Istvan Albert <iua1 at psu.edu> wrote:
> A response mentioned that Gmail's email threading works just as well
> ... ?well it doesn't help anyone who has not already been subscribed
> to the messages to begin with. ?If you come to a discussion later you
> cannot get that.

True - but that becomes less and less of an issue once you
have signed up.

> ... Get someone who is 20 and has never heard of sending
> emails to an address then see what they say about it...

Do 20 year olds really not know how to use email these days?
I do talk to graduate students, and hadn't noticed a trend.
I must be getting old(er). Maybe we need a "Dummies
Guide to setting up a GoogleMail/Thunderbird/Outlook
filter"? e.g. I have one to move things from the inbox to a
"Biopython" folder automatically.

I do take you point that making the mailing list more
accessible to novices (especially university students) is a
good idea - and you may be right that *mirroring* it on
GoogleGroups could be a solution. I don't know enough
about how that works to have an informed viewpoint, but
I trust Hilmar to look into it.

Peter


From iua1 at psu.edu  Wed Dec 16 13:57:39 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:57:39 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>
Message-ID: <c878cd560912161057l1fc52636nef4ab79d64cd0643@mail.gmail.com>

2009/12/16 Tiago Ant?o <tiagoantao at gmail.com>:

> If google turns bad, we loose a lot of history as google groups
> is not inherently distributed and thus neither resilient

No, on a second thought it actually is.

Sign up to the group such that is sends an email for every single
message (if you wish so). Google goes under, go back to the site the
way it is right now.

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From iua1 at psu.edu  Wed Dec 16 13:59:11 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:59:11 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912161055l38b8e27dpbb4c19be7c23b18b@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
	<c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>
	<320fb6e00912161055l38b8e27dpbb4c19be7c23b18b@mail.gmail.com>
Message-ID: <c878cd560912161059s1d06eff1j4cf7eabd23c03c0d@mail.gmail.com>

On Wed, Dec 16, 2009 at 1:55 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> Do 20 year olds really not know how to use email these days?
> I do talk to graduate students, and hadn't noticed a trend.
> I must be getting old(er). Maybe we need a "Dummies

Not email but interacting with a listserver via emails.

Ask your students what a list server is.


-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From iua1 at psu.edu  Wed Dec 16 14:14:21 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 14:14:21 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <c878cd560912161114h391b7673tf9e26ad0d9745705@mail.gmail.com>

On Wed, Dec 16, 2009 at 2:07 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Just curious, but does anyone know whether Google groups are more or less susceptible to spamming?
> The current mailman setup does keep out a vast majority of spam (I can't recall the last instance, actually).


The effective way to deal with it is white listing. There is a setting
that requires that the first message from a given email be approved by
mods.

That being said spam, popularity and ease of access all correlate.



-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From cjfields at illinois.edu  Wed Dec 16 14:05:46 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 13:05:46 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161057l1fc52636nef4ab79d64cd0643@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>
	<c878cd560912161057l1fc52636nef4ab79d64cd0643@mail.gmail.com>
Message-ID: <CE55BF20-B8A3-4BAF-AC72-10A3DB8890C6@illinois.edu>


On Dec 16, 2009, at 12:57 PM, Istvan Albert wrote:

> 2009/12/16 Tiago Ant?o <tiagoantao at gmail.com>:
> 
>> If google turns bad, we loose a lot of history as google groups
>> is not inherently distributed and thus neither resilient
> 
> No, on a second thought it actually is.
> 
> Sign up to the group such that is sends an email for every single
> message (if you wish so). Google goes under, go back to the site the
> way it is right now.
> 
> Istvan

...and in the meantime we lose any content only present on the google group list.  Whereas if the group is a mirror of this list, then nothing is lost.

chris

From hlapp at drycafe.net  Wed Dec 16 14:20:21 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 14:20:21 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <307922E9-8DD9-408F-8D39-D259186B3568@drycafe.net>

It's the mailing list moderator volunteers that keep the spam out,  
actually. It's gotten so bad though that most OBF lists are set to  
reject non-member posts.

What Google might be better at is to reject the spam well enough that  
one could open up the lists again to non-member posting.

-hilmar

Sent from away

On Dec 16, 2009, at 2:07 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Just curious, but does anyone know whether Google groups are more or  
> less susceptible to spamming?  The current mailman setup does keep  
> out a vast majority of spam (I can't recall the last instance,  
> actually).

From cjfields at illinois.edu  Wed Dec 16 14:07:39 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 13:07:39 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
Message-ID: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>

On Dec 16, 2009, at 12:40 PM, Istvan Albert wrote:

> On Wed, Dec 16, 2009 at 1:28 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>> Agreed.  With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.
> 
> My fault for being insufficiently clear. I am not saying that having
> archives is useless.
> 
> It all needs to be framed in the mindset of an unexpected event
> causing an archive to be  lost. Is that irreparable harm? For example
> would having a hundred more active participants be worth the small
> risk of losing the archives?

Not that I think Google is in any danger of going under, or that Google Groups will cease to exist, but they have discontinued services in the past (notebook was one, and I recall others going away).

> I am just putting the 100 as a number out there, just to get you to
> think. I think you all agree that at some level of extra participation
> the risks would be well worth it.

I understand your point, but I'm not really convinced this is something that can't be accomplished by simply mirroring the group and redirecting new users to sign up on the obf forums.

> Now I am convinced that a Google group would get more participation.
> But is that 10 more people, one hundred, one thousand? That I do not
> dare to guesstimate.
> 
> (definitely more than 10, ;-) )
> 
> Istvan

I think mirroring the list is the best compromise.  I can't envision moving everything wholesale over to Google Groups for the reasons Hilmar has outlined.

Just curious, but does anyone know whether Google groups are more or less susceptible to spamming?  The current mailman setup does keep out a vast majority of spam (I can't recall the last instance, actually).  

chris

From iua1 at psu.edu  Wed Dec 16 14:21:05 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 14:21:05 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>

On Wed, Dec 16, 2009 at 2:07 PM, Chris Fields <cjfields at illinois.edu> wrote:

> I understand your point, but I'm not really convinced this is something that can't be accomplished by simply mirroring the group and redirecting new users to sign up on the obf forums.

Great idea! While you are at it, why not allow people to post as well?

Sign up the current list so that when someone posts on Google Groups
it also goes to the current biopython list. When people reply-all from
biopython group it will go to both lists.

Maybe it is possible to get both worlds and using them in parallel!

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From hlapp at drycafe.net  Wed Dec 16 14:29:14 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 14:29:14 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
	<c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
Message-ID: <C1D71945-4ACB-450D-9B55-39D5699B3C83@drycafe.net>

That's included in the mirroring. You can post through either  
interface and join at either interface, it's transparent.

-hilmar

Sent from away

On Dec 16, 2009, at 2:21 PM, Istvan Albert <iua1 at psu.edu> wrote:

> Great idea! While you are at it, why not allow people to post as well?

From pingou at pingoured.fr  Wed Dec 16 14:35:07 2009
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 16 Dec 2009 20:35:07 +0100
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
	<c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
Message-ID: <1260992107.5993.0.camel@localhost.localdomain>

On Wed, 2009-12-16 at 14:21 -0500, Istvan Albert wrote:
> 
> Sign up the current list so that when someone posts on Google Groups
> it also goes to the current biopython list 
that implies that people are suscribed to both list and that won't be
always the case

Pierre


From richard_w_g_price at academia.edu  Wed Dec 16 17:50:05 2009
From: richard_w_g_price at academia.edu (Richard Price)
Date: Wed, 16 Dec 2009 14:50:05 -0800
Subject: [Biopython] New Academia.edu feature for Biopython
In-Reply-To: <cc0d7cc0912021721g660b39a2ga13c8213ec701454@mail.gmail.com>
References: <cc0d7cc0912021721g660b39a2ga13c8213ec701454@mail.gmail.com>
Message-ID: <cc0d7cc0912161450u7e188b9cm6eb85e24afc6458@mail.gmail.com>

Dear Biopython members,

I just wanted to let you know that there are now 5 members of Biopython on
Academia.edu listing their research interests such as Analytical
Chemistry, Computational Biology, and Bioinformatics. They have also
listed contacts, photos and papers.

There are thousands of people listing the same research interests as
the Biopython
members on Academia.edu, so there are lots of researchers for Biopython
members to discover.

To see the 5 members of Biopython on Academia.edu, and their research
interests and papers, follow the link below:

http://lists.academia.edu/See-members-of-Biopython

Richard

Dr. Richard Price, post-doc, Philosophy Dept, Oxford University.
Founder of Academia.edu

On Wed, Dec 2, 2009 at 5:21 PM, Richard Price
<richard_w_g_price at academia.edu> wrote:
> Dear Biopython members,
>
>
> I wanted to tell the list about a new feature on Academia.edu.
> Academia.edu launched 12 months ago and now helps 300,000 academics a
> month answer the question 'who's researching what?'
>
>
> We have built a dedicated page on Academia.edu for the Biopython mailing list:
>
>
> http://lists.academia.edu/See-members-of-Biopython
>
>
> This page will show you fellow members already on Academia.edu. ?You
> can see their papers, research interests, and other information.
>
>
> Visit the link below, sign up with Academia.edu, and see who else from
> Biopython is on Academia.edu.
>
>
>
> http://lists.academia.edu/See-members-of-Biopython
>
>
> Richard
>
>
> Dr. Richard Price, post-doc, Philosophy Dept, Oxford University.
> Founder of Academia.edu
>


From lpritc at scri.ac.uk  Thu Dec 17 04:35:56 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Thu, 17 Dec 2009 09:35:56 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <C74FABFC.2DBF9%lpritc@scri.ac.uk>

Hi,

On 16/12/2009 16:49, "Istvan Albert" <iua1 at psu.edu> wrote:

> [the mailing list] feels like a throwback to the 90s. [...]
> Of course  python has comp.lang.python and it is a nice and
> thriving group.

<stir>

comp.lang.python is a Usenet group, and Usenet is a throwback to the 70s. ;)

</stir>

> I can't even imagine what it would look like to have a popular
> newsgroup being delivered to my mailbox.

Mailing lists are far more convenient - for me - than having to navigate to
a website especially to check new messages on a particular subject.  Mailing
lists bring new posts and issues to my attention via a single always-on
interface in a timely manner.  The current mailing list also has the
advantage of grabbing the attention, specifically, of many people who might
be able to do something about a query.

As it happens, when I used to still read Usenet groups, I would do so from
my mail client, with exactly the same threaded interface as I used for
mailing lists and all other email.

Biopython is never likely to be more than a niche interest, so I wouldn't
expect it to ever reach the traffic of - say - alt.binaries.  To be honest,
the traffic doesn't even seem to approach that of numpy-discussion.  And
while we're talking about numpy-discussion, it illustrates one of Hilmar's
and Chris' points:

On 16/12/2009 16:56, "Hilmar Lapp" <hlapp at drycafe.net> wrote:

> what is your solution to Google all of a sudden deciding to take
> Google Groups down, or to make it a paid subscription service, or if
> Google goes out of business?

On 16/12/2009 19:07, "Chris Fields" <cjfields at illinois.edu> wrote:

> Not that I think Google is in any danger of going under, or that Google Groups
> will cease to exist, but they have discontinued services in the past (notebook
> was one, and I recall others going away).

http://groups.google.com/group/numpy-discussion/unlock?_done=/group/numpy-di
scussion/

That mailing list was taken down from Google Groups for 'violating terms of
service' - why, I don't know: it's a mailing list for a specialist Python
library.  It does illustrate though, how control can be (irrevocably) lost
over communication via Google Groups.  Notably, the mailing list itself
persists without interruption.

On 16/12/2009 17:36, "Istvan Albert" <iua1 at psu.edu> wrote:

> One thing is seems clear to me and I do not think that you are aware
> of it. This mailman setup is a throttle - it imposes a negative
> feedback on the amount of messages that it can handle.
> 
> This system of messages cannot grow over a certain limit. Just imagine
> regularly getting a dozen new emails a day plus their followups, yet
> you are just a casual user.
> 
> This would be unbearable for many people whose inboxes are already
> overflowing.

This issue - that some people don't like to receive lots of messages at once
- is already solved in mailman.  There is a 'daily digest' option on the
mailing list that collates the messages for a day, and sends them out as a
single email for you.

As a mailing list, mailman is deliberately designed to be relatively low
volume in terms of content, but to reach many readers directly; the idea is
to send relatively few messages to many people - but to push those messages
through to the reader.

Forums, wikis and website-based discussion lists require a deliberate effort
on the part of the reader either to find what they're interested in, or to
visit the site regularly.  Otherwise they just end up signing up to receive
updates by email, much like mailman.

On 16/12/2009 17:40, "Hilmar Lapp" <hlapp at drycafe.net> wrote:

> That all being said, if what's at issue here is to have a Google Group
> interface to the Biopython mailing list, then that's actually easy to
> achieve.

FWIW, I think that archiving the mailing list on Google Groups is not a bad
idea - so long as the current registration scheme continues to prevent the
inevitable waves of spam from Google Groups users.

The Biopython mailing lists appear already to have been archived - with
various degrees of usable interface, and likely intermittent coverage, too -
at sites such as:

http://www.mailinglistarchive.com/biopython at biopython.org/index.html

and

http://osdir.com/ml/search.html?cx=008059810939676512379%3Af5owd_2hq3u&cof=F
ORID%3A10&q=%5Bbiopython%5D&sa=Search

amongst others.

On 16/12/2009 18:02, "Istvan Albert" <iua1 at psu.edu> wrote:

> All of you who responded - frankly I think you are too close to this
> issue to be able judge it correctly. [...] Get
> someone who is 20 and has never heard of sending emails to an address
> then see what they say about it...

<stir>

If they've never heard of emailing an address, and/or can't use a mail
client to filter their email, I'm not sure the immediate problem is
necessarily with the mailing list... ;)

</stir>

I don't think that anyone here wants to restrict access to Biopython, or to
prevent discussion, even inadvertently.  That we've had 28 posts on this
issue in about 12 hours suggests that the list can handle issues of some
interest.  Sure, it would be nice to have a convenient, web-accessible and
searchable archive with a pretty and robust interface (and Google Groups
could give us that).  But I'm not convinced that the current mailing list is
a particular barrier to participation.


+1 for mirroring/archiving on Google Groups:
http://groups.google.com/support/bin/answer.py?hl=en&answer=46387


L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

From lpritc at scri.ac.uk  Thu Dec 17 05:14:54 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Thu, 17 Dec 2009 10:14:54 +0000
Subject: [Biopython] Is there any in silico PCR tool on biopython?
In-Reply-To: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
Message-ID: <C74FB51E.2DBFD%lpritc@scri.ac.uk>

Hi Carlos,

There's an interface to the EMBOSS package primersearch, which might be what
you're looking for.

http://embossgui.sourceforge.net/demo/manual/primersearch.html

http://github.com/biopython/biopython/blob/master/Bio/Emboss/Applications.py

Cheers,

L.


On 16/12/2009 16:57, "Carlos Javier Borroto" <carlos.borroto at gmail.com>
wrote:

> Hi there,
> 
> I'm looking for a way to show some information on the specificity of
> sets of primers I'm designing, I'll love to have a way to run an in
> silico PCR reaction and parse the results with biopython.
> 
> Is there something to use with one of the available PCR simulation tools?
> 
> regards,

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

From biopython at maubp.freeserve.co.uk  Thu Dec 17 05:42:16 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 10:42:16 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <C74FABFC.2DBF9%lpritc@scri.ac.uk>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<C74FABFC.2DBF9%lpritc@scri.ac.uk>
Message-ID: <320fb6e00912170242p7caa551eh91c2aa7beabc00f1@mail.gmail.com>

On Thu, Dec 17, 2009 at 9:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
>
> On 16/12/2009 16:56, "Hilmar Lapp" <hlapp at drycafe.net> wrote:
>
>> what is your solution to Google all of a sudden deciding to take
>> Google Groups down, or to make it a paid subscription service,
>> or if Google goes out of business?
>
> On 16/12/2009 19:07, "Chris Fields" <cjfields at illinois.edu> wrote:
>
>> Not that I think Google is in any danger of going under, or that Google Groups
>> will cease to exist, but they have discontinued services in the past (notebook
>> was one, and I recall others going away).
>
> http://groups.google.com/group/numpy-discussion/unlock?_done=/group/numpy-di
> scussion/
>
> That mailing list was taken down from Google Groups for 'violating terms of
> service' - why, I don't know: it's a mailing list for a specialist Python
> library. ?It does illustrate though, how control can be (irrevocably) lost
> over communication via Google Groups. ?Notably, the mailing list itself
> persists without interruption.

I remembered that example later - if NumPy had *switched*
that would have been a major upset to their community. As it
was, it seems people who were using the Google Groups
interface switched to using plain old email:
http://mail.scipy.org/pipermail/numpy-discussion/2009-October/045855.html

Peter


From biopython at maubp.freeserve.co.uk  Thu Dec 17 05:55:51 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 10:55:51 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <C74FABFC.2DBF9%lpritc@scri.ac.uk>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<C74FABFC.2DBF9%lpritc@scri.ac.uk>
Message-ID: <320fb6e00912170255y3968a6e4s3bd904071910251@mail.gmail.com>

On Wed, Dec 16, 2009 at 6:55 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> I do take you point that making the mailing list more
> accessible to novices (especially university students) is a
> good idea - and you may be right that *mirroring* it on
> GoogleGroups could be a solution. I don't know enough
> about how that works to have an informed viewpoint, but
> I trust Hilmar to look into it.
>

On Thu, Dec 17, 2009 at 9:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
>
> +1 for mirroring/archiving on Google Groups:
> http://groups.google.com/support/bin/answer.py?hl=en&answer=46387
>

It looks like we can see mirroring/archiving on Google Groups in action -
Hilmar and Chris have got this up and running for the main BioPerl list,

http://lists.open-bio.org/pipermail/bioperl-l/2009-December/031789.html
http://groups.google.com/group/bioperl-l

It is a shame there isn't any obvious way to import the existing archive
though.

Peter

From biopython at maubp.freeserve.co.uk  Thu Dec 17 07:27:59 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 12:27:59 +0000
Subject: [Biopython] Entrez.efetch Service unavailable!
In-Reply-To: <5b6410e0912160125j4f034218x263e6ab90b4afd47@mail.gmail.com>
References: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>
	<320fb6e00912160058i57acc020nba7c61c53a4ec64b@mail.gmail.com>
	<5b6410e0912160125j4f034218x263e6ab90b4afd47@mail.gmail.com>
Message-ID: <320fb6e00912170427q6b31ee33x6b161323d24f3027@mail.gmail.com>

On Wed, Dec 16, 2009 at 9:25 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi Peter,
> Thanks for the suggestion. It was also an exercise for me since I am new to
> Biopython and add to the fact that I do not need the Archaea sequences as I
> am looking for pathogenic bacteria. I admit I am lazy ha! All the same,
> thanks for being so helpful to a newbie to biopython.
> Cheers
> Kevin

No problem. I've been trying Entrez EFtech on and off over the last 24
hours, and it has been unavailable for a while. It seems to be back now.

Peter

P.S. Mailing list CC'd

From giles.weaver at googlemail.com  Thu Dec 17 08:25:18 2009
From: giles.weaver at googlemail.com (Giles Weaver)
Date: Thu, 17 Dec 2009 13:25:18 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <4B2A313E.3050300@googlemail.com>

I urge extreme caution with regards to using Google Groups.
My experiences with Google Groups have been less than satisfactory. I've 
administered several small groups and they have been plagued with 
delivery issues for a small subset of users. I've also known members to 
be unable to access a group that they are a member of, and find that 
Google Groups has "disappeared" their profile - despite having an 
otherwise fully functioning Google account (Gmail etc).

I'm not a fan of mailman, but at least the open-bio administrators have 
full control over the lists. I've known Chris to solve issues with the 
bioperl mailman list within minutes. You won't get that kind of service 
(if any) from Google.

Having looked at alternatives to Google Groups myself, the two things 
that have caught my attention are bbPress (a wordpress derived bulletin 
board) and Google Wave. Both are still under development.
bbPress <http://bbpress.org/> boards can be subscribed to via RSS (and 
possibly email), so users can have messages drop into their mail/news 
reader.
Wave looks promising, but I wouldn't touch it with a barge pole until 
mature Google free implementations take off, and that could be some time 
away.

Mirroring the open-bio mailman lists onto Google Groups seems to me the 
right way to go, but I think there should be a health warning on the 
list home pages!

Giles

On 16/12/2009 19:07, Chris Fields wrote:
> On Dec 16, 2009, at 12:40 PM, Istvan Albert wrote:
>
>    
>> On Wed, Dec 16, 2009 at 1:28 PM, Chris Fields<cjfields at illinois.edu>  wrote:
>>      
>>> Agreed.  With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.
>>>        
>> My fault for being insufficiently clear. I am not saying that having
>> archives is useless.
>>
>> It all needs to be framed in the mindset of an unexpected event
>> causing an archive to be  lost. Is that irreparable harm? For example
>> would having a hundred more active participants be worth the small
>> risk of losing the archives?
>>      
> Not that I think Google is in any danger of going under, or that Google Groups will cease to exist, but they have discontinued services in the past (notebook was one, and I recall others going away).
>
>    
>> I am just putting the 100 as a number out there, just to get you to
>> think. I think you all agree that at some level of extra participation
>> the risks would be well worth it.
>>      
> I understand your point, but I'm not really convinced this is something that can't be accomplished by simply mirroring the group and redirecting new users to sign up on the obf forums.
>
>    
>> Now I am convinced that a Google group would get more participation.
>> But is that 10 more people, one hundred, one thousand? That I do not
>> dare to guesstimate.
>>
>> (definitely more than 10, ;-) )
>>
>> Istvan
>>      
> I think mirroring the list is the best compromise.  I can't envision moving everything wholesale over to Google Groups for the reasons Hilmar has outlined.
>
> Just curious, but does anyone know whether Google groups are more or less susceptible to spamming?  The current mailman setup does keep out a vast majority of spam (I can't recall the last instance, actually).
>
> chris
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>    

From biopython at maubp.freeserve.co.uk  Thu Dec 17 08:35:25 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 13:35:25 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <4B2A313E.3050300@googlemail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
	<4B2A313E.3050300@googlemail.com>
Message-ID: <320fb6e00912170535r3a6d2a4cv37d852aff3671e6e@mail.gmail.com>

On Thu, Dec 17, 2009 at 1:25 PM, Giles Weaver
<giles.weaver at googlemail.com> wrote:
> I urge extreme caution with regards to using Google Groups.
> My experiences with Google Groups have been less than satisfactory.
> ...
>
> Mirroring the open-bio mailman lists onto Google Groups seems to me the
> right way to go, but I think there should be a health warning on the list
> home pages!

Thanks for the hard earned advice. I absolutely agree that *moving* to
GoogleGroups is a bad idea, and accept that *mirroring* may be worth
a try.

Given the BioPerl list is already trying this out, let's give that a week
or so, and if they think it works nicely then we could do the same for
Biopython.

Peter

From David.Lapointe at umassmed.edu  Thu Dec 17 07:42:15 2009
From: David.Lapointe at umassmed.edu (Lapointe, David)
Date: Thu, 17 Dec 2009 07:42:15 -0500
Subject: [Biopython] EMBOSS and Python
Message-ID: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>

I haven't used EMBOSS though the python module before so this hasn't
been an issue but even though I have  a working install of EMBOSS, all
of the EMBOSS tests seem to fail. I haven't seen any instructions for
this.

David 




From biopython at maubp.freeserve.co.uk  Thu Dec 17 12:04:11 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 17:04:11 +0000
Subject: [Biopython] EMBOSS and Python
In-Reply-To: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
Message-ID: <320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>

On Thu, Dec 17, 2009 at 12:42 PM, Lapointe, David
<David.Lapointe at umassmed.edu> wrote:
> I haven't used EMBOSS though the python module before so this hasn't
> been an issue but even though I have ?a working install of EMBOSS, all
> of the EMBOSS tests seem to fail. I haven't seen any instructions for
> this.

What version of Biopython do you have? And if you are talking about the
Biopython unit tests, could you post the output please?

What version of EMBOSS do you have? Some of the Biopython tests did
flag issues in EMBOSS which are fixed in their latest release.

Thanks,

Peter


From iua1 at psu.edu  Thu Dec 17 12:29:17 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Thu, 17 Dec 2009 12:29:17 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <C74FABFC.2DBF9%lpritc@scri.ac.uk>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<C74FABFC.2DBF9%lpritc@scri.ac.uk>
Message-ID: <c878cd560912170929k2dc7fe72sa3de81bc058e00@mail.gmail.com>

On Thu, Dec 17, 2009 at 4:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:

> Mailing lists are far more convenient - for me - than having to navigate to
> a website especially to check new messages on a particular subject.

Just for clarity:  nobody is suggesting to take that away. You can
*always* get the messages delivered via email. I think some of you get
a little bit defensive because you assume that the suggestion is about
messing with your system.

> Biopython is never likely to be more than a niche interest,

You are perfectly right here and that echoes my original sentiment!
What keeps biopython a niche interest is exactly the lack of community
building features. There obstacles in getting into it, so most won't.
It doesn't take much to discourage a newcomer.

best,

Istvan

-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From dalloliogm at gmail.com  Thu Dec 17 12:48:18 2009
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Thu, 17 Dec 2009 18:48:18 +0100
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com> 
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
Message-ID: <5aa3b3570912170948k1890aa5ft3c30c760718c3cbd@mail.gmail.com>

On Wed, Dec 16, 2009 at 6:26 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
>>
>> The alternative such as Google groups would be far superior in
>> attracting and building a community of developers and users as well.
>> Is this an idea that ?the owners of the list would entertain?
>>
>
> As far as I can tell from the limited documentation I found on
> Google Groups (maybe I was looking in the wrong place?) there
> is no way to import our existing decade long mail archives.
> That would be a major downside.


It seems that you can use a google/group to archive the messages from
a remote mailing list, but you can't import the older messages to the
google group:
- http://groups.google.com/support/bin/answer.py?hl=en&answer=46387

Maybe you can give it a try: just create a group on google and use it
as a mirror for the current mailing list. This way google users will
be able to use the google interface to search and read messages, but
they won't be able to post messages by mail. It won't arm anyone to
have a mirror of the messages in GG, except that it may be a bit
confusing for new users.

About other possibilities, it seems that there is not yet a way to
import a whole archive go GG:
- http://groups.google.com/group/Groups-Suggestions/browse_thread/thread/3eb3ed32dee6b97e

I have tried google/wave (I have invitations if anyone wants) but
please, avoid to switch to it yet because it is still very very buggy
and it will take them at least one year or so to make it useful.


> Also, using Google Groups would *require* all posters to have
> a Google Account - a potential sticking point for some.

I am still not sure about this: it seems that you can subscribe with
another address if you are invited, but you have to create a google
account (not necessarily a google mail) to subscribe to it manually.

It is a nice idea to switch to a fancier program for managing the
list, but maybe it would require too much time to switch to
google/groups.

>
> Peter
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it


From lpritc at scri.ac.uk  Thu Dec 17 12:55:52 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Thu, 17 Dec 2009 17:55:52 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <c878cd560912170929k2dc7fe72sa3de81bc058e00@mail.gmail.com>
Message-ID: <C7502128.2DC9B%lpritc@scri.ac.uk>

Hi,

On 17/12/2009 17:29, "Istvan Albert" <iua1 at psu.edu> wrote:

> On Thu, Dec 17, 2009 at 4:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> 
>> Mailing lists are far more convenient - for me - than having to navigate to
>> a website especially to check new messages on a particular subject.
> 
> Just for clarity:  nobody is suggesting to take that away. You can
> *always* get the messages delivered via email.

I wasn't worried that anyone would 'take it away'.  Though it must be said
that not all discussion systems allow email tracking.

> I think some of you get a little bit defensive because you assume that the
> suggestion is about messing with your system.

I don't think that's a fair characterisation.  So far, what I've seen is
open and thoughtful discussion of a comment you've made, and general
agreement that mirroring/archiving on Google Groups is a good idea.  Just
because someone doesn't agree with every point you make, that doesn't make
them defensive.

>> Biopython is never likely to be more than a niche interest,
> 
> You are perfectly right here and that echoes my original sentiment!
> What keeps biopython a niche interest is exactly the lack of community
> building features. There obstacles in getting into it, so most won't.
> It doesn't take much to discourage a newcomer.

That's not what I meant when I wrote that it's a niche interest.

Biopython is a niche interest because a user likely fulfils three - rather
unusual - criteria.  I believe that these are the big obstacles to
participation - not the software used for the mailing list:

- they program in Python
- they have an interest (likely professional or educational - not many
bioinformatics hobbyists out there) in bioinformatics
- they have bothered to investigate an existing general library for
bioinformatics in Python, rather than try to solve their problem from
scratch ;)

Add to that, that the mailing list is a forum for discussion which - along
with all other online fora for discussion, including Google Groups - is
inherently self-selecting for active members.  Taken together, this sets its
own upper limit to the user base, which in turn helps define what is a
sensible system to convey information between, and to, users.

The three criteria listed above do suggest a sufficient level of comfort
with the problem domain, such that Biopython's presence on Google Groups is
- in my opinion - unlikely to be the major draw for new contributors or
users.

I do worry for the future of research if signing up to a mailing list (which
you can do via the website; no subscription email is required) is an
insurmountable hurdle for young, apparently computer-literate scientists.
If that sort of thing really is a problem, it should at least keep
conference attendances down in years to come, as navigating their Byzantine
registration systems must drive them to endless despair...

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

From iua1 at psu.edu  Thu Dec 17 13:47:23 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Thu, 17 Dec 2009 13:47:23 -0500
Subject: [Biopython] some eye opening stats
Message-ID: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>

Hello Everyone,

So I ran some statistics on this group (see below) that includes the
entire past year. Make you own decisions based on it.

Here is one of my observation:  I find it saddening that I made the
list at number 18!  That's some niche list where one person posting
ten messages in a whole year gets to be at number 18. In fact I only
need three more posts to make myself top ten poster! Would you still
claim this to be a good way to establish, grow and interact with a
community?

I said this many times before, and I'll try for this to be the last
time I bring this up:

I believe biopython is a niche software tool because *YOU* are
limiting its reach *YOURSELVES* by making inappropriate decisions as
far as accessibility and community goes. It will stay so as long as
you don't recognize and act on this.

best regards,

Istvan Albert

=================================

Statistics from 1.12.2008 to 17.12.2009
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
***** People who have written most messages:
+----+-----Author-----------------------------------+--Msg-+-Percent-+
|  1 | biopython at maubp.freeserve.co.uk (Peter)   |  472 | 39.70 % |
|  2 | chapmanb at 50mail.com (Brad Chapman)        |   53 |  4.46 % |
|  3 | p.j.a.cock at googlemail.com (Peter Cock)    |   36 |  3.03 % |
|  4 | lueck at ipk-gatersleben.de (=?iso-8859-1?Q? |   27 |  2.27 % |
|  5 | mjldehoon at yahoo.com (Michiel de Hoon)     |   23 |  1.93 % |
|  6 | cjfields at illinois.edu (Chris Fields)      |   22 |  1.85 % |
|  7 | dalloliogm at gmail.com (Giovanni Marco Dall |   21 |  1.77 % |
|  8 | winda002 at student.otago.ac.nz (David Winte |   15 |  1.26 % |
|  9 | lpritc at scri.ac.uk (Leighton Pritchard)    |   14 |  1.18 % |
| 10 | cmckay at u.washington.edu (Cedar McKay)     |   13 |  1.09 % |
| 11 | italo.maia at gmail.com (Italo Maia)         |   12 |  1.01 % |
| 12 | kellrott at gmail.com (Kyle Ellrott)         |   12 |  1.01 % |
| 13 | rodrigo_faccioli at uol.com.br (Rodrigo facc |   12 |  1.01 % |
| 14 | bartek at rezolwenta.eu.org (Bartek Wilczyns |   12 |  1.01 % |
| 15 | anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Ro |   11 |  0.93 % |
| 16 | bartomas at gmail.com (bar tomas)            |   11 |  0.93 % |
| 17 | pzs at dcs.gla.ac.uk (Peter Saffrey)         |   11 |  0.93 % |
| 18 | iua1 at psu.edu (Istvan Albert)              |   10 |  0.84 % |
| 19 | dejmail at gmail.com (Liam Thompson)         |   10 |  0.84 % |
| 20 | stran104 at chapman.edu (Matthew Strand)     |   10 |  0.84 % |
| 21 | ibdeno at gmail.com (Miguel Ortiz Lombardia) |    9 |  0.76 % |
| 22 | pengyu.ut at gmail.com (Peng Yu)             |    9 |  0.76 % |
| 23 | yvan.strahm at bccs.uib.no (Yvan Strahm)     |    9 |  0.76 % |
| 24 | kelly.oakeson at utah.edu (Kelly F Oakeson)  |    9 |  0.76 % |
| 25 | carlos.borroto at gmail.com (Carlos Javier B |    9 |  0.76 % |
+----+----------------------------------------------+------+---------+
|    | other                                        |  337 | 28.34 % |
+----+----------------------------------------------+------+---------+

***** Best authors, by total size of their messages (w/o quoting):
+----+-----Author-------------------------------------------+-KBytes-+
|  1 | biopython at maubp.freeserve.co.uk (Peter)           |  391.4 |
|  2 | chapmanb at 50mail.com (Brad Chapman)                |   48.1 |
|  3 | lpritc at scri.ac.uk (Leighton Pritchard)            |   39.1 |
|  4 | p.j.a.cock at googlemail.com (Peter Cock)            |   35.7 |
|  5 | lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie |   27.9 |
|  6 | matzke at berkeley.edu (Nick Matzke)                 |   21.2 |
|  7 | animesh.agrawal at anu.edu.au (Animesh Agrawal)      |   21.1 |
|  8 | kelly.oakeson at utah.edu (Kelly F Oakeson)          |   16.7 |
|  9 | pzs at dcs.gla.ac.uk (Peter Saffrey)                 |   15.4 |
| 10 | dalloliogm at gmail.com (Giovanni Marco Dall'Olio)   |   14.7 |
| 11 | natassa_g_2000 at yahoo.com (natassa)                |   12.7 |
| 12 | hlapp at gmx.net (Hilmar Lapp)                       |   12.7 |
| 13 | mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydG |   12.5 |
| 14 | cjfields at illinois.edu (Chris Fields)              |   12.0 |
| 15 | bartek at rezolwenta.eu.org (Bartek Wilczynski)      |   11.6 |
| 16 | winda002 at student.otago.ac.nz (David Winter)       |   11.3 |
| 17 | cmckay at u.washington.edu (Cedar McKay)             |   11.0 |
| 18 | mjldehoon at yahoo.com (Michiel de Hoon)             |   10.9 |
| 19 | dejmail at gmail.com (Liam Thompson)                 |   10.6 |
| 20 | rodrigo_faccioli at uol.com.br (Rodrigo faccioli)    |   10.3 |
| 21 | anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues? |    9.7 |
| 22 | fufezan at uni-muenster.de (Christian Fufezan)       |    9.6 |
| 23 | kellrott at gmail.com (Kyle Ellrott)                 |    9.2 |
| 24 | peter at maubp.freeserve.co.uk (Peter)               |    8.9 |
| 25 | ibdeno at gmail.com (Miguel Ortiz Lombardia)         |    8.3 |
+----+------------------------------------------------------+--------+

***** Best authors, by average size of their message (w/o quoting):
+----+-----Author--------------------------------------------+-bytes-+
|  1 | agarbino at gmail.com (Alex Garbino)                  |  7991 |
|  2 | aduran at fhcrc.org (Duran, Alysha M)                 |  3893 |
|  3 | n.j.loman at bham.ac.uk (Nick Loman)                  |  3877 |
|  4 | mmueller at python-academy.de (=?ISO-8859-15?Q?Mike_M |  3816 |
|  5 | animesh.agrawal at anu.edu.au (Animesh Agrawal)       |  3598 |
|  6 | ivan at biodec.com (Ivan Rossi)                       |  2947 |
|  7 | thomas.e.keller at gmail.com (Thomas Keller)          |  2937 |
|  8 | lpritc at scri.ac.uk (Leighton Pritchard)             |  2860 |
|  9 | matzke at berkeley.edu (Nick Matzke)                  |  2717 |
| 10 | jhcepas at gmail.com (Jaime Huerta Cepas)             |  2705 |
| 11 | fufezan at uni-muenster.de (Christian Fufezan)        |  2447 |
| 12 | natassa_g_2000 at yahoo.com (natassa)                 |  2175 |
| 13 | bav853 at bham.ac.uk (Bhima A van der Molen)          |  1987 |
| 14 | kteague at bcgsc.ca (Kevin Teague)                    |  1932 |
| 15 | danielchubb at gmail.com (Daniel Chubb)               |  1923 |
| 16 | lueck at ipk-gatersleben.de (=?utf-8?Q?Stefanie_L=C3= |  1919 |
| 17 | dalloliogm at fastwebnet.it (Giovanni Marco Dall'Olio |  1915 |
| 18 | kelly.oakeson at utah.edu (Kelly F Oakeson)           |  1895 |
| 19 | bav853 at bham.ac.uk (Bhima Auro van der Molen)       |  1874 |
| 20 | darnells at dnastar.com (Steve Darnell)               |  1768 |
| 21 | gatoygata at hotmail.com (Joaquin Abian Monux)        |  1744 |
| 22 | srini_iyyer_bio at yahoo.com (Srinivas Iyyer)         |  1733 |
| 23 | bassbabyface at yahoo.com (Ben O'Loghlin)             |  1698 |
| 24 | hlapp at gmx.net (Hilmar Lapp)                        |  1624 |
| 25 | mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGl |  1603 |
+----+-------------------------------------------------------+-------+

***** Table showing the most successful subjects:
+----+----Subject-----------------------------------+--Msg-+-Percent-+
|  1 | [Biopython] suggestion: moving to the discus |   33 |  2.78 % |
|  2 | [Biopython] Problems parsing with PSIBlastPa |   32 |  2.69 % |
|  3 | [BioPython] The count method of a Seq (or Mu |   23 |  1.93 % |
|  4 | [Biopython] Biopython and Snow Leopard       |   21 |  1.77 % |
|  5 | [Biopython] Phylogenetic trees with biopytho |   16 |  1.35 % |
|  6 | [Biopython] Indexing large sequence files    |   15 |  1.26 % |
|  7 | [Biopython] SQL Alchemy based BioSQL         |   14 |  1.18 % |
|  8 | [BioPython] AlignIO: Sequences of different  |   13 |  1.09 % |
|  9 | [Biopython] searching for a human chromosome |   13 |  1.09 % |
| 10 | [Biopython] BLAST against mouse genome only  |   12 |  1.01 % |
| 11 | [Biopython] How to get sequences upstream of |   12 |  1.01 % |
| 12 | [Biopython] Parsing large blast files        |   11 |  0.93 % |
| 13 | [Biopython] Additions to the SeqRecord       |   11 |  0.93 % |
| 14 | [Biopython] Biopython & p3d                  |   11 |  0.93 % |
| 15 | [BioPython] Feedback from Biopython 1.50 bet |   10 |  0.84 % |
| 16 | [BioPython] Adding startswith and endswith m |   10 |  0.84 % |
| 17 | [Biopython] Bio.Sequencing.Ace               |   10 |  0.84 % |
| 18 | [Biopython] Entrez.read return value is type |   10 |  0.84 % |
| 19 | [Biopython] SeqIO for fasta conversion of Il |   10 |  0.84 % |
| 20 | [Biopython] Parsing problem                  |    9 |  0.76 % |
| 21 | [Biopython] Fasta.index_file: functionality  |    9 |  0.76 % |
| 22 | [Biopython] Adaptor trimmer and dimers       |    9 |  0.76 % |
| 23 | [BioPython] Is query_length really the lengt |    8 |  0.67 % |
| 24 | [BioPython] Reading Roche 454 binary SFF fil |    8 |  0.67 % |
| 25 | [Biopython] Writing into a PDB file using PD |    8 |  0.67 % |
+----+----------------------------------------------+------+---------+
|    | other                                        |  851 | 71.57 % |
+----+----------------------------------------------+------+---------+

***** Most used email clients:
+----+----Mailer------------------------------------+--Msg-+-Percent-+
|  1 | (unknown)                                    | 1189 |100.00 % |
+----+----------------------------------------------+------+---------+
|    | other                                        |    0 |  0.00 % |
+----+----------------------------------------------+------+---------+

***** Table of maximal quoting:
+----+-----Author------------------------------------------+-Percent-+
|  1 | golubchi at stats.ox.ac.uk (Tanya Golubchik)        | 94.68 % |
|  2 | fredgca at hotmail.com (Frederico Arnoldi)          | 92.56 % |
|  3 | srikrishnamohan at gmail.com (km)                   | 92.28 % |
|  4 | cmckay at u.washington.edu (Cedar Mckay)            | 88.19 % |
|  5 | harekrishna at gmail.com (Austin Davis-Richar       | 87.51 % |
|  6 | biopython.chen at gmail.com (chen Ku)               | 86.14 % |
|  7 | wgheath at gmail.com (William Heath)                | 85.12 % |
|  8 | jkhilmer at gmail.com (Jonathan Hilmer)             | 82.50 % |
|  9 | andrea at biodec.com (Andrea)                       | 80.82 % |
| 10 | nuin at genedrift.org (Paulo Nuin)                  | 79.90 % |
| 11 | lueck at ipk-gatersleben.de (lueck at ipk-gat       | 78.81 % |
| 12 | ibdeno at gmail.com (Miguel Ortiz Lombardia)        | 78.57 % |
| 13 | oda at georgetown.edu (Ogan ABAAN)                  | 75.33 % |
| 14 | sean.maceach at gmail.com (Sean MacEachern)         | 75.09 % |
| 15 | pengyu.ut at gmail.com (Peng Yu)                    | 73.17 % |
| 16 | fungazid at yahoo.com (Fungazid)                    | 71.57 % |
| 17 | yvan.strahm at bccs.uib.no (Yvan Strahm)            | 70.23 % |
| 18 | cjfields at illinois.edu (Chris Fields)             | 70.18 % |
| 19 | sdavis2 at mail.nih.gov (Sean Davis)                | 68.54 % |
| 20 | thomas.hamelryck at gmail.com (Thomas Hamelry       | 68.31 % |
| 21 | mjldehoon at yahoo.com (Michiel de Hoon)            | 66.49 % |
| 22 | mavata at gmail.com (Manu Tamminen)                 | 66.42 % |
| 23 | eric.talevich at gmail.com (Eric Talevich)          | 65.92 % |
| 24 | bsouthey at gmail.com (Bruce Southey)               | 64.70 % |
| 25 | biopythonlist at gmail.com (dr goettel)             | 64.53 % |
+----+-----------------------------------------------------+---------+
|    | average                                             | 44.57 % |
+----+-----------------------------------------------------+---------+

***** Graph showing number of messages written during hours of day:

100% ---------------------#--------------------------- - 146
 90% ---------------------#--------------------------- msgs
 80% ---------------------#---------------------------
 70% ---------------------#-#-------------------------
 60% ---------------------#-#-#-#-#---#---------------
 50% ---------------------#-#-#-#-#-#-#-#-------------
 40% ---------------------#-#-#-#-#-#-#-#-#-----------
 30% -----------------#-#-#-#-#-#-#-#-#-#-#-#---------
 20% -----------------#-#-#-#-#-#-#-#-#-#-#-#---------
 10% ---------------#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-
      * * * * * * * * * * * * * * * * * * * * * * * *
hour  0         5           11          17          23


***** Graph showing number of messages written during days of month:

100% -----------------------------#--------------------------------- - 74
 90% -----------------------------#-#------------------------------- msgs
 80% -----------------#-----------#-#-------------------------------
 70% -#---------------#---------#-#-#---#---------------------------
 60% -#-------#-#-----#---------#-#-#-#-#-#-#-----------------#-----
 50% -#-------#-#-----#-------#-#-#-#-#-#-#-#-----#-#---------#-----
 40% -#-#-----#-#-----#-----#-#-#-#-#-#-#-#-#-#---#-#---#---#-#-----
 30% -#-#-#-#-#-#---#-#-#---#-#-#-#-#-#-#-#-#-#---#-#-#-#-#-#-#-----
 20% -#-#-#-#-#-#-#-#-#-#---#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-
 10% -#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-
      * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 day  1         6           12          18          24            31


***** Graph showing number of messages written during days of week:

100% -------------#--------------- - 262
 90% ---------#---#--------------- msgs
 80% ---------#---#---#-----------
 70% -#---#---#---#---#-----------
 60% -#---#---#---#---#-----------
 50% -#---#---#---#---#-----------
 40% -#---#---#---#---#-----------
 30% -#---#---#---#---#-----------
 20% -#---#---#---#---#-----------
 10% -#---#---#---#---#---#---#---
      *   *   *   *   *   *   *
     Mon Tue Wed Thu Fri Sat Sun


***** Maximal quoting:
      Author     : andrea at biodec.com (Andrea)
      Subject    : [Biopython] Problems parsing with PSIBlastParser
      Date       : Thu, 15 Oct 2009 17:39:48 +0200
      Quote ratio: 98.63% / 15890 bytes

***** Longest message:
      Author     : chapmanb at 50mail.com (Brad Chapman)
      Subject    : [Biopython] Skipping over blank/erroneous Entrez.esummary()
      Date       : Wed, 7 Oct 2009 16:29:11 -0400
      Size       : 18503 bytes

***** Most successful subject:
      Subject    : [Biopython] suggestion: moving to the discussion
list to Google
      No. of msgs: 33
      Total size : 43527 bytes

***** Final summary:
      Total number of messages:             1189
      Total number of different authors:    159
      Total number of different subjects:   332
      Total size of messages (w/o headers): 1992170 bytes
      Average size of a message:            1675 bytes

***** Generated by MailListStat v1.3, (C) 2001-2003 <marki (at) nexin.sk>
***** See http://freshmeat.net/projects/mls for details...

-- 
Istvan Albert
http://www.personal.psu.edu/iua1

From mailinglist.honeypot at gmail.com  Thu Dec 17 14:08:55 2009
From: mailinglist.honeypot at gmail.com (Steve Lianoglou)
Date: Thu, 17 Dec 2009 14:08:55 -0500
Subject: [Biopython] some eye opening stats
In-Reply-To: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
References: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
Message-ID: <6E3B0A7F-476A-4417-A580-0FBCF4512763@gmail.com>

Hi Istvan,

On Dec 17, 2009, at 1:47 PM, Istvan Albert wrote:

> Hello Everyone,
> 
> So I ran some statistics on this group (see below) that includes the
> entire past year. Make you own decisions based on it.
> 
> Here is one of my observation:  I find it saddening that I made the
> list at number 18!  That's some niche list where one person posting
> ten messages in a whole year gets to be at number 18. In fact I only
> need three more posts to make myself top ten poster! Would you still
> claim this to be a good way to establish, grow and interact with a
> community?
> 
> I said this many times before, and I'll try for this to be the last
> time I bring this up:
> 
> I believe biopython is a niche software tool because *YOU* are
> limiting its reach *YOURSELVES* by making inappropriate decisions as
> far as accessibility and community goes. It will stay so as long as
> you don't recognize and act on this.

I haven't said much so far because (1) I'm not really actively using biopython atm, and (2) I'm largely indifferent about the choice of mailing list vs. web interface, but let's be serious here ... how can you be so confident in drawing any causality between your stats and the fact that biopython is using a mailing list?

You're arguing that since you are at # 18 w/ only 10 posts, it must be due to discussion about this project is confined to a mailing-list instead of a more "open" and "accessible" web group and the community needs to "act now" or ignore this at its peril.

Try doing the same experiment with the bioconductor mailing list, or (depending on how bold you're feeling)  the R-user mailing list. Discussion on both groups is via mailing-list only (or through gmane --- same can be said with this list) and come back with that report.

Now, go try your same experiment on the networkx or igraph user group. Both are hosted on google groups. With 10 posts, you'll likely be somewhere in the top 10 posters for the year.

Oh, even better: igraph just set up the mirror-do-hicky-whatever so you can access their mailing list via GG sometime in July:

http://groups.google.com/group/network-analysis-with-igraph/browse_thread/thread/77305d9b6bc6d35/c6a694e287936049?lnk=gst&q=google+groups#c6a694e287936049

Perhaps you'd like to see how traffic has changed on that list before and after that fact. I'm going to guess it wasn't by all that much, but that would at least be a better experiment you can use to base your hunches on.

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact



From cjfields at illinois.edu  Thu Dec 17 14:46:08 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Dec 2009 13:46:08 -0600
Subject: [Biopython] some eye opening stats
In-Reply-To: <6E3B0A7F-476A-4417-A580-0FBCF4512763@gmail.com>
References: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
	<6E3B0A7F-476A-4417-A580-0FBCF4512763@gmail.com>
Message-ID: <1ED2ED4E-F87E-4229-8D6A-8EF56C837D73@illinois.edu>

On Dec 17, 2009, at 1:08 PM, Steve Lianoglou wrote:

> Hi Istvan,
> 
> On Dec 17, 2009, at 1:47 PM, Istvan Albert wrote:
> 
>> Hello Everyone,
>> 
>> So I ran some statistics on this group (see below) that includes the
>> entire past year. Make you own decisions based on it.
>> 
>> Here is one of my observation:  I find it saddening that I made the
>> list at number 18!  That's some niche list where one person posting
>> ten messages in a whole year gets to be at number 18. In fact I only
>> need three more posts to make myself top ten poster! Would you still
>> claim this to be a good way to establish, grow and interact with a
>> community?
>> 
>> I said this many times before, and I'll try for this to be the last
>> time I bring this up:
>> 
>> I believe biopython is a niche software tool because *YOU* are
>> limiting its reach *YOURSELVES* by making inappropriate decisions as
>> far as accessibility and community goes. It will stay so as long as
>> you don't recognize and act on this.
> 
> I haven't said much so far because (1) I'm not really actively using biopython atm, and (2) I'm largely indifferent about the choice of mailing list vs. web interface, but let's be serious here ... how can you be so confident in drawing any causality between your stats and the fact that biopython is using a mailing list?
> 
> You're arguing that since you are at # 18 w/ only 10 posts, it must be due to discussion about this project is confined to a mailing-list instead of a more "open" and "accessible" web group and the community needs to "act now" or ignore this at its peril.
> 
> Try doing the same experiment with the bioconductor mailing list, or (depending on how bold you're feeling)  the R-user mailing list. Discussion on both groups is via mailing-list only (or through gmane --- same can be said with this list) and come back with that report.
> 
> Now, go try your same experiment on the networkx or igraph user group. Both are hosted on google groups. With 10 posts, you'll likely be somewhere in the top 10 posters for the year.
> 
> Oh, even better: igraph just set up the mirror-do-hicky-whatever so you can access their mailing list via GG sometime in July:
> 
> http://groups.google.com/group/network-analysis-with-igraph/browse_thread/thread/77305d9b6bc6d35/c6a694e287936049?lnk=gst&q=google+groups#c6a694e287936049
> 
> Perhaps you'd like to see how traffic has changed on that list before and after that fact. I'm going to guess it wasn't by all that much, but that would at least be a better experiment you can use to base your hunches on.
> 
> -steve
> 
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  |  Memorial Sloan-Kettering Cancer Center
>  |  Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact

This also doesn't factor participation via other means, such as other mail lists, IRC, etc.  As an example, the Perl Moose mail list is fairly low traffic, with a few posts a week, but the IRC channel is much more active.  Conversely, we in BioPerl tend to use the mail list over #bioperl (though I do use both if time permits). 

I think way too much time has been pushed into this topic, considering we've reached a pretty viable option, namely mirroring the list to Google Groups.  That seems satisfactory to everyone.  I fail to see the reason to press the issue (and everyone's ire) more?

chris




From jtomkins at ICR.org  Thu Dec 17 14:43:19 2009
From: jtomkins at ICR.org (Jeff Tomkins)
Date: Thu, 17 Dec 2009 13:43:19 -0600
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
Message-ID: <C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>

I installed biopython 1.52 as directed for OS X leopard.  Everything imports using the python prompt in the terminal, idle, ipython, wing ide, etc.  But when I run a standard python script (#!/usr/bin/python) in the shell it cannot locate Bio.  What setup feature have I missed?

Thanks, Jeff

From villahozbale at wisc.edu  Thu Dec 17 15:23:30 2009
From: villahozbale at wisc.edu (ANGEL VILLAHOZ-BALETA)
Date: Thu, 17 Dec 2009 14:23:30 -0600
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <7065_1261079798_ZZg0M1E7a5Xoa.00_C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<7065_1261079798_ZZg0M1E7a5Xoa.00_C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
Message-ID: <6f80a33d6a3f0.4b2a3ee2@wiscmail.wisc.edu>

Jeff,

Have you added the path of the libraries of Biopython to the shell variable called as PYTHONPATH?

Angel Villahoz-Baleta
Bioinformatics Programmer
University of Wisconsin-Madison

----- Original Message -----
From: Jeff Tomkins <jtomkins at ICR.org>
Date: Thursday, December 17, 2009 1:56 pm
Subject: [Biopython] Bio won't import in *.py scripts
To: "Biopython at lists.open-bio.org" <Biopython at lists.open-bio.org>

> I installed biopython 1.52 as directed for OS X leopard.  Everything 
> imports using the python prompt in the terminal, idle, ipython, wing 
> ide, etc.  But when I run a standard python script (#!/usr/bin/python) 
> in the shell it cannot locate Bio.  What setup feature have I missed?
> 
> Thanks, Jeff
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

From daniel at dim.fm.usp.br  Thu Dec 17 14:49:28 2009
From: daniel at dim.fm.usp.br (Daniel Silvestre)
Date: Thu, 17 Dec 2009 17:49:28 -0200
Subject: [Biopython] Why so few recipes in the cookbook?
Message-ID: <4B2A8B48.50302@dim.fm.usp.br>

Greeting everybody,

Is there a reason to the existence of so few recipes in Biopython
cookbook? Is there a task force to improve the documentation and related
stuff?

Usually I see perfect reusable and instructional recipes in blogs of
biopython users. But, they simply don't get to the cookbook.

Att.
Daniel


-- 
+---------------------------------------+
Daniel de A. M. M. Silvestre
LIM01 - Laborat?rio de Inform?tica M?dica - HCFMUSP
Sala 1349 - Depto. de Patologia
Faculdade de Medicina
Universidade de S?o Paulo
Av. Dr. Arnaldo, 455                | e-mail:  daniel at dim.fm.usp.br
Cerqueira C?sar                     |    Tel: +55-11-3061-7381
01246-903  -  S?o Paulo  -  SP      |    Cel: +55-11-8042-9369
BRASIL                              |  Skype: jarretinha

---------------------------------------------------------------------
Esta mensagem pode conter informacao confidencial.
Se voce nao for o destinatario ou a pessoa autorizada a receber
esta mensagem, nao podera usar, copiar ou divulgar as informacoes nela
contidas ou tomar qualquer acao baseada nessas informacoes. Se
voce recebeu esta mensagem por engano, favor avisar imediatamente o
remetente, respondendo o e-mail e, em seguida, apague-o.
Agradecemos sua cooperacao.

This message may contain confidential information.
If you are not the addressee or authorized person to receive it for the
addressee, you must not use, copy, disclose or take any action based on
this message or any information herein. If you have received this message
in error, please advise the sender immediately by replying this e-mail 
message and delete it.
Thanks in advance for your cooperation.
----------------------------------------------------------------------
               DIM   Faculdade de Medicina USP
----------------------------------------------------------------------

-------------- next part --------------
A non-text attachment was scrubbed...
Name: daniel.vcf
Type: text/x-vcard
Size: 375 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091217/a6313b8c/attachment.vcf>

From biopython at maubp.freeserve.co.uk  Thu Dec 17 16:16:42 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 21:16:42 +0000
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <4B2A8B48.50302@dim.fm.usp.br>
References: <4B2A8B48.50302@dim.fm.usp.br>
Message-ID: <320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>

2009/12/17 Daniel Silvestre <daniel at dim.fm.usp.br>:
> Greeting everybody,
>
> Is there a reason to the existence of so few recipes in Biopython
> cookbook? Is there a task force to improve the documentation
> and related stuff?

The cookbook wiki is still quite new (6 months or so), but the
idea was to encourage user participation. What would you like
to write about ;)

http://news.open-bio.org/news/2009/04/biopython-cookbook-wiki/

> Usually I see perfect reusable and instructional recipes in blogs of
> biopython users. But, they simply don't get to the cookbook.

Any specific examples? We can ask blog authors to put
some of their finished receipes on the wiki (with a link
back to the original).

Peter

P.S. Your message was delayed for moderation - probably the attachment?

From p.j.a.cock at googlemail.com  Thu Dec 17 17:59:07 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 17 Dec 2009 22:59:07 +0000
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
Message-ID: <320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>

Hi Jeff,

On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins <jtomkins at icr.org> wrote:
> I installed biopython 1.52 as directed for OS X leopard.
> ?Everything imports using the python prompt in the terminal,
> idle, ipython, wing ide, etc.

Good :)

> But when I run a standard python script (#!/usr/bin/python)
> in the shell it cannot locate Bio. ?What setup feature have I missed?

That does seem odd. You didn't call your script Bio.py did you?
Could you show us the error message?

Peter


From mjldehoon at yahoo.com  Fri Dec 18 03:35:40 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Dec 2009 00:35:40 -0800 (PST)
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>
Message-ID: <274100.45967.qm@web62402.mail.re1.yahoo.com>

If you start python in the terminal, does it start /usr/bin/python or a different python?

--- On Thu, 12/17/09, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [Biopython] Bio won't import in *.py scripts
> To: "Jeff Tomkins" <jtomkins at icr.org>
> Cc: "Biopython at lists.open-bio.org" <Biopython at lists.open-bio.org>
> Date: Thursday, December 17, 2009, 5:59 PM
> Hi Jeff,
> 
> On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins <jtomkins at icr.org>
> wrote:
> > I installed biopython 1.52 as directed for OS X
> leopard.
> > ?Everything imports using the python prompt in the
> terminal,
> > idle, ipython, wing ide, etc.
> 
> Good :)
> 
> > But when I run a standard python script
> (#!/usr/bin/python)
> > in the shell it cannot locate Bio. ?What setup
> feature have I missed?
> 
> That does seem odd. You didn't call your script Bio.py did
> you?
> Could you show us the error message?
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list? -? Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 


      


From lpritc at scri.ac.uk  Fri Dec 18 03:49:51 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Fri, 18 Dec 2009 08:49:51 +0000
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>
Message-ID: <C750F2AF.2DD39%lpritc@scri.ac.uk>

Hi,

On 17/12/2009 22:59, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> Hi Jeff,
> 
> On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins <jtomkins at icr.org> wrote:
>> I installed biopython 1.52 as directed for OS X leopard.
>> ?Everything imports using the python prompt in the terminal,
>> idle, ipython, wing ide, etc.
> 
> Good :)
> 
>> But when I run a standard python script (#!/usr/bin/python)
>> in the shell it cannot locate Bio. ?What setup feature have I missed?

It could be a $PATH issue.

On my Mac, /usr/bin/python is where Apple's Python lives.  I leave that
installation alone, and don't replace it to avoid problems with the OS's
potential use of Python (I had horrors with it back at 10.2).  My 'working'
version of Python is installed as /usr/local/bin/python.

lpmacpro:scripts lpritc$ /usr/bin/python
Python 2.5.1 (r251:54863, Feb  6 2009, 19:02:12)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
lpmacpro:scripts lpritc$ which python
/usr/local/bin/python
lpmacpro:scripts lpritc$ python
Python 2.6 (trunk:66714:66715M, Oct  1 2008, 18:36:04)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 
lpmacpro:scripts lpritc$ /usr/local/bin/python
Python 2.6 (trunk:66714:66715M, Oct  1 2008, 18:36:04)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 

You could check to see if your setup is similar.

What this means is that, as I have /usr/local/bin ahead of /usr/bin in my
$PATH (don't shout at me, everyone!), command-line invocation and module
installations with 'python setup.py' use the 'working' version, so install
modules under that version of Python only.  This would mean that if I had
#!/usr/bin/python at the head of my script, it would use Apple's Python, and
not see modules installed under my 'working' Python.  This would give the
same error you seem to describe:

lpmacpro:scripts lpritc$ python
Python 2.6 (trunk:66714:66715M, Oct  1 2008, 18:36:04)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> 
lpmacpro:scripts lpritc$ /usr/bin/python
Python 2.5.1 (r251:54863, Feb  6 2009, 19:02:12)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named Bio
>>> 

If this is the issue, then one way to get around the problem is to use
#!/usr/bin/env python at the top of your script so that it uses the Python
you would get from the command-line.  This is better in some ways, as you
don't have to make guesses about where the Python executable is installed
when you move the script to another machine, though it probably won't matter
on Windows, and there may be security issues that arise from this shortcut
under some circumstances.  If you're at all worried about those, just try
'which python' at the command-line, and substitute that location for
/usr/bin/python.

Cheers,

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________


From lpritc at scri.ac.uk  Fri Dec 18 05:16:42 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Fri, 18 Dec 2009 10:16:42 +0000
Subject: [Biopython] some eye opening stats
In-Reply-To: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
Message-ID: <C751070A.2DD4E%lpritc@scri.ac.uk>

On 17/12/2009 18:47, "Istvan Albert" <iua1 at psu.edu> wrote:
 
> Statistics from 1.12.2008 to 17.12.2009
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ***** People who have written most messages:
> +----+-----Author-----------------------------------+--Msg-+-Percent-+
[...]
> |  9 | lpritc at scri.ac.uk (Leighton Pritchard)    |   14 |  1.18 % |

> 
> ***** Best authors, by total size of their messages (w/o quoting):
> +----+-----Author-------------------------------------------+-KBytes-+
[...]
> |  3 | lpritc at scri.ac.uk (Leighton Pritchard)            |   39.1 |

Hmm... Peter has suggested privately that I do have a somewhat prolix and
flowery writing style - I guess he's right... ;)

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

From daniel at dim.fm.usp.br  Fri Dec 18 07:55:15 2009
From: daniel at dim.fm.usp.br (Daniel Silvestre)
Date: Fri, 18 Dec 2009 10:55:15 -0200
Subject: [Biopython] [Fwd: Re:  Why so few recipes in the cookbook?]
Message-ID: <4B2B7BB3.6090505@dim.fm.usp.br>


-- 
+---------------------------------------+
Daniel de A. M. M. Silvestre
LIM01 - Laborat?rio de Inform?tica M?dica - HCFMUSP
Sala 1349 - Depto. de Patologia
Faculdade de Medicina
Universidade de S?o Paulo
Av. Dr. Arnaldo, 455                | e-mail:  daniel at dim.fm.usp.br
Cerqueira C?sar                     |    Tel: +55-11-3061-7381
01246-903  -  S?o Paulo  -  SP      |    Cel: +55-11-8042-9369
BRASIL                              |  Skype: jarretinha

---------------------------------------------------------------------
Esta mensagem pode conter informacao confidencial.
Se voce nao for o destinatario ou a pessoa autorizada a receber
esta mensagem, nao podera usar, copiar ou divulgar as informacoes nela
contidas ou tomar qualquer acao baseada nessas informacoes. Se
voce recebeu esta mensagem por engano, favor avisar imediatamente o
remetente, respondendo o e-mail e, em seguida, apague-o.
Agradecemos sua cooperacao.

This message may contain confidential information.
If you are not the addressee or authorized person to receive it for the
addressee, you must not use, copy, disclose or take any action based on
this message or any information herein. If you have received this message
in error, please advise the sender immediately by replying this e-mail 
message and delete it.
Thanks in advance for your cooperation.
----------------------------------------------------------------------
               DIM   Faculdade de Medicina USP
----------------------------------------------------------------------

-------------- next part --------------
An embedded message was scrubbed...
From: unknown sender
Subject: no subject
Date: no date
Size: 6202
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091218/cd8bf70b/attachment.eml>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: daniel.vcf
Type: text/x-vcard
Size: 375 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091218/cd8bf70b/attachment.vcf>

From biopython at maubp.freeserve.co.uk  Fri Dec 18 07:57:30 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 12:57:30 +0000
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <4B2B6DE2.3080500@dim.fm.usp.br>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<sfid-+20091217-191648-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
Message-ID: <320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>

2009/12/18 Daniel Silvestre <daniel at dim.fm.usp.br>:
> Greetings again,
>
> There are some blogs like Programming for Scientists and Yokofakun with
> some usable code and tips.
>
> I do want to contribute, but there are no clear objectives stated to the
> cookbook writing process. What's the gist? Just some code snippets?
> Complete examples?

I would personally prefer concrete examples. The name "cookbook"
suggests a collection of complete recipes (rather than snippets).

> My teaching experience says that complete (and real) examples are the
> most wanted. For instance, even in the bioperl community only code
> snippets are available. So, the first question students ask me after a
> brief looking at the tutorials is smth like "Well, how do I use this in
> a directory tree?".
>
> What about a bioinformatics recipes in (bio)python?

Yes please :)

Are there any examples in the main "Biopython Tutorial and
Cookbook" which would in your opinion be better in the wiki?

> Att,
> Daniel
>
> P.S.:Is there a problem with my vcard? I can use a different sig.

Could you try no vcard attachment at all?

Peter

From biopython at maubp.freeserve.co.uk  Fri Dec 18 10:00:13 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 15:00:13 +0000
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <4B2B8CC3.3090307@dim.fm.usp.br>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
	<sfid-+20091218-105736-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>
	<4B2B8CC3.3090307@dim.fm.usp.br>
Message-ID: <320fb6e00912180700w49d3be87r53b1a5201c84461b@mail.gmail.com>

2009/12/18 Daniel Silvestre <daniel at dim.fm.usp.br>:
> Hi people,
>
> Actually, even the tutorial is a collection of snippets. I do consider
> and regard the effort. But, in order to attract biologists like myself
> and my colleagues we need something more pragmatic, problem
> driven.

Most of the tutorial is by its nature "snippets" but the Cookbook
chapter examples are more self standing. I suspect you are
looking for even more self contained things - complete examples
with a motivating rational, sample input data, etc.

> The prototipical workflow of a molecular biologist is:
>
> ?- Select a bunch of interesting genes in Entrez by clicking buttons and
> boxes;
>
> ?- BLAST some sequences and save the results in separated directories,
> normally one for each gene;
>
> ?- Struggle to extract useful statistics from the results, wich usually
> end in sorting and selecting the first few results;
>
> ?- Apply some analytical method (phylogeny reconstruction, mutation
> analysis, etc.) over the "filtered" results;
>
> ?- Restart the cycle until get satisfied or bored;
>
> By the way, in one of my classes I just taught the students (which can
> be grad students and professors) to use the fields of Entrez (molecular
> weight, range search, organism name, etc.) and they felt really powerful
> after that. For instance, they used to retrieve sequence lists of papers
> ?by hand !!!

I confess I don't know or use the full power of the Entrez website,
although that is in part since I can do clever stuff via their API ;)

> On the other hand, the ones who dare to use biopython tipically don't
> know how to glob things and other administrivia. So, without a real
> example only biology geeks like me get to the next step.
>
> There is a list of good recipes to start the cookbook:
>
> ?- How to retrieve and organize sequences and annotations from online
> databases using you own custom command line tool;

We touch on some of this already, e.g. search and retrieve examples
in the Bio.Entrez chapter of the tutorial. Are you looking for something
more in depth? Or using other databases?

> ?- How to setup/insert/retrieve a bunch of results into a local
> (personal) database (SQL);

Done, although not tagged as a cookbook specifically:
http://www.biopython.org/wiki/BioSQL

(The tutorial also points to this page)

> ?- How to annotate retrieved results with your own results;

Now here I'd like a little clarification about what you want to do.

My guess would be something I have considered working up
into a cookbook recipe, based one stuff I have already done:
Taking a small genome (viral or prokaryote), doing simple
gene predictions (e.g. ORF finding, pick first start codon,
or maybe calling a command line tool to do it for us), then
taking the predicted peptides and BLASTing them, then
making a GenBank file with these predicted features and
stick a summary of the BLAST results in their annotation.

However, while this is a reasonable first step, there are
downsides to encouraging this sort of naive approach to
annotation - the example would ideally have "Further
Reading" section, see for example Schnoes et al 2009.
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000605

> These are real problems faced by the common biologist. The proposed
> snippets in the tutorial and the cookbook is already dealt by a lot of
> web tools. It's absolutely necessary to show that biopython can increase
> the power and range of a biologist everyday work, and can possibly be
> automated.
>
> I have some examples to obtain statistics over genome sequences which
> address complete examples (including globbing filelists, retrieving from
> online databases, etc.) and can prepare them as a recipe. But, I could
> use some help . . .

If you start a cookbook entry on the wiki, and some outline
code, I'm sure we can as a group contribute ideas and tips
(particularly in the code, but maybe in the approach too). Or,
if you would rather, discuss some specific ideas here on the
mailing list first.

Note that some of these topics would be ideal for an OBF
project wide set of examples, with reference solutions in
Biopython, BioPerl, BioJava, BioRuby, etc. That is however
a much much bigger task.

Peter


From rjalves at igc.gulbenkian.pt  Fri Dec 18 12:17:44 2009
From: rjalves at igc.gulbenkian.pt (Renato Alves)
Date: Fri, 18 Dec 2009 17:17:44 +0000
Subject: [Biopython] SeqIO.index improvement suggestions
Message-ID: <4B2BB938.5030709@igc.gulbenkian.pt>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

[I tried submitting this message to the dev mailing list, but got
rejected since I'm not yet authorized to post there, so here it goes]

Hi everyone,

I'm working on changes to the Bio.SeqIO.index() function to make it more
consistent with the .read and .parse i.e. accept a filehandle instead of
a filename and also to include a way to cache the index into a file to
speed up the process.

The reason why we are implementing these two is because we were going to
implement our own index solution until we realized this was added to 1.52.

However the implementation in 1.52 has a few limitations.

One limitation is that we are using a gzipped database for the sake of
space and using gzip.open() to create the file-handle that would then be
passed to .parse(). The same was not doable with .index().
This is already implemented in
http://github.com/Unode/biopython/commit/6fc390151452e3ddf26a117269132125a3ffb3fe

The second is that we are going to use this feature to quick search the
database in a web application. Here we have the limitation that we don't
have persistence across web requests, which means that we would need to
recalculate the index on every web request.

The details of how we plan to implement this are the following:

cPickle the internal dictionary of offsets and save it on the database
folder with the same name as the database + .index. The consistency
check on whether the file has changed will be performed based on name
and timestamp. By default .index() will search for this file, check the
timestamp and use the cache if they match, otherwise they will be
recalculated. The save function will be available like:

>>> >>> d = SeqIO.index(...)
>>> >>> d.save(filename)

where filename is optional and defaults to "%s.index" % _handle.name

We already have a solution like this implemented with subclasses of
SeqIO._index, it's just a matter of reworking that and merge it into
BioPython if you consider a good addition to the code.

I would like to hear your comments and suggestions on this.

Regards,
Renato
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iEYEARECAAYFAksruTIACgkQYh11EUYTX9TymgCeL6hu3Uz//itSHx38k9KjfZJg
dGUAmwVCgaI9G/19VKiUolrXogelgrPs
=M+xw
-----END PGP SIGNATURE-----

From biopython at maubp.freeserve.co.uk  Fri Dec 18 16:39:11 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 21:39:11 +0000
Subject: [Biopython] SeqIO.index improvement suggestions
In-Reply-To: <4B2BB938.5030709@igc.gulbenkian.pt>
References: <4B2BB938.5030709@igc.gulbenkian.pt>
Message-ID: <320fb6e00912181339o1a5c4100w6f1957fd4d78d20d@mail.gmail.com>

Hi Renato,

I'm cooking dinner while writing this, so it won't be as in depth as
usual...

On Fri, Dec 18, 2009 at 5:17 PM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
>
> [I tried submitting this message to the dev mailing list, but got
> rejected since I'm not yet authorized to post there, so here it goes]

Have you definitely subscribed to the dev list? That should be all that
is required to post there, and this discussion would be better suited
there.

> Hi everyone,
>
> I'm working on changes to the Bio.SeqIO.index() function to make it more
> consistent with the .read and .parse i.e. accept a filehandle instead of
> a filename and also to include a way to cache the index into a file to
> speed up the process.
>
> The reason why we are implementing these two is because we were going to
> implement our own index solution until we realized this was added to 1.52.
>
> However the implementation in 1.52 has a few limitations.

Yes, this was designed to cover basic use cases in a general way,
but with the option in future to do other things - and in particular
saving the index to disk was kept in mind.

> One limitation is that we are using a gzipped database for the sake of
> space and using gzip.open() to create the file-handle that would then be
> passed to .parse(). The same was not doable with .index().
> This is already implemented in
> http://github.com/Unode/biopython/commit/6fc390151452e3ddf26a117269132125a3ffb3fe

That was a deliberate choice in that the index code wants to "own"
the handle. If other code has access to the handle, there is a risky
of different bits of code moving the handle pointer etc. But, if you
are careful it could be done.

There are also issues here in combination with saving the index.
With a filename, the code can easily reopen the file in the same
mode. With a handle, things are more tricky. You have non-file
handles to consider - such as the gzip example. There is also the
problem of recording the file mode (normal text, universal text,
or binary - which we will need for SFF files - code already written).

If we do change the code to allow handles, it would have to be
to allow handles OR filenames to be compatible with Biopython
1.52 and 1.53 (which take just filenames). This could be handled
as in Bio.SeqIO.convert(), which also allows both (which was the
subject of some discussion!).

> The second is that we are going to use this feature to quick search the
> database in a web application. Here we have the limitation that we don't
> have persistence across web requests, which means that we would need to
> recalculate the index on every web request.
>
> The details of how we plan to implement this are the following:
>
> cPickle the internal dictionary of offsets and save it on the database
> folder with the same name as the database + .index. The consistency
> check on whether the file has changed will be performed based on name
> and timestamp. By default .index() will search for this file, check the
> timestamp and use the cache if they match, otherwise they will be
> recalculated. The save function will be available like:
>
>>>> >>> d = SeqIO.index(...)
>>>> >>> d.save(filename)
>
> where filename is optional and defaults to "%s.index" % _handle.name
>
> We already have a solution like this implemented with subclasses of
> SeqIO._index, it's just a matter of reworking that and merge it into
> BioPython if you consider a good addition to the code.
>
> I would like to hear your comments and suggestions on this.

Yes, saving indexes is an obvious addition. I have explored
using pickle via shelve, and also SQLite - there are
implementations of this on my github respository, plus
begun to look into the existing OBF Open Biological
Database Access (OBDA) specification for cross project
compatibility. Other potential benefits here are reduced
memory usage if we don't keep the dictionary
of offsets in RAM.

http://github.com/peterjc/biopython/tree/index-shelve
http://github.com/peterjc/biopython/tree/index-sqlite

There is a potential complication with index sub-classes
which do more specialised indexing (e.g. GenBank files,
and for a more extreme case, SFF files). See:
http://github.com/peterjc/biopython/tree/sff-seqio

Anyway - great to see you are finding the code useful,
and have some quite similar ideas for how to extend
it further.

Peter

From biopython at maubp.freeserve.co.uk  Fri Dec 18 17:26:43 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 22:26:43 +0000
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <F10A5C1D-E3EF-48FF-BA43-715161600296@ICR.org>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
	<320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>
	<F10A5C1D-E3EF-48FF-BA43-715161600296@ICR.org>
Message-ID: <320fb6e00912181426i44b93b2co96a1a171a404dc5f@mail.gmail.com>

On Fri, Dec 18, 2009 at 6:25 PM, Jeff Tomkins <jtomkins at icr.org> wrote:
> I got some advice from Angel V. and added the following lines to my
> profile and the scripts now import Bio - it looks like ?it worked and
> fixed the issue. ?Thanks for getting back with me!
> -jeff
>
> PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/biopython-1.52-py2.5-macosx-10.3-fat.egg:${PYTHONPATH}"
> export PYTHONPATH
>

Excellent - and well done Angel for coming up with a working solution.

Peter


From pedro.al at fenhi.uh.cu  Fri Dec 18 17:25:29 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Fri, 18 Dec 2009 17:25:29 -0500
Subject: [Biopython] Superpose structures
Message-ID: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>

Hi all!!

I want to superpose some structures on a reference one.
The fixed selection is the backbone atoms of two residues and i want  
to superpose the rest of structures based in this atoms (for the same  
residues in the others structures, of course)

Reference selection:
[[<Atom O>, <Atom C>, <Atom CA>, <Atom N>], [<Atom O>, <Atom C>, <Atom  
CA>, <Atom N>]]

The moving selection is a similar nested list, with the list of the  
residues backbone atoms to move in the query structures....

How can i superpose these structures based in the backbone atoms of  
two residues?

Please help me...
Thanks




-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI





From p.j.a.cock at googlemail.com  Fri Dec 18 17:55:44 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 18 Dec 2009 22:55:44 +0000
Subject: [Biopython] Superpose structures
In-Reply-To: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
References: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
Message-ID: <320fb6e00912181455g680a8dbmdfa166bd820f06ed@mail.gmail.com>

2009/12/18 Yasser Almeida Hern?ndez <pedro.al at fenhi.uh.cu>:
> Hi all!!
>
> I want to superpose some structures on a reference one.
> The fixed selection is the backbone atoms of two residues and i want to
> superpose the rest of structures based in this atoms (for the same residues
> in the others structures, of course)
>
> Reference selection:
> [[<Atom O>, <Atom C>, <Atom CA>, <Atom N>], [<Atom O>, <Atom C>, <Atom CA>,
> <Atom N>]]
>
> The moving selection is a similar nested list, with the list of the residues
> backbone atoms to move in the query structures....
>
> How can i superpose these structures based in the backbone atoms of two
> residues?
>
> Please help me...
> Thanks

Does this example help?
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/

Peter


From mjldehoon at yahoo.com  Fri Dec 18 18:54:52 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Dec 2009 15:54:52 -0800 (PST)
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <1D3CBE1D-A7A9-4337-BE0A-E073C2B9A3CC@ICR.org>
Message-ID: <138394.60837.qm@web62408.mail.re1.yahoo.com>

Good to hear you found a solution.
Just for some background information:
The reason /usr/bin/python couldn't find Biopython is that you have Biopython installed with the python in /Library/Frameworks/Python.framework/Versions/2.5/bin/python. These two pythons don't know about each other, so anything you install for one python is not seen by the other python. If you want to use /usr/bin/python in your scripts, another solution would have been to install Biopython for that python using /usr/bin/python setup.py build followed by /usr/bin/python setup.py install. But usually it's better to leave the Apple-installed python in /usr/bin/python alone, and to install modules for /Library/Frameworks/Python.framework/Versions/2.5/bin/python, and use that python.

--Michiel. 


--- On Fri, 12/18/09, Jeff Tomkins <jtomkins at ICR.org> wrote:

> From: Jeff Tomkins <jtomkins at ICR.org>
> Subject: Re: [Biopython] Bio won't import in *.py scripts
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Date: Friday, December 18, 2009, 1:27 PM
> I got some advice from Angel V. and
> added the following lines to my .profile and the scripts now
> import Bio - it looks like? it worked and fixed the
> issue.? Thanks for getting back with me! 
> -jeff
> 
> PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/biopython-1.52-py2.5-macosx-10.3-fat.egg:${PYTHONPATH}"
> export PYTHONPATH
> 
> 
> On Dec 18, 2009, at 2:35 AM, Michiel de Hoon wrote:
> 
> > If you start python in the terminal, does it start
> /usr/bin/python or a different python?
> > 
> > --- On Thu, 12/17/09, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > 
> >> From: Peter Cock <p.j.a.cock at googlemail.com>
> >> Subject: Re: [Biopython] Bio won't import in *.py
> scripts
> >> To: "Jeff Tomkins" <jtomkins at icr.org>
> >> Cc: "Biopython at lists.open-bio.org"
> <Biopython at lists.open-bio.org>
> >> Date: Thursday, December 17, 2009, 5:59 PM
> >> Hi Jeff,
> >> 
> >> On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins
> <jtomkins at icr.org>
> >> wrote:
> >>> I installed biopython 1.52 as directed for OS
> X
> >> leopard.
> >>>? Everything imports using the python
> prompt in the
> >> terminal,
> >>> idle, ipython, wing ide, etc.
> >> 
> >> Good :)
> >> 
> >>> But when I run a standard python script
> >> (#!/usr/bin/python)
> >>> in the shell it cannot locate Bio.? What
> setup
> >> feature have I missed?
> >> 
> >> That does seem odd. You didn't call your script
> Bio.py did
> >> you?
> >> Could you show us the error message?
> >> 
> >> Peter
> >> 
> >> _______________________________________________
> >> Biopython mailing list? -? Biopython at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biopython
> >> 
> > 
> > 
> > 
> 
> 


      


From schafer at rostlab.org  Fri Dec 18 18:57:52 2009
From: schafer at rostlab.org (=?ISO-8859-1?Q?Christian_Sch=E4fer?=)
Date: Fri, 18 Dec 2009 18:57:52 -0500
Subject: [Biopython] Superpose structures
In-Reply-To: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
References: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
Message-ID: <4B2C1700.6080704@rostlab.org>

Hey,

an alternative would be to use the program ProFit 
(http://www.bioinf.org.uk/software/profit/index.html), which does a 
least-square fitting based on aligned residues of one reference and one 
or more mobile structures. It comes with an extensive yet easy 
comprehensible set of commands.
I'm currently using it myself within my Python code.

Chris

On 12/18/2009 05:25 PM, Yasser Almeida Hern?ndez wrote:
> Hi all!!
>
> I want to superpose some structures on a reference one.
> The fixed selection is the backbone atoms of two residues and i want to
> superpose the rest of structures based in this atoms (for the same
> residues in the others structures, of course)
>
> Reference selection:
> [[<Atom O>, <Atom C>, <Atom CA>, <Atom N>], [<Atom O>, <Atom C>, <Atom
> CA>, <Atom N>]]
>
> The moving selection is a similar nested list, with the list of the
> residues backbone atoms to move in the query structures....
>
> How can i superpose these structures based in the backbone atoms of two
> residues?
>
> Please help me...
> Thanks
>
>
>
>

From bjorn_johansson at bio.uminho.pt  Sat Dec 19 06:00:19 2009
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Sat, 19 Dec 2009 11:00:19 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
Message-ID: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>

Hi,

I am trying to get a restriction batch tha is limited to some enzymes with a
certain size.
I think that the lambdasplit might be used for this.

I have not found any examples of the use of the restrictionbatch.lambdasplit

rb = RestrictionBatch(first=[],suppliers=['F','R'])

rb2= rb.lambdasplit(lambda x: x.size==6)

this code does not work. Could someone give me an example on how to use
this?
I have tried to see docs on the lambda function in python, but I still could
not solve this.
grateful for any answer!
/bjorn

From biopython at maubp.freeserve.co.uk  Sat Dec 19 06:17:33 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 19 Dec 2009 11:17:33 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
Message-ID: <320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>

2009/12/19 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Hi,
>
> I am trying to get a restriction batch tha is limited to some enzymes with a
> certain size.
> I think that the lambdasplit might be used for this.
>
> I have not found any examples of the use of the restrictionbatch.lambdasplit
>
> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>
> rb2= rb.lambdasplit(lambda x: x.size==6)
>
> this code does not work. Could someone give me an example on how to use
> this?
> I have tried to see docs on the lambda function in python, but I still could
> not solve this.
> grateful for any answer!
> /bjorn

Hmm, no mention of lambdasplit in this doc:
http://biopython.org/DIST/docs/cookbook/Restriction.html

Also no mention in Tests/test_Restriction.py

Looking at the code, you need a function (which could
be defined with a python lambda but need not be)
which will be given as single argument and must
return a boolean (or rather, something which will be
evaluated as a boolean). You code looks fine:

>>> from Bio.Restriction import *
>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>> len(rb)
228
>>> len([x for x in rb if x.size==6])
128
>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>> len(rb2)
0

Either we have both misunderstood the point of
this function, or there is a bug in lambdasplit.

Please file a bug report:
http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython

Thanks,

Peter


From sohm at inaf.cnrs-gif.fr  Sat Dec 19 12:53:35 2009
From: sohm at inaf.cnrs-gif.fr (=?ISO-8859-1?Q?Fr=E9d=E9ric_Sohm?=)
Date: Sat, 19 Dec 2009 18:53:35 +0100
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
Message-ID: <4B2D131F.1080302@inaf.cnrs-gif.fr>

Hi Bj?rn, Peter,

The code is working for me.
I can't reproduce the bug.


 >>> from Bio.Restriction import *
 >>> rb = RestrictionBatch(first=[], suppliers=['F','R'])
 >>> len(rb)
228
 >>> len([x for x in rb if x.size == 6])
128
 >>> rb2 = rb.lambdasplit(lambda x : x.size == 6)
 >>> len(rb2)
128
 >>> len([x for x in rb if len(x) == 6])
128
 >>> rb3 = rb.lambdasplit(lambda x : len(x) == 6)
 >>> len(rb3)
128
 >>> rb2 == rb3
True
 >>> EcoRI in rb
True
 >>> EcoRI in rb2 and EcoRI in rb3
True
 >>> EcoRI.size == len(EcoRI) == 6
True
 >>>


I am a bit puzzled there, Peter's code should work (and is effectively 
working on my machine) ...

My setup is :

Debian Lenny
python 2.5.2 or python 2.4.6 (both tested)
Biopython : 1.45

What about yours ?


Best regards

Fred



Peter wrote:
> 2009/12/19 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
>> Hi,
>>
>> I am trying to get a restriction batch tha is limited to some enzymes with a
>> certain size.
>> I think that the lambdasplit might be used for this.
>>
>> I have not found any examples of the use of the restrictionbatch.lambdasplit
>>
>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>
>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>
>> this code does not work. Could someone give me an example on how to use
>> this?
>> I have tried to see docs on the lambda function in python, but I still could
>> not solve this.
>> grateful for any answer!
>> /bjorn
> 
> Hmm, no mention of lambdasplit in this doc:
> http://biopython.org/DIST/docs/cookbook/Restriction.html
> 
> Also no mention in Tests/test_Restriction.py
> 
> Looking at the code, you need a function (which could
> be defined with a python lambda but need not be)
> which will be given as single argument and must
> return a boolean (or rather, something which will be
> evaluated as a boolean). You code looks fine:
> 
>>>> from Bio.Restriction import *
>>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>>> len(rb)
> 228
>>>> len([x for x in rb if x.size==6])
> 128
>>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>>> len(rb2)
> 0
> 
> Either we have both misunderstood the point of
> this function, or there is a bug in lambdasplit.
> 
> Please file a bug report:
> http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython
> 
> Thanks,
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 

-- 
Fr?d?ric Sohm
GIS AMAGEN CNRS INRA
Equipe INRA U1126 "Morphogen?se du syst?me nerveux des Chord?s"
UPR 2197 DEPSN, CNRS
Institut de Neurobiologie A. Fessard
1 Avenue de la Terrasse
91 198 GIF-SUR -YVETTE
FRANCE
Phone: 33 1 69 82 34 12
Fax: 33 1 69 82 41 67
email: sohm at inaf.cnrs-gif.fr

From bjorn_johansson at bio.uminho.pt  Sun Dec 20 01:58:43 2009
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Sun, 20 Dec 2009 06:58:43 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <4B2D131F.1080302@inaf.cnrs-gif.fr>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
	<4B2D131F.1080302@inaf.cnrs-gif.fr>
Message-ID: <c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>

Hi,
I copied the output from running Frederics example on my machine below:

bjorn at bjorn-laptop:~/wikidpad/user_extensions/SeqTools$ python
Python 2.6.4 (r264:75706, Dec  7 2009, 18:45:15)
[GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.Restriction import *
>>> rb = RestrictionBatch(first=[], suppliers=['F','R'])
>>> len(rb)
228
>>> len([x for x in rb if x.size == 6])
128
>>> rb2 = rb.lambdasplit(lambda x : x.size == 6)
>>> len(rb2)
0
>>> len([x for x in rb if len(x) == 6])
128
>>> len([x for x in rb if len(x) == 6])
128
>>> rb3 = rb.lambdasplit(lambda x : len(x) == 6)
>>> len(rb3)
0
>>> rb2 == rb3
True
>>> EcoRI in rb
True
>>> EcoRI in rb2 and EcoRI in rb3
False
>>> EcoRI.size == len(EcoRI) == 6
True
>>>

The lambdasplit does not seem to be working for me. I use python 2.6.4 on
ubuntu karmic
How can I print the biooython version?
thansk for your help!
/bjorn


2009/12/19 Fr?d?ric Sohm <sohm at inaf.cnrs-gif.fr>

> Hi Bj?rn, Peter,
>
> The code is working for me.
> I can't reproduce the bug.
>
>
>
> >>> from Bio.Restriction import *
> >>> rb = RestrictionBatch(first=[], suppliers=['F','R'])
> >>> len(rb)
> 228
> >>> len([x for x in rb if x.size == 6])
> 128
> >>> rb2 = rb.lambdasplit(lambda x : x.size == 6)
> >>> len(rb2)
> 128
> >>> len([x for x in rb if len(x) == 6])
> 128
> >>> rb3 = rb.lambdasplit(lambda x : len(x) == 6)
> >>> len(rb3)
> 128
> >>> rb2 == rb3
> True
> >>> EcoRI in rb
> True
> >>> EcoRI in rb2 and EcoRI in rb3
> True
> >>> EcoRI.size == len(EcoRI) == 6
> True
> >>>
>
>
> I am a bit puzzled there, Peter's code should work (and is effectively
> working on my machine) ...
>
> My setup is :
>
> Debian Lenny
> python 2.5.2 or python 2.4.6 (both tested)
> Biopython : 1.45
>
> What about yours ?
>
>
> Best regards
>
> Fred
>
>
>
> Peter wrote:
>
>> 2009/12/19 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
>>
>>> Hi,
>>>
>>> I am trying to get a restriction batch tha is limited to some enzymes
>>> with a
>>> certain size.
>>> I think that the lambdasplit might be used for this.
>>>
>>> I have not found any examples of the use of the
>>> restrictionbatch.lambdasplit
>>>
>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>>
>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>>
>>> this code does not work. Could someone give me an example on how to use
>>> this?
>>> I have tried to see docs on the lambda function in python, but I still
>>> could
>>> not solve this.
>>> grateful for any answer!
>>> /bjorn
>>>
>>
>> Hmm, no mention of lambdasplit in this doc:
>> http://biopython.org/DIST/docs/cookbook/Restriction.html
>>
>> Also no mention in Tests/test_Restriction.py
>>
>> Looking at the code, you need a function (which could
>> be defined with a python lambda but need not be)
>> which will be given as single argument and must
>> return a boolean (or rather, something which will be
>> evaluated as a boolean). You code looks fine:
>>
>>  from Bio.Restriction import *
>>>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>>>> len(rb)
>>>>>
>>>> 228
>>
>>> len([x for x in rb if x.size==6])
>>>>>
>>>> 128
>>
>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>>>> len(rb2)
>>>>>
>>>> 0
>>
>> Either we have both misunderstood the point of
>> this function, or there is a bug in lambdasplit.
>>
>> Please file a bug report:
>> http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython
>>
>> Thanks,
>>
>> Peter
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>>
> --
> Fr?d?ric Sohm
> GIS AMAGEN CNRS INRA
> Equipe INRA U1126 "Morphogen?se du syst?me nerveux des Chord?s"
> UPR 2197 DEPSN, CNRS
> Institut de Neurobiologie A. Fessard
> 1 Avenue de la Terrasse
> 91 198 GIF-SUR -YVETTE
> FRANCE
> Phone: 33 1 69 82 34 12
> Fax: 33 1 69 82 41 67
> email: sohm at inaf.cnrs-gif.fr
>



-- 
______O_________oO________oO______o_______oO__
Bj?rn Johansson
Assistant Professor
Departament of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL
http://www.bio.uminho.pt
http://sites.google.com/site/bjornhome
Work (direct) +351-253 601517
Private mob. +351-967 147 704
Dept of Biology (secretariate) +351-253 60 4310
Dept of Biology (fax) +351-253 678980


From biopython at maubp.freeserve.co.uk  Sun Dec 20 13:01:56 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 20 Dec 2009 18:01:56 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
	<4B2D131F.1080302@inaf.cnrs-gif.fr>
	<c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>
Message-ID: <320fb6e00912201001j24acc005uf7ad6d88f25bbf3d@mail.gmail.com>

2009/12/20 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Hi,
> I copied the output from running Frederics example on my machine below:
>
> bjorn at bjorn-laptop:~/wikidpad/user_extensions/SeqTools$ python
> Python 2.6.4 (r264:75706, Dec ?7 2009, 18:45:15)
> [GCC 4.4.1] on linux2
> ...
> The lambdasplit does not seem to be working for me. I use python
> 2.6.4 on ubuntu karmic

I was using the same version of Python (also on Linux Ubuntu Karmic).
This looks like it could be a Python 2.6 specific problem.

> How can I print the biooython version?
> thansk for your help!
> /bjorn

Its in the FAQ in the Tutorial, at the Python prompt just do:

import Bio
print Bio.__version__

Peter


From biopython at maubp.freeserve.co.uk  Mon Dec 21 07:03:34 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 21 Dec 2009 12:03:34 +0000
Subject: [Biopython] Fwd:  Why so few recipes in the cookbook?
In-Reply-To: <320fb6e00912181442r60348fcwf15776a0451bc6a1@mail.gmail.com>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
	<320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>
	<4B2B8CC3.3090307@dim.fm.usp.br>
	<sfid-+20091218-130021-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912180700w49d3be87r53b1a5201c84461b@mail.gmail.com>
	<4B2BAE35.2070404@dim.fm.usp.br>
	<320fb6e00912181442r60348fcwf15776a0451bc6a1@mail.gmail.com>
Message-ID: <320fb6e00912210403q5dd4c0d7xf06c9a850ecde9db@mail.gmail.com>

I just checked with Daniel to make sure he was happy for me to
forward this back to the mailing list.

Peter
---------- Forwarded message ----------
From: Peter <biopython at maubp.freeserve.co.uk>
Date: Fri, Dec 18, 2009 at 10:42 PM
Subject: Re: [Biopython] Why so few recipes in the cookbook?
To: Daniel Silvestre <daniel at dim.fm.usp.br>


Hi Daniel,

Do you mind if I send this to the list too?

2009/12/18 Daniel Silvestre <daniel at dim.fm.usp.br>:
>>
>> I confess I don't know or use the full power of the Entrez website,
>> although that is in part since I can do clever stuff via their API ;)
>
> This is exactly what we want to do when get to the Entrez interface.
> But, the information "How to submit complex query" is hidden (and
> scattered) under many layers of web pages.
>
> The ability to do such things in a more customized way is the dream of
> all life science guy.

This is partly down to the NCBI's Entrez documentation - a lots of
the examples in the Biopython tutorial took some serious exploration
to get working, including trawling the net for other Entrez users (in
other languages). I hope that we've managed to make things clearer.

> While this tutorial is enough to CS-oriented guys, it's a really big
> step to grasp such information for people from other communities.
> That's why I'm always a little confused about the idea behind bio
> projects. If the idea is programming of scientists, the approach is
> way too CS.

You are probably right in that the Bio* projects do cater more to a
programming scientist than a wet biologist - not that there aren't
people that can and do both. You have to be able to program to
take full advantage of any of the Bio* kits. However, there are a
number of front ends, webpages, etc which use them internally.

>> Now here I'd like a little clarification about what you want to do.
>>
>> My guess would be something I have considered working up
>> into a cookbook recipe, based one stuff I have already done:
>> Taking a small genome (viral or prokaryote), doing simple
>> gene predictions (e.g. ORF finding, pick first start codon,
>> or maybe calling a command line tool to do it for us), then
>> taking the predicted peptides and BLASTing them, then
>> making a GenBank file with these predicted features and
>> stick a summary of the BLAST results in their annotation.
>>
>> However, while this is a reasonable first step, there are
>> downsides to encouraging this sort of naive approach to
>> annotation - the example would ideally have "Further
>> Reading" section, see for example Schnoes et al 2009.
>> http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000605
>>
>
> That's exactly my point. Without a complete recipe with a
> specific motivation and a clear stated problem behinf it,
> people will continue with this kind of behavior.

We agree here.

> And I don't see why one need to start simple. The first time I've
> entered in a molbio lab was to carry on a old fashioned gene cloning
> procedure. This is a simple procedure. How do this compares to the
> simple examples we see on bio project tutorials?

I see the tutorial as a teaching aid, and many of the cookbook
examples also. For someone learning to program, an overly
complicated example is intimidating. This is not to say we can't
have some complex cookbook entries too.

i.e. I thank for learning to program, you need to start simple,
and build up the complexity gradually.

>>> These are real problems faced by the common biologist. The proposed
>>> snippets in the tutorial and the cookbook is already dealt by a lot of
>>> web tools. It's absolutely necessary to show that biopython can increase
>>> the power and range of a biologist everyday work, and can possibly be
>>> automated.
>>>
>>> I have some examples to obtain statistics over genome sequences which
>>> address complete examples (including globbing filelists, retrieving from
>>> online databases, etc.) and can prepare them as a recipe. But, I could
>>> use some help . . .
>>
>> If you start a cookbook entry on the wiki, and some outline
>> code, I'm sure we can as a group contribute ideas and tips
>> (particularly in the code, but maybe in the approach too). Or,
>> if you would rather, discuss some specific ideas here on the
>> mailing list first.
>>
>> Note that some of these topics would be ideal for an OBF
>> project wide set of examples, with reference solutions in
>> Biopython, BioPerl, BioJava, BioRuby, etc. That is however
>> a much much bigger task.
>
> I think that there is no need to worry about big things right now. By
> the very nature of programming, people will mirror ideas from one
> another. I've tried a similar approach in the bioperl community. But,
> for the pragmatic life scientist, perl is over expressive while python
> has a much higher first encounter acceptance rate (I'm not sure why,
> tough...).
>
> My idea is not a master blaster cookbook, just to assemble simple ideas
> that work for the everyday user, be this guy a CS or a life scientist.
>
> How do this sound to you?

Wonderful :)

(And I would agree with you that Python is probably easier to teach
to beginners than Perl)

Peter

From chapmanb at 50mail.com  Mon Dec 21 08:11:48 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 21 Dec 2009 08:11:48 -0500
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <320fb6e00912210403q5dd4c0d7xf06c9a850ecde9db@mail.gmail.com>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
	<320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>
	<4B2B8CC3.3090307@dim.fm.usp.br>
	<sfid-+20091218-130021-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912180700w49d3be87r53b1a5201c84461b@mail.gmail.com>
	<4B2BAE35.2070404@dim.fm.usp.br>
	<320fb6e00912181442r60348fcwf15776a0451bc6a1@mail.gmail.com>
	<320fb6e00912210403q5dd4c0d7xf06c9a850ecde9db@mail.gmail.com>
Message-ID: <20091221131148.GB21580@sobchak.mgh.harvard.edu>

Peter and Daniel;
Really interesting discussion. Documentation is an area that can
always use more work to appeal to a wider audience.

Daniel:
> > While this tutorial is enough to CS-oriented guys, it's a really big
> > step to grasp such information for people from other communities.
> > That's why I'm always a little confused about the idea behind bio
> > projects. If the idea is programming of scientists, the approach is
> > way too CS.

This stresses why we actively encourage contributions from biologists
as well. Many of the contributors to Biopython tend more towards the
programming/bioinformatics side, since that experience helps in building
up and appreciating a re-usable toolkit. When those same people write
documentation, it is going to be naturally biased towards the sort of
work they do.

I'd definitely encourage you, and anyone else who might be
interested, to build up examples that are more intuitive to those
coming at the work from a different starting point. This is exactly
the idea behind starting up the cookbook on the wiki; it's all
freely editable, so dig right in.

Brad

From biopython at maubp.freeserve.co.uk  Tue Dec 22 11:22:24 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 22 Dec 2009 16:22:24 +0000
Subject: [Biopython] EMBOSS and Python
In-Reply-To: <5ECA525B88314B48870E4AC72E3B9AF2045A70FE@EDUNIVMAIL05.ad.umassmed.edu>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<5ECA525B88314B48870E4AC72E3B9AF2045A70FE@EDUNIVMAIL05.ad.umassmed.edu>
Message-ID: <320fb6e00912220822m7e1c81c5h113a642f1336b328@mail.gmail.com>

Hi David,

I cc'd the mailing list again.

On Tue, Dec 22, 2009 at 4:02 PM, Lapointe, David
<David.Lapointe at umassmed.edu> wrote:
>
> Hi Peter,
>
> I have current version for both EMBOSS (6.1.0) and BioPython (1.53).

Do you have the original unpatched EMBOSS 6.1.0, or the latest
patched version, currently EMBOSS 6.1.0 patch 3? See:
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch

> I looked at the
> code for the unit tests (asis) and the problem might be there, as I could run the
> test fine by hand.

Could you clarify what you meant by "I could run the test fine by hand"?

> Shouldn't there be a '-' in front of asequence?
>
> ? ?def test_water_file(self):
> ? ? ? ?"""water with the asis trick, output to a file."""
> ? ? ? ?#Setup, try a mixture of keyword arguments and later additions:
> ? ? ? ?cline = WaterCommandline(cmd=exes["water"],
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? gapopen="10", gapextend="0.5")
> ? ? ? ?#Try using both human readable names, and the literal ones:
> ? ? ? ?cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
> ? ? ? ?cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
>
> David

Good question, but no. The test is confirming the set_parameter method
supports both these ways of setting the parameters. This is now a semi-
obsolete method - the preferred way would be to use bsequence in the
constructor arguments, or the bsequence property.

Interestingly the test output also indicates issues calling dnal (which
is nothing to do with EMBOSS), yet at least one other command line
tool test seem to be running OK (Clustalw).

Peter


From silvio.tschapke at googlemail.com  Wed Dec 23 05:57:58 2009
From: silvio.tschapke at googlemail.com (Silvio Tschapke)
Date: Wed, 23 Dec 2009 11:57:58 +0100
Subject: [Biopython] cannot find elink_090910.dtd
Message-ID: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>

Hi all,

I am using ubuntu 9.10, python 2.6 and biopython 1.53
But while running these two lines of code

pmid = "14630660"
results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid)

I get the following error message posted at the bottom.
So I searched at the proposed websites and in the web for
"elink_090910.dtd" without success.
I only found the files for elink_020511.dtd and something for 2010. But
nothing related to elink_090910.dtd.
Could you please help me how I can solve this problem?

Cheers and merry christmas,
Silvio


Traceback (most recent call last):
  File "/home/silvio/programming/python/first steps/biopythonTutorial.py",
line 17, in <module>
    results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid))
  File
"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/__init__.py",
line 258, in read
    record = handler.read(handle)
  File
"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
line 108, in read
    self.parser.ParseFile(handle)
  File
"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
line 377, in externalEntityRefHandler
    raise RuntimeError(message)
RuntimeError: Unable to load DTD file eLink_090910.dtd.

From biopython at maubp.freeserve.co.uk  Wed Dec 23 07:10:17 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 12:10:17 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
Message-ID: <320fb6e00912230410hf895e3sa999b0489e0b9e5e@mail.gmail.com>

On Wed, Dec 23, 2009 at 10:57 AM, Silvio Tschapke
<silvio.tschapke at googlemail.com> wrote:
> Hi all,
>
> I am using ubuntu 9.10, python 2.6 and biopython 1.53
> But while running these two lines of code
>
> pmid = "14630660"
> results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid)
>
> I get the following error message posted at the bottom.
> So I searched at the proposed websites and in the web for
> "elink_090910.dtd" without success.
> I only found the files for elink_020511.dtd and something for 2010. But
> nothing related to elink_090910.dtd.
> Could you please help me how I can solve this problem?
>
> Cheers and merry christmas,
> Silvio

Hi Silvio,

Yep, I don't have that file either, it looks like we missed it :(
The NCBI website don't make it easy to find (as far as I could
tell, none of the DTD pages list this file). However, the XML
tells us where to try:
http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/eLink_090910.dtd

I've added this to our repository, and it will be in the next release.

You'll need to download that DTD file. How did you install Biopython?
It looks like the file would need to go inside the egg - so it might
be easier to (re)install from source with this extra file in the source
code subdirectory Bio/Entrez/DTDs. Or start by grabbing the latest
Biopython code from git. Does that make sense?

However, even with the DTD file, I'm getting "Error 111
(Connection refused)" for your example. Maybe the NCBI are
doing some maintenance work at the moment?

Merry Christmas,

Peter

From konrad.koehler at mac.com  Wed Dec 23 06:22:32 2009
From: konrad.koehler at mac.com (Konrad Koehler)
Date: Wed, 23 Dec 2009 12:22:32 +0100
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
Message-ID: <11374559688483741089292458484266867741-Webmail@me.com>

Hi  Silvio,

This appears to be a temporary glitch with the Entrez database and not biopython.  For example, the following link should display the abstract, but current does not:

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=14630660&dopt=Abstract

A lot of other things in Entrez appear to be broken. For example internal links to RefSeq records from EntrezGene do not currently work.  For example, the RefSeq link from here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2645

to here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2645

doesn't work either.

Hopefully the problems in the Entrez database will be sorted out shortly.  Cheers,

Konrad

On Wednesday, December 23, 2009, at 11:57AM, "Silvio Tschapke" <silvio.tschapke at googlemail.com> wrote:
>Hi all,
>
>I am using ubuntu 9.10, python 2.6 and biopython 1.53
>But while running these two lines of code
>
>pmid = "14630660"
>results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid)
>
>I get the following error message posted at the bottom.
>So I searched at the proposed websites and in the web for
>"elink_090910.dtd" without success.
>I only found the files for elink_020511.dtd and something for 2010. But
>nothing related to elink_090910.dtd.
>Could you please help me how I can solve this problem?
>
>Cheers and merry christmas,
>Silvio
>
>
>Traceback (most recent call last):
>  File "/home/silvio/programming/python/first steps/biopythonTutorial.py",
>line 17, in <module>
>    results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid))
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/__init__.py",
>line 258, in read
>    record = handler.read(handle)
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
>line 108, in read
>    self.parser.ParseFile(handle)
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
>line 377, in externalEntityRefHandler
>    raise RuntimeError(message)
>RuntimeError: Unable to load DTD file eLink_090910.dtd.
>_______________________________________________
>Biopython mailing list  -  Biopython at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biopython
>
>

From biopython at maubp.freeserve.co.uk  Wed Dec 23 07:28:37 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 12:28:37 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <11374559688483741089292458484266867741-Webmail@me.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
Message-ID: <320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>

On Wed, Dec 23, 2009 at 11:22 AM, Konrad Koehler wrote:
> Hi ?Silvio,
>
> This appears to be a temporary glitch with the Entrez database and not biopython.
>

Your URLs seem to be working now :)

On Wed, Dec 23, 2009 at 12:10 PM, Peter wrote:
>
> However, even with the DTD file, I'm getting "Error 111
> (Connection refused)" for your example. Maybe the NCBI are
> doing some maintenance work at the moment?

This is also working now. Its looks like both a temporary glitch at the
NCBI, and the problem with Biopython missing eLink_090910.dtd

Peter


From biopython at maubp.freeserve.co.uk  Wed Dec 23 09:03:04 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 14:03:04 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
	<320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>
	<d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
Message-ID: <320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>

On Wed, Dec 23, 2009 at 1:29 PM, Silvio Tschapke
<silvio.tschapke at googlemail.com> wrote:
>
> I have copied the DTD file in
> /usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/DTDs/
> now and it seems to work. Great! I have installed Biopython with
>
> python setup.py build
> python setup.py test
> sudo python setup.py install

OK - good :)

> But will I have the same problems when I use eSearch, or eQuery and so
> on? Because all of the DTD will not be up to date. So far I only
> copied this DTD for eLink you posted.

I *hope* that this was the only DTD file we were missing. If
not, please do let us know so we can fix this for other users.

In the short term, you would again need to download and fetch
other missing DTD files in the same way. You can generally look
at the start of the XML file to see where the DTD can be found, e.g.

>>> from Bio import Entrez
>>> Entrez.email = "your.name.here at example.com"
>>> print Entrez.elink(dbfrom="pubmed", id="12345678").read(300)
<?xml version="1.0"?>
<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 10 August
2009//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_090910.dtd">
<eLinkResult>
...

Thanks,

Peter

From bjorn_johansson at bio.uminho.pt  Wed Dec 23 09:42:37 2009
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Wed, 23 Dec 2009 14:42:37 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <320fb6e00912201001j24acc005uf7ad6d88f25bbf3d@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
	<4B2D131F.1080302@inaf.cnrs-gif.fr>
	<c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>
	<320fb6e00912201001j24acc005uf7ad6d88f25bbf3d@mail.gmail.com>
Message-ID: <c3ee7c590912230642v6efddad2laf766de37071ee0a@mail.gmail.com>

Hi, my Biopython version seems to be 1.52
bjorn at bjorn-laptop:~$ python
Python 2.6.4 (r264:75706, Dec  7 2009, 18:45:15)
[GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> Bio.__version__
'1.52'

This works really well to get only five cutters and above (rb is a
restriction batch):

rb = [x for x in rb if len(x) > 4]

which was what I wanted initially.
Thanks for all help!
Happy hollidays!
/bjorn


2009/12/20 Peter <biopython at maubp.freeserve.co.uk>

> 2009/12/20 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> > Hi,
> > I copied the output from running Frederics example on my machine below:
> >
> > bjorn at bjorn-laptop:~/wikidpad/user_extensions/SeqTools$ python
> > Python 2.6.4 (r264:75706, Dec  7 2009, 18:45:15)
> > [GCC 4.4.1] on linux2
> > ...
> > The lambdasplit does not seem to be working for me. I use python
> > 2.6.4 on ubuntu karmic
>
> I was using the same version of Python (also on Linux Ubuntu Karmic).
> This looks like it could be a Python 2.6 specific problem.
>
> > How can I print the biooython version?
> > thansk for your help!
> > /bjorn
>
> Its in the FAQ in the Tutorial, at the Python prompt just do:
>
> import Bio
> print Bio.__version__
>
> Peter
>



-- 
______O_________oO________oO______o_______oO__
Bj?rn Johansson
Assistant Professor
Departament of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL
http://www.bio.uminho.pt
http://sites.google.com/site/bjornhome
Work (direct) +351-253 601517
Private mob. +351-967 147 704
Dept of Biology (secretariate) +351-253 60 4310
Dept of Biology (fax) +351-253 678980


From cjfields at illinois.edu  Wed Dec 23 10:08:31 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 23 Dec 2009 09:08:31 -0600
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
	<320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>
	<d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
	<320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>
Message-ID: <9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>

On Dec 23, 2009, at 8:03 AM, Peter wrote:

> On Wed, Dec 23, 2009 at 1:29 PM, Silvio Tschapke
> <silvio.tschapke at googlemail.com> wrote:
>> 
>> I have copied the DTD file in
>> /usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/DTDs/
>> now and it seems to work. Great! I have installed Biopython with
>> 
>> python setup.py build
>> python setup.py test
>> sudo python setup.py install
> 
> OK - good :)
> 
>> But will I have the same problems when I use eSearch, or eQuery and so
>> on? Because all of the DTD will not be up to date. So far I only
>> copied this DTD for eLink you posted.
> 
> I *hope* that this was the only DTD file we were missing. If
> not, please do let us know so we can fix this for other users.
> 
> In the short term, you would again need to download and fetch
> other missing DTD files in the same way. You can generally look
> at the start of the XML file to see where the DTD can be found, e.g.
> 
>>>> from Bio import Entrez
>>>> Entrez.email = "your.name.here at example.com"
>>>> print Entrez.elink(dbfrom="pubmed", id="12345678").read(300)
> <?xml version="1.0"?>
> <!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 10 August
> 2009//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_090910.dtd">
> <eLinkResult>
> ...
> 
> Thanks,
> 
> Peter

Just a quick question: is there any particular reason you need the DTDs?  The BioPerl eutils interface doesn't use them at all, primarily b/c they aren't required on our end.

chris




From biopython at maubp.freeserve.co.uk  Wed Dec 23 10:14:06 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 15:14:06 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
	<320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>
	<d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
	<320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>
	<9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>
Message-ID: <320fb6e00912230714y5893143dhd262a6732536c87@mail.gmail.com>

On Wed, Dec 23, 2009 at 3:08 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
> Just a quick question: is there any particular reason you need the DTDs?
> The BioPerl eutils interface doesn't use them at all, primarily b/c they
> aren't required on our end.

Our parser uses the DTDs (local copies) to know the expected data
structure, which gets turned into Python lists, dicts, strings etc using
that information. I don't know too much about the implementation details,
but this doesn't work on Jython (Python under Java) since they haven't
implemented the DTD parsing support we expect.

Peter

From mjldehoon at yahoo.com  Thu Dec 24 10:11:48 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 24 Dec 2009 07:11:48 -0800 (PST)
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>
Message-ID: <439227.21985.qm@web62403.mail.re1.yahoo.com>

--- On Wed, 12/23/09, Chris Fields <cjfields at illinois.edu> wrote:
> Just a quick question: is there any particular reason you
> need the DTDs?? The BioPerl eutils interface doesn't
> use them at all, primarily b/c they aren't required on our
> end.
> 
The DTDs are needed to figure out the data structure of the XML file. In other words, what is a list, what is a dictionary, what is plain data, etcetera. How does the BioPerl eutils interface know how to store the information in the XML file?

--Michiel.


      


From cjfields at illinois.edu  Thu Dec 24 13:54:14 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 24 Dec 2009 12:54:14 -0600
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <439227.21985.qm@web62403.mail.re1.yahoo.com>
References: <439227.21985.qm@web62403.mail.re1.yahoo.com>
Message-ID: <5569562A-372E-414C-889A-9E75B344BA21@illinois.edu>


On Dec 24, 2009, at 9:11 AM, Michiel de Hoon wrote:

> --- On Wed, 12/23/09, Chris Fields <cjfields at illinois.edu> wrote:
>> Just a quick question: is there any particular reason you
>> need the DTDs?  The BioPerl eutils interface doesn't
>> use them at all, primarily b/c they aren't required on our
>> end.
>> 
> The DTDs are needed to figure out the data structure of the XML file. In other words, what is a list, what is a dictionary, what is plain data, etcetera. How does the BioPerl eutils interface know how to store the information in the XML file?
> 
> --Michiel.

We have classes designed to hold the information generically; docsums has docsum items, elink has linkouts, einfo has field/link information, so on.  Has worked fairly well with eutils changes over the last four yeqrs w/o directly relying on the DTDs in a release.

chris



From pedro.al at fenhi.uh.cu  Thu Dec 24 16:05:41 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Thu, 24 Dec 2009 16:05:41 -0500
Subject: [Biopython] Superpose structures...
Message-ID: <20091224160541.4d9f8d4so4g4gcss@correo.fenhi.uh.cu>

Hi all...
I've superpose two structures.. Now i want to compute the RMSD between  
2 residues after the superposition (with the transformed coordinates  
of the moving structure)
How can i do that...?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI





From pedro.al at fenhi.uh.cu  Thu Dec 24 16:37:12 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Thu, 24 Dec 2009 16:37:12 -0500
Subject: [Biopython] Superpose structures...
Message-ID: <20091224163712.mg5fgthu04gcgcgk@correo.fenhi.uh.cu>

I know i made that question already but this time is a quite  
different. I already superpose the structures (Profit isn't so  
suitable for my project), but now i want to compute the RMSD betweeen  
2 residues in the superposed position. When i do that, the RMSD that i  
get is the same that if i superpose the structures according to that  
residue, and what i really want is the "deviation of 2 residues when  
its structures are superposed according to its binding sites  
residues", and i want to know how to do that in Biopython...

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI





From schafer at rostlab.org  Thu Dec 24 17:11:10 2009
From: schafer at rostlab.org (=?ISO-8859-1?Q?Christian_Sch=E4fer?=)
Date: Thu, 24 Dec 2009 17:11:10 -0500
Subject: [Biopython] Superpose structures...
In-Reply-To: <20091224163712.mg5fgthu04gcgcgk@correo.fenhi.uh.cu>
References: <20091224163712.mg5fgthu04gcgcgk@correo.fenhi.uh.cu>
Message-ID: <4B33E6FE.3090709@rostlab.org>

So, what you want to do is to superpose two structures by minimizing the 
RMSD between aligned residues and after that calculating the RMSD 
between two residues? Is that right? If so, ProFit is able to do that. 
Superimpostion is done by the ZONE command (which then returns the 
overall RMSD over the aligned regions after superimpostion); and 
calculating the RMSD between specific residues (after superimposition) 
is done via the RZONE command. You can even chose which kind of atoms to 
consider for RMSD calculation with the ATOMS and RATOMS commands.
I'm not sure if something that specific could be done with plain 
BioPython. But again, you can always write a wrapper for the ProFit part 
in Python.

Chris

On 12/24/2009 04:37 PM, Yasser Almeida Hern?ndez wrote:
> I know i made that question already but this time is a quite different.
> I already superpose the structures (Profit isn't so suitable for my
> project), but now i want to compute the RMSD betweeen 2 residues in the
> superposed position. When i do that, the RMSD that i get is the same
> that if i superpose the structures according to that residue, and what i
> really want is the "deviation of 2 residues when its structures are
> superposed according to its binding sites residues", and i want to know
> how to do that in Biopython...
>
> Thanks
>

From bioinformaticsing at gmail.com  Sat Dec 26 09:37:31 2009
From: bioinformaticsing at gmail.com (ning luwen)
Date: Sat, 26 Dec 2009 22:37:31 +0800
Subject: [Biopython] need help! how to retrieve full text from Pubmed
	central ?
Message-ID: <90247fbe0912260637n7553bdf7wbce10a627c0a124c@mail.gmail.com>

Dear everyone,
?? I need to download full text from Pubmed central. After see the
Entrez manual, maybe Entrez(not the web interface) doesn't give a way
to?download .pdf full text file, is this true?




--
regards,
ningluwen


From bioinformaticsing at gmail.com  Sat Dec 26 09:54:23 2009
From: bioinformaticsing at gmail.com (ning luwen)
Date: Sat, 26 Dec 2009 22:54:23 +0800
Subject: [Biopython] need help! how to retrieve full text from Pubmed
	central ?
In-Reply-To: <90247fbe0912260637n7553bdf7wbce10a627c0a124c@mail.gmail.com>
References: <90247fbe0912260637n7553bdf7wbce10a627c0a124c@mail.gmail.com>
Message-ID: <90247fbe0912260654scd2b0ceyb37d54f36a3531fa@mail.gmail.com>

more about the problem.

     From http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html,
I can learn:
      PubMed Central contains a number of articles classified as "open
access" for which you may download the full text as XML. For the
remaining articles in PMC you may download only the abstracts as XML.

but when try to
handle=Entrez.efetch(db='pmc',id=idlist,rettype='full',retmode='xml')
record=Entrez.read(handle)

got following errors:
    Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.6/dist-packages/Bio/Entrez/__init__.py",
line 258, in read
    record = handler.read(handle)
  File "/usr/local/lib/python2.6/dist-packages/Bio/Entrez/Parser.py",
line 114, in read
    raise CorruptedXMLError
Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data.
Please make sure that the input data are in XML format, and that the
data are not corrupted.

the python version is 1.53 and my system is ubuntu 9.10.

On Sat, Dec 26, 2009 at 10:37 PM, ning luwen
<bioinformaticsing at gmail.com> wrote:
> Dear everyone,
> ?? I need to download full text from Pubmed central. After see the
> Entrez manual, maybe Entrez(not the web interface) doesn't give a way
> to?download .pdf full text file, is this true?
>
>
>
>
> --
> regards,
> ningluwen
>



-- 
regards,
luwening,bioinformatics center in uestc:
www.bioinformaticsinuestc.cz.cc


From pedro.al at fenhi.uh.cu  Mon Dec 28 09:06:38 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Mon, 28 Dec 2009 09:06:38 -0500
Subject: [Biopython] Superpose structures... DONE
Message-ID: <20091228090638.y05tos1p8g0gk08c@correo.fenhi.uh.cu>

The problem with the calculus of the RMSD after the superposition is  
solved. This is done with the class SVDSuperimposer (Bio >  
SVDSuperimposer > SVDSuperimposer.py). This class has the method  
get_init_rms() that compute the structures RMSD after the  
superposition...
Now i have another question. It is possible in Biopython read gziped  
pdb files (.pdb.gz)?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI





From mjldehoon at yahoo.com  Mon Dec 28 12:27:23 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Mon, 28 Dec 2009 09:27:23 -0800 (PST)
Subject: [Biopython] Superpose structures... DONE
In-Reply-To: <20091228090638.y05tos1p8g0gk08c@correo.fenhi.uh.cu>
Message-ID: <363342.11278.qm@web62406.mail.re1.yahoo.com>

--- On Mon, 12/28/09, Yasser Almeida Hern?ndez <pedro.al at fenhi.uh.cu> wrote:
> Now i have another question. It is possible in Biopython
> read gziped pdb files (.pdb.gz)?

I am not a Bio.PDB user, but from its documentation it looks like it uses the file name to open a PDB file instead of a handle. Thomas, how do you feel about modifying Bio.PDB so it uses a file handle instead of a file name? Then Bio.PDB can parse gzipped and bzipped files.

--Michiel.


      


From pedro.al at fenhi.uh.cu  Tue Dec 29 09:18:38 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Tue, 29 Dec 2009 09:18:38 -0500
Subject: [Biopython] Remove hydrogens...
Message-ID: <20091229091838.fnyk66sayos8swww@correo.fenhi.uh.cu>

Hi all...
How can i remove hydrogens atoms from the structures objects?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI





From pengyu.ut at gmail.com  Tue Dec 29 11:08:09 2009
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 29 Dec 2009 10:08:09 -0600
Subject: [Biopython] Comparison between bioperl and biopython?
Message-ID: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>

May I ask somebody who are versitile in both bioperl and biopython
comment on the pros and cons of bioperl and biopython? I'm sending
this email to both bioperl and biopython mailing lists. But I hope
that it will not result in any contention.

I assume that the functionality between bioperl or biopython is the
same, i.e., tasks can be done in bioperl can be done biopython and
vice versa, as both libraries have been out there over 10 years.
Please correct me if my understanding is not true.

Given that a task that can be done with either bioperl or biopython,
I, in particularly, want to know how long it will take to write the
code for the task in bioperl and biopython, with the same readability
requirement (see below) and the assumption that users have the same
fluency in perl and python.

python is claimed to be good for maintainability. But perl is
criticized for there-are-many-ways-for-a-given-task. Since there are
multiple ways in perl, let us assume that we always use perl in a
readable way.

From jason at bioperl.org  Tue Dec 29 11:49:20 2009
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 29 Dec 2009 08:49:20 -0800
Subject: [Biopython] [Bioperl-l] Comparison between bioperl and
	biopython?
In-Reply-To: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
Message-ID: <2B85EF86-8A84-491B-8C33-7EC16CCB8CBC@bioperl.org>

Are you asking for the purposes of choosing a toolkit for your work or  
just curious about the advantages/disadvantages of language choice?

-jason
On Dec 29, 2009, at 8:08 AM, Peng Yu wrote:

> May I ask somebody who are versitile in both bioperl and biopython
> comment on the pros and cons of bioperl and biopython? I'm sending
> this email to both bioperl and biopython mailing lists. But I hope
> that it will not result in any contention.
>
> I assume that the functionality between bioperl or biopython is the
> same, i.e., tasks can be done in bioperl can be done biopython and
> vice versa, as both libraries have been out there over 10 years.
> Please correct me if my understanding is not true.
>
> Given that a task that can be done with either bioperl or biopython,
> I, in particularly, want to know how long it will take to write the
> code for the task in bioperl and biopython, with the same readability
> requirement (see below) and the assumption that users have the same
> fluency in perl and python.
>
> python is claimed to be good for maintainability. But perl is
> criticized for there-are-many-ways-for-a-given-task. Since there are
> multiple ways in perl, let us assume that we always use perl in a
> readable way.
> _______________________________________________
> 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
http://fungalgenomes.org/


From sdavis2 at mail.nih.gov  Tue Dec 29 12:03:40 2009
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Tue, 29 Dec 2009 12:03:40 -0500
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
Message-ID: <264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>

On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> May I ask somebody who are versitile in both bioperl and biopython
> comment on the pros and cons of bioperl and biopython? I'm sending
> this email to both bioperl and biopython mailing lists. But I hope
> that it will not result in any contention.
>
> I assume that the functionality between bioperl or biopython is the
> same, i.e., tasks can be done in bioperl can be done biopython and
> vice versa, as both libraries have been out there over 10 years.
> Please correct me if my understanding is not true.

The two projects have similar goals, but saying that the functionality
is the same would be an extreme oversimplification.  You will need to
define what you want to do and then check to see what the two projects
have to offer.  This will, in general, require perusing the websites
for both projects as well as the relevant documentation.

> Given that a task that can be done with either bioperl or biopython,
> I, in particularly, want to know how long it will take to write the
> code for the task in bioperl and biopython, with the same readability
> requirement (see below) and the assumption that users have the same
> fluency in perl and python.

Again, you will want to define the task(s) to be accomplished and then
weigh the pros and cons of each project combined with local expertise.
 If you don't know what you want to do, then you can certainly read
some examples on the websites and see which project strikes you as a
"winner" for you.

> python is claimed to be good for maintainability. But perl is
> criticized for there-are-many-ways-for-a-given-task. Since there are
> multiple ways in perl, let us assume that we always use perl in a
> readable way.

These two statements are generalizations that provide little insight
into the strengths or weaknesses of the languages.  In other words,
one can write good or bad code in both languages.

Hope that helps.

Sean

From eric.talevich at gmail.com  Tue Dec 29 13:37:43 2009
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 29 Dec 2009 10:37:43 -0800
Subject: [Biopython] Superpose structures... DONE
Message-ID: <3f6baf360912291037o5313b9f0s2acdc481c9989ce1@mail.gmail.com>

On Mon, 28 Dec 2009, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

>
> I am not a Bio.PDB user, but from its documentation it looks like it uses
> the file name to open a PDB file instead of a handle. Thomas, how do you
> feel about modifying Bio.PDB so it uses a file handle instead of a file
> name? Then Bio.PDB can parse gzipped and bzipped files.
>
> --Michiel.
>
>
I guess PDB requires a file name because it wants full control over the file
handle -- the handle is passed between PDBParser and parse_pdb_header, for
instance. But control still isn't as crucial as in SeqIO.index (for
example), so I don't think using a handle directly would lead to catastrophe
in general.

In addition, do you think a StructIO module would be worthwhile?

Benefits:
- Accept either a file name or file handle
- Wouldn't necessarily need to specify the structure object's name as a
separate argument (as PDBParser requires)
- No need to instantiate a Parser object before parsing
- PDB, PDBXML and mmCIF parsing would be called the same way

Drawbacks:
- Integrating parse_pdb_headers would become more important/tricky
- Thin wrappers still require effort, and I'm currently tied up with TreeIO
-- I'd get to it some months from now

Cheers,
Eric

From pengyu.ut at gmail.com  Tue Dec 29 13:58:59 2009
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 29 Dec 2009 12:58:59 -0600
Subject: [Biopython] [Bioperl-l] Comparison between bioperl and
	biopython?
In-Reply-To: <2B85EF86-8A84-491B-8C33-7EC16CCB8CBC@bioperl.org>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<2B85EF86-8A84-491B-8C33-7EC16CCB8CBC@bioperl.org>
Message-ID: <366c6f340912291058t6c601e57re0c35e69fe81e09d@mail.gmail.com>

To choose a toolkit for my work.

On Tue, Dec 29, 2009 at 10:49 AM, Jason Stajich <jason at bioperl.org> wrote:
> Are you asking for the purposes of choosing a toolkit for your work or just
> curious about the advantages/disadvantages of language choice?
>
> -jason
> On Dec 29, 2009, at 8:08 AM, Peng Yu wrote:
>
>> May I ask somebody who are versitile in both bioperl and biopython
>> comment on the pros and cons of bioperl and biopython? I'm sending
>> this email to both bioperl and biopython mailing lists. But I hope
>> that it will not result in any contention.
>>
>> I assume that the functionality between bioperl or biopython is the
>> same, i.e., tasks can be done in bioperl can be done biopython and
>> vice versa, as both libraries have been out there over 10 years.
>> Please correct me if my understanding is not true.
>>
>> Given that a task that can be done with either bioperl or biopython,
>> I, in particularly, want to know how long it will take to write the
>> code for the task in bioperl and biopython, with the same readability
>> requirement (see below) and the assumption that users have the same
>> fluency in perl and python.
>>
>> python is claimed to be good for maintainability. But perl is
>> criticized for there-are-many-ways-for-a-given-task. Since there are
>> multiple ways in perl, let us assume that we always use perl in a
>> readable way.
>> _______________________________________________
>> 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
> http://fungalgenomes.org/
>
>

From pengyu.ut at gmail.com  Tue Dec 29 14:15:14 2009
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 29 Dec 2009 13:15:14 -0600
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
Message-ID: <366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>

On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
>> May I ask somebody who are versitile in both bioperl and biopython
>> comment on the pros and cons of bioperl and biopython? I'm sending
>> this email to both bioperl and biopython mailing lists. But I hope
>> that it will not result in any contention.
>>
>> I assume that the functionality between bioperl or biopython is the
>> same, i.e., tasks can be done in bioperl can be done biopython and
>> vice versa, as both libraries have been out there over 10 years.
>> Please correct me if my understanding is not true.
>
> The two projects have similar goals, but saying that the functionality
> is the same would be an extreme oversimplification. ?You will need to
> define what you want to do and then check to see what the two projects
> have to offer. ?This will, in general, require perusing the websites
> for both projects as well as the relevant documentation.

According to your experience, are there some tasks that are easier
with one than with another?

>> Given that a task that can be done with either bioperl or biopython,
>> I, in particularly, want to know how long it will take to write the
>> code for the task in bioperl and biopython, with the same readability
>> requirement (see below) and the assumption that users have the same
>> fluency in perl and python.
>
> Again, you will want to define the task(s) to be accomplished and then
> weigh the pros and cons of each project combined with local expertise.
> ?If you don't know what you want to do, then you can certainly read
> some examples on the websites and see which project strikes you as a
> "winner" for you.
>
>> python is claimed to be good for maintainability. But perl is
>> criticized for there-are-many-ways-for-a-given-task. Since there are
>> multiple ways in perl, let us assume that we always use perl in a
>> readable way.
>
> These two statements are generalizations that provide little insight
> into the strengths or weaknesses of the languages. ?In other words,
> one can write good or bad code in both languages.
>
> Hope that helps.
>
> Sean
>


From jkhilmer at gmail.com  Tue Dec 29 14:55:18 2009
From: jkhilmer at gmail.com (Jonathan Hilmer)
Date: Tue, 29 Dec 2009 12:55:18 -0700
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
	<366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
Message-ID: <81277ce10912291155x6dde10ewe2055b9692d077c1@mail.gmail.com>

Personally, I think that the differences between Python and Perl
(although substantial) are not large enough to make the language
itself the deciding factor.

Instead, consider the larger community of software.  I haven't yet
found a situation in which Python cannot be applied: it can be used
with R (statistics); lower-level code C or fortran; visualization
software such as PyMol, Chimera, Blender, VTK; plotting with
matplotlib; and scipy/numpy or sage, which provide innumerable
benefits for computation, data-processing, etc.

Although I don't claim to have a great deal of experience with Perl, I
haven't seen the same integration with that language: I'm assuming it
can be used with R and VTK (not sure about C or fortran?).  For this
reason, unless your work is highly targeted and you have no use
programming language integration with other software, I would
recommend Python.

For perl experts, I would truly appreciate any corrections you could
offer to these observations of mine, since I wouldn't mind using perl
if it offers benefits either in general or for specific applications.


Jonathan

On Tue, Dec 29, 2009 at 12:15 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
>>> May I ask somebody who are versitile in both bioperl and biopython
>>> comment on the pros and cons of bioperl and biopython? I'm sending
>>> this email to both bioperl and biopython mailing lists. But I hope
>>> that it will not result in any contention.
>>>
>>> I assume that the functionality between bioperl or biopython is the
>>> same, i.e., tasks can be done in bioperl can be done biopython and
>>> vice versa, as both libraries have been out there over 10 years.
>>> Please correct me if my understanding is not true.
>>
>> The two projects have similar goals, but saying that the functionality
>> is the same would be an extreme oversimplification. ?You will need to
>> define what you want to do and then check to see what the two projects
>> have to offer. ?This will, in general, require perusing the websites
>> for both projects as well as the relevant documentation.
>
> According to your experience, are there some tasks that are easier
> with one than with another?
>
>>> Given that a task that can be done with either bioperl or biopython,
>>> I, in particularly, want to know how long it will take to write the
>>> code for the task in bioperl and biopython, with the same readability
>>> requirement (see below) and the assumption that users have the same
>>> fluency in perl and python.
>>
>> Again, you will want to define the task(s) to be accomplished and then
>> weigh the pros and cons of each project combined with local expertise.
>> ?If you don't know what you want to do, then you can certainly read
>> some examples on the websites and see which project strikes you as a
>> "winner" for you.
>>
>>> python is claimed to be good for maintainability. But perl is
>>> criticized for there-are-many-ways-for-a-given-task. Since there are
>>> multiple ways in perl, let us assume that we always use perl in a
>>> readable way.
>>
>> These two statements are generalizations that provide little insight
>> into the strengths or weaknesses of the languages. ?In other words,
>> one can write good or bad code in both languages.
>>
>> Hope that helps.
>>
>> Sean
>>
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From wgheath at gmail.com  Tue Dec 29 15:16:39 2009
From: wgheath at gmail.com (William Heath)
Date: Tue, 29 Dec 2009 12:16:39 -0800
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <81277ce10912291155x6dde10ewe2055b9692d077c1@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
	<366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
	<81277ce10912291155x6dde10ewe2055b9692d077c1@mail.gmail.com>
Message-ID: <f08ddf990912291216h32988b8cv20830c1b6701caf6@mail.gmail.com>

The biggest reason to go with python is the ease of use.  Biologists are not
programmers and the learning curve for python is much smaller than that of
perl.  I like perl but choose python because of this issue.  Perl 6 does
address some of these issues however but this has not been fully implemented
as of yet.

-Tim

P.S.

I love, love, love cpan though which is only for perl right now :(

On Tue, Dec 29, 2009 at 11:55 AM, Jonathan Hilmer <jkhilmer at gmail.com>wrote:

> Personally, I think that the differences between Python and Perl
> (although substantial) are not large enough to make the language
> itself the deciding factor.
>
> Instead, consider the larger community of software.  I haven't yet
> found a situation in which Python cannot be applied: it can be used
> with R (statistics); lower-level code C or fortran; visualization
> software such as PyMol, Chimera, Blender, VTK; plotting with
> matplotlib; and scipy/numpy or sage, which provide innumerable
> benefits for computation, data-processing, etc.
>
> Although I don't claim to have a great deal of experience with Perl, I
> haven't seen the same integration with that language: I'm assuming it
> can be used with R and VTK (not sure about C or fortran?).  For this
> reason, unless your work is highly targeted and you have no use
> programming language integration with other software, I would
> recommend Python.
>
> For perl experts, I would truly appreciate any corrections you could
> offer to these observations of mine, since I wouldn't mind using perl
> if it offers benefits either in general or for specific applications.
>
>
> Jonathan
>
> On Tue, Dec 29, 2009 at 12:15 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> > On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov>
> wrote:
> >> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> >>> May I ask somebody who are versitile in both bioperl and biopython
> >>> comment on the pros and cons of bioperl and biopython? I'm sending
> >>> this email to both bioperl and biopython mailing lists. But I hope
> >>> that it will not result in any contention.
> >>>
> >>> I assume that the functionality between bioperl or biopython is the
> >>> same, i.e., tasks can be done in bioperl can be done biopython and
> >>> vice versa, as both libraries have been out there over 10 years.
> >>> Please correct me if my understanding is not true.
> >>
> >> The two projects have similar goals, but saying that the functionality
> >> is the same would be an extreme oversimplification.  You will need to
> >> define what you want to do and then check to see what the two projects
> >> have to offer.  This will, in general, require perusing the websites
> >> for both projects as well as the relevant documentation.
> >
> > According to your experience, are there some tasks that are easier
> > with one than with another?
> >
> >>> Given that a task that can be done with either bioperl or biopython,
> >>> I, in particularly, want to know how long it will take to write the
> >>> code for the task in bioperl and biopython, with the same readability
> >>> requirement (see below) and the assumption that users have the same
> >>> fluency in perl and python.
> >>
> >> Again, you will want to define the task(s) to be accomplished and then
> >> weigh the pros and cons of each project combined with local expertise.
> >>  If you don't know what you want to do, then you can certainly read
> >> some examples on the websites and see which project strikes you as a
> >> "winner" for you.
> >>
> >>> python is claimed to be good for maintainability. But perl is
> >>> criticized for there-are-many-ways-for-a-given-task. Since there are
> >>> multiple ways in perl, let us assume that we always use perl in a
> >>> readable way.
> >>
> >> These two statements are generalizations that provide little insight
> >> into the strengths or weaknesses of the languages.  In other words,
> >> one can write good or bad code in both languages.
> >>
> >> Hope that helps.
> >>
> >> Sean
> >>
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>

From jason at bioperl.org  Tue Dec 29 16:57:49 2009
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 29 Dec 2009 13:57:49 -0800
Subject: [Biopython] [Bioperl-l] Comparison between bioperl and
	biopython?
In-Reply-To: <366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
	<366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
Message-ID: <02851B8A-E74E-453E-9725-6FA8F3995F82@bioperl.org>


On Dec 29, 2009, at 11:15 AM, Peng Yu wrote:

> On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov>  
> wrote:
>> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com>  
>> wrote:
>>> May I ask somebody who are versitile in both bioperl and biopython
>>> comment on the pros and cons of bioperl and biopython? I'm sending
>>> this email to both bioperl and biopython mailing lists. But I hope
>>> that it will not result in any contention.
>>>
>>> I assume that the functionality between bioperl or biopython is the
>>> same, i.e., tasks can be done in bioperl can be done biopython and
>>> vice versa, as both libraries have been out there over 10 years.
>>> Please correct me if my understanding is not true.
>>
>> The two projects have similar goals, but saying that the  
>> functionality
>> is the same would be an extreme oversimplification.  You will need to
>> define what you want to do and then check to see what the two  
>> projects
>> have to offer.  This will, in general, require perusing the websites
>> for both projects as well as the relevant documentation.
>
> According to your experience, are there some tasks that are easier
> with one than with another?

As you have still failed to give much insight into the 'tasks' it is  
hard to give you a better answer.

If there is a module or set of routines already written then yes one  
might be easier than the other. Otherwise it just depends on your  
strengths in the programming language.
We discussed the strengths of the different toolkits briefly on the  
podcast last month.  http://twit.tv/floss96

I echo Sean. Use whichever language you are a better programmer in.   
BioPerl is more mature in some facets than is BioPython, but BioPython  
has some components that are more heavily developed and supported than  
BioPerl (structures being one of those and interfacing that to pyMol  
would be a strength).   I personally think the Gbrowse, Bio-Graphics,  
and Bio::DB::GFF/Bio::DB::SeqFeature::Store interface to Sequence  
databases and Features is a critical aspect of mining  genomic data  
and features and use these heavily in my work, making BioPerl easy and  
powerful for my tasks. That and sequence and alignment parsing and  
reformatting.  But there are comparable tools written in python with  
and without BioPython that you can also use so mainly it is about  
building up an expertise in a toolkit and going forward.  The BioPerl  
faithful will probably say it is more useful toolkit to us, but we are  
of course a biased sample.

Both projects can benefit from more users and developers contributing  
code and documentation so I would just jump in and give it a try if  
you are unsure which will be easier for you.

>
>>> Given that a task that can be done with either bioperl or biopython,
>>> I, in particularly, want to know how long it will take to write the
>>> code for the task in bioperl and biopython, with the same  
>>> readability
>>> requirement (see below) and the assumption that users have the same
>>> fluency in perl and python.
>>
>> Again, you will want to define the task(s) to be accomplished and  
>> then
>> weigh the pros and cons of each project combined with local  
>> expertise.
>>  If you don't know what you want to do, then you can certainly read
>> some examples on the websites and see which project strikes you as a
>> "winner" for you.
>>
>>> python is claimed to be good for maintainability. But perl is
>>> criticized for there-are-many-ways-for-a-given-task. Since there are
>>> multiple ways in perl, let us assume that we always use perl in a
>>> readable way.
>>
>> These two statements are generalizations that provide little insight
>> into the strengths or weaknesses of the languages.  In other words,
>> one can write good or bad code in both languages.
>>
>> Hope that helps.
>>
>> Sean
>>
>
> _______________________________________________
> 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
http://fungalgenomes.org/


From mitlox at op.pl  Tue Dec 29 21:42:07 2009
From: mitlox at op.pl (xyz)
Date: Wed, 30 Dec 2009 12:42:07 +1000
Subject: [Biopython] fastq-solexa index
In-Reply-To: <320fb6e00911260248w1f6a29b1ucc0bfecec897c67b@mail.gmail.com>
References: <4B0DD08B.6070607@op.pl>
	<320fb6e00911260248w1f6a29b1ucc0bfecec897c67b@mail.gmail.com>
Message-ID: <4B3ABDFF.8030809@op.pl>

Peter wrote:
> In Bio.SeqIO we give each file format a name, in this case "fastq-solexa"
> means the old Solexa FASTQ files (also used by Illumina up to and
> including pipeline 1.2) which use Solexa scores with an ASCII offset
> of 64 (not PHRED scores). The table on the SeqIO wiki page tries to
> summarise this. See also: http://en.wikipedia.org/wiki/FASTQ_format
>
> The "index" column on that table on the SeqIO wiki page indicates if
> each file format can be used with the Bio.SeqIO.index(...) function
> included in Biopython 1.52 onwards. See:
> http://news.open-bio.org/news/2009/09/biopython-seqio-index/
>
> There are also examples in the main Tutorial,
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>
> And in the Bio.SeqIO module's built in help, online here:
> http://biopython.org/DIST/docs/api/Bio.SeqIO-module.html
>
> >From within Python:
>
>   
>>>> from Bio import SeqIO
>>>> help(SeqIO)
>>>>         
> ...
>   
>>>> help(SeqIO.index)
>>>>         
> ...
>
> Peter
>
>   
Thank you.

From mitlox at op.pl  Tue Dec 29 21:51:45 2009
From: mitlox at op.pl (xyz)
Date: Wed, 30 Dec 2009 12:51:45 +1000
Subject: [Biopython] Strand
Message-ID: <4B3AC041.2070008@op.pl>

Hello,
I downloaded data from Phytozome Biomart:

>AC159145_38|MtChr2|AC159145_38|Mtruncatula|17915949|17918990|-1
ATTTCCTCCAGACTTGTTAAAGAAGTTGAGTACAGATTGTATTGTCATGCAAAATCATCA
ATATGGCATATCCCCAGTAAAACTCCTGGGAAATCAAAAGCTATCGAGTTTTTTCGAGAT
CTTGACAACTTCCAACGATCAAGATGATAAGGTTTATGTCTCTACAGTACGTTCACGTAA
CTATCCCGTGACTGGCTTCCAATGGCATCCTGAGAAAAATGCCTTCGAATGGGGCTCACC
AAGCATTCCACACACAGAGGATGCCATTCGAACAACTCAGTATGCTGCAAACTATTTGGT
CAGTGAAGCGAGGAAGTCCTTAAACAGACCAGTTGCTCAGGAATTGTTAGACAATCTCAT
ATACAATTACAGACCCACTTATTGTGGGTATGCAGGTTGTCCACCGCCTAATCCGAACCT
CTACTACCAGCCGGTCATTGGAATTCTCAGCCACCCCGGCGATGGCACTTCAGGCCGCCA
CAGTAATGCTACGGGCGCTTCCTTCATTCACGCCTCTTATGTGAAATTCGTGGAGGCTGC
TGGCGCTAGAGTAGTTCCTCTCATTTACAACGAACCGGAGGAGAAGATTCTCAAGGTATC
AGAAAAGGCCAAAGCTTGA


The above data is from -1 strand, but how could I convert it +1 strand?

Thank you in advance.

Best regards,


From p.j.a.cock at googlemail.com  Wed Dec 30 07:13:42 2009
From: p.j.a.cock at googlemail.com (Peter)
Date: Wed, 30 Dec 2009 12:13:42 +0000
Subject: [Biopython] programming errors
In-Reply-To: <4788465e0912252205l1ac3f26ds98739898ff83dbd9@mail.gmail.com>
References: <4788465e0912252205l1ac3f26ds98739898ff83dbd9@mail.gmail.com>
Message-ID: <389810B4-4CAB-4375-8964-5ABDA9749FFB@googlemail.com>

Hi Rocky,

To send a query to the mailing list please use the Biopython at ...  
address, not the Biopython-owner at ... address. You need to sign up to  
the mailing list first.

Thanks,

Peter

On 26 Dec 2009, at 06:05, Rocky Parida <nirulinga at gmail.com> wrote:

> Hi
> My name is Rocky. I am student at the Grand Valley State University.  
> I am
> doing MS in Bioinformatics. I am currently using python 2.6.I was  
> trying to
> follow a documentation(
> http://www.inb.mu-luebeck.de/biosoft/biopython/tut/Tutorial002.html#toc10 
> )in<http://www.inb.mu-luebeck.de/biosoft/biopython/tut/Tutorial002.html#toc10%29in 
> >
> order to connect to a biological databases. I am facing some troubles
> regarding importing data from NCBI. I am attaching my snipped word  
> doc with
> this email.
> Can you please suggest me on how to perform statistical data  
> analysis using
> python. I am very much interested to learn but i am facing some  
> troubles
> following the documentation. Is there a step by step documentation  
> that has
> all the information regarding what to write, what to download and  
> how to do
> statistics using python codes. If you please refer those sites and  
> books in
> you reply. I have very little back ground in programming. So, please  
> keep
> that in you consideration as well.
> Thanking you
> Rocky

From chapmanb at 50mail.com  Wed Dec 30 07:59:42 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Wed, 30 Dec 2009 07:59:42 -0500
Subject: [Biopython] Strand
In-Reply-To: <4B3AC041.2070008@op.pl>
References: <4B3AC041.2070008@op.pl>
Message-ID: <20091230125942.GB39741@sobchak.mgh.harvard.edu>

Hello;

> I downloaded data from Phytozome Biomart:
> 
> >AC159145_38|MtChr2|AC159145_38|Mtruncatula|17915949|17918990|-1
> ATTTCCTCCAGACTTGTTAAAGAAGTTGAGTACAGATTGTATTGTCATGCAAAATCATCA
> ATATGGCATATCCCCAGTAAAACTCCTGGGAAATCAAAAGCTATCGAGTTTTTTCGAGAT
> CTTGACAACTTCCAACGATCAAGATGATAAGGTTTATGTCTCTACAGTACGTTCACGTAA
> CTATCCCGTGACTGGCTTCCAATGGCATCCTGAGAAAAATGCCTTCGAATGGGGCTCACC
> AAGCATTCCACACACAGAGGATGCCATTCGAACAACTCAGTATGCTGCAAACTATTTGGT
> CAGTGAAGCGAGGAAGTCCTTAAACAGACCAGTTGCTCAGGAATTGTTAGACAATCTCAT
> ATACAATTACAGACCCACTTATTGTGGGTATGCAGGTTGTCCACCGCCTAATCCGAACCT
> CTACTACCAGCCGGTCATTGGAATTCTCAGCCACCCCGGCGATGGCACTTCAGGCCGCCA
> CAGTAATGCTACGGGCGCTTCCTTCATTCACGCCTCTTATGTGAAATTCGTGGAGGCTGC
> TGGCGCTAGAGTAGTTCCTCTCATTTACAACGAACCGGAGGAGAAGATTCTCAAGGTATC
> AGAAAAGGCCAAAGCTTGA
> 
> The above data is from -1 strand, but how could I convert it +1 strand?

If you got this from BioMart and retrieved something like cDNA
sequence or transcript, this is probably already reverse
complemented for you. In this case it looks like a coding sequence
starting at base 47 and proceeding to the stop codon at the end.

To answer your question, please see the Tutorial documentation,
specifically Chapter 5 Sequence Input/Output:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc44

and section 3.7 Nucleotide sequences and (reverse) complements:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc23

This should lead you to:

in_file = "your_data.fa"
with open(in_file) as in_handle:
    rec = SeqIO.read(in_handle, "fasta")

rc = rec.seq.reverse_complement()

Hope this helps,
Brad

From pedro.al at fenhi.uh.cu  Wed Dec 30 15:05:55 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Wed, 30 Dec 2009 15:05:55 -0500
Subject: [Biopython] Save custom structure...
Message-ID: <20091230150555.ojbth0gp34g088os@correo.fenhi.uh.cu>

Hi all...
I've extracted a residue and an atom as two separated objects...
How can i save them as a single structure .pdb file?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI





From johncumbers at gmail.com  Tue Dec  1 07:10:16 2009
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 30 Nov 2009 23:10:16 -0800
Subject: [Biopython] MuscleCommandline and phyiout
Message-ID: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>

Hello,

I'm using the MuscleCommandline wrapper and I'm having trouble getting the
Phylip interleaved output format.  For the Muscle command line I would type
"muscle -in myinputfile -phyiout myoutputfile" and this command in python:
cline = MuscleCommandline (input=output_file_name_FASTA,
out=output_file_name_aligned)

But for phyiout, this doesn't work:
cline = MuscleCommandline (input=output_file_name_FASTA,
phyiout=output_file_name_aligned)
returning: ValueError: Option name phyiout was not found.

I tried to lookup the possibilities here:
http://www.biopython.org/DIST/docs/api/Bio.Align.Applications._Muscle.MuscleCommandline-class.html

but couldn't find them, any help appreciated,
cheers,
John


John Cumbers, Ph.D Candidate
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.
cell +1 (401) 523 8190, office +1 (650) 604-1914, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA


From biopython at maubp.freeserve.co.uk  Tue Dec  1 09:23:54 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 09:23:54 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
Message-ID: <320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>

On Tue, Dec 1, 2009 at 7:10 AM, John Cumbers <johncumbers at gmail.com> wrote:
> Hello,
>
> I'm using the MuscleCommandline wrapper and I'm having trouble getting the
> Phylip interleaved output format. ?For the Muscle command line I would type
> "muscle -in myinputfile -phyiout myoutputfile"

What version of MUSCLE do you have? v3.7 doesn't mention this
option in the command line help, nor does the current manual:
http://www.drive5.com/muscle/muscle.html

Peter



From biopython at maubp.freeserve.co.uk  Tue Dec  1 09:52:19 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 09:52:19 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
Message-ID: <320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>

On Tue, Dec 1, 2009 at 9:23 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Dec 1, 2009 at 7:10 AM, John Cumbers <johncumbers at gmail.com> wrote:
>> Hello,
>>
>> I'm using the MuscleCommandline wrapper and I'm having trouble getting the
>> Phylip interleaved output format. ?For the Muscle command line I would type
>> "muscle -in myinputfile -phyiout myoutputfile"
>
> What version of MUSCLE do you have? v3.7 doesn't mention this
> option in the command line help, nor does the current manual:
> http://www.drive5.com/muscle/muscle.html

It looks like an undocumented option, much like -phyi (which I guessed)
for PHYLIP interlaced and -phys for PHYLIP sequential. These match
the documented format options (e.g. -msf, -html, -clw and -clwstrict).
i.e. You can use this:

"muscle -in myinputfile -phyi -out myoutputfile"

I think we should ask the MUSCLE author which of these
undocumented arguments are actually supported rather than
adding them all.

Peter



From bartomas at gmail.com  Tue Dec  1 16:25:36 2009
From: bartomas at gmail.com (bar tomas)
Date: Tue, 1 Dec 2009 16:25:36 +0000
Subject: [Biopython] Host_organism field in SwissProt
Message-ID: <fdcd75820912010825w76a8aa55q4385cae0c8e0b49@mail.gmail.com>

Hi,
I'm using BioPython for processing protein sequences from SwissProt database.
I'm following the excellent tutorial documentation on SwissProt querying (p.107)
I'm just wondering about the meaning of the field 'host_organism' in a
swissprot record, as I haven't yet found a record where the value of
this field is supplied.
If the record concerns the protein sequence of a bacteria, for
instance, does the host_organism field contain a list of taxonomic ids
of possible host organisms where the bacteria can be found?
Many thanks


From biopython at maubp.freeserve.co.uk  Tue Dec  1 19:19:23 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 19:19:23 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
	<320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
Message-ID: <320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>

On Tue, Dec 1, 2009 at 9:52 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> It looks like an undocumented option, much like -phyi (which I guessed)
> for PHYLIP interlaced and -phys for PHYLIP sequential. These match
> the documented format options (e.g. -msf, -html, -clw and -clwstrict).
> i.e. You can use this:
>
> "muscle -in myinputfile -phyi -out myoutputfile"
>
> I think we should ask the MUSCLE author which of these
> undocumented arguments are actually supported rather than
> adding them all.

Robert Edgar agreed the documentation was out of sync, and has
confirmed these are safe arguments to include in our wrapper.

Peter


From biopython at maubp.freeserve.co.uk  Tue Dec  1 19:21:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 19:21:35 +0000
Subject: [Biopython] Host_organism field in SwissProt
In-Reply-To: <fdcd75820912010825w76a8aa55q4385cae0c8e0b49@mail.gmail.com>
References: <fdcd75820912010825w76a8aa55q4385cae0c8e0b49@mail.gmail.com>
Message-ID: <320fb6e00912011121o41237344v61d1570a919d54b4@mail.gmail.com>

On Tue, Dec 1, 2009 at 4:25 PM, bar tomas <bartomas at gmail.com> wrote:
> Hi,
> I'm using BioPython for processing protein sequences from SwissProt database.
> I'm following the excellent tutorial documentation on SwissProt querying (p.107)
> I'm just wondering about the meaning of the field 'host_organism' in a
> swissprot record, as I haven't yet found a record where the value of
> this field is supplied.
> If the record concerns the protein sequence of a bacteria, for
> instance, does the host_organism field contain a list of taxonomic ids
> of possible host organisms where the bacteria can be found?
> Many thanks

I suspect (without checking) that this field only applies to viruses
(or perhaps pathogens) and so will usually be empty.

Peter

P.S. Page numbers (and even section numbers) in the tutorial do
change from release to release - the section names are usually
stable.


From biopython at maubp.freeserve.co.uk  Tue Dec  1 19:34:19 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Dec 2009 19:34:19 +0000
Subject: [Biopython] Fwd: [Utilities-announce] NCBI E-Utility Policy Change
In-Reply-To: <320fb6e00912011129j68dda3b2p6df9a232f0462458@mail.gmail.com>
References: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov>
	<320fb6e00912011129j68dda3b2p6df9a232f0462458@mail.gmail.com>
Message-ID: <320fb6e00912011134u2481644aw5dfdfe9f9a3049f0@mail.gmail.com>

Hi all,

Attention NCBI Entrez users - the NCBI really do want you to include
your email address, and it will be mandatory in future! See below...

If using Bio.Entrez, the tool parameter will by default be set to
Biopython, but the email is omitted. We already encourage the email
to be included in our documentation but given the new NCBI guidance
I'd suggest we make omitting the email issue a warning in the next
release (and an error in the subsequent release of Biopython?).

Peter


---------- Forwarded message ----------
From: ?<utilities-announce at ncbi.nlm.nih.gov>
Date: Tue, Dec 1, 2009 at 6:59 PM
Subject: [Utilities-announce] NCBI E-Utility Policy Change
To: utilities-announce at ncbi.nlm.nih.gov


As part of an ongoing effort to ensure efficient access to the Entrez
Utilities (E-utilities) by all users, NCBI has decided to change the
usage policy for the E-utilities effective June 1, 2010. Effective on
June 1, 2010, all E-utility requests, either using standard URLs or
SOAP, must contain non-null values for both the &tool and &email
parameters. Any E-utility request made after June 1, 2010 that does
not contain values for both parameters will return an error explaining
that these parameters must be included in E-utility requests.



The value of the &tool parameter should be a URI-safe string that is
the name of the software package, script or web page producing the
E-utility request.



The value of the &email parameter should be a valid e-mail address for
the appropriate contact person or group responsible for maintaining
the tool producing the E-utility request.



NCBI uses these parameters to contact users whose use of the
E-utilities violates the standard usage policies described at
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements.
These usage policies are designed to prevent excessive requests from a
small group of users from reducing or eliminating the wider
community's access to the E-utilities. NCBI will attempt to contact a
user at the e-mail address provided in the &email parameter prior to
blocking access to the E-utilities.



NCBI realizes that this policy change will require many of our users
to change their code. Based on past experience, we anticipate that
most of our users should be able to make the necessary changes before
the June 1, 2010 deadline. If you have any concerns about making these
changes by that date, or if you have any questions about these
policies, please contact eutilities at ncbi.nlm.nih.gov.



Thank you for your understanding and cooperation in helping us
continue to deliver a reliable and efficient web service.



_______________________________________________
Utilities-announce mailing list
http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce
-------------- next part --------------
_______________________________________________
Utilities-announce mailing list
http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce

From cjfields at illinois.edu  Tue Dec  1 19:54:48 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 1 Dec 2009 13:54:48 -0600
Subject: [Biopython] Fwd: [Utilities-announce] NCBI E-Utility Policy
	Change
In-Reply-To: <320fb6e00912011134u2481644aw5dfdfe9f9a3049f0@mail.gmail.com>
References: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov>
	<320fb6e00912011129j68dda3b2p6df9a232f0462458@mail.gmail.com>
	<320fb6e00912011134u2481644aw5dfdfe9f9a3049f0@mail.gmail.com>
Message-ID: <1EE2400D-D3F7-49DC-82D7-001EE18F2030@illinois.edu>

I'll be following the same (exclusion of the email a warning in next bioperl release in Jan, and an error for the spring release).

chris

On Dec 1, 2009, at 1:34 PM, Peter wrote:

> Hi all,
> 
> Attention NCBI Entrez users - the NCBI really do want you to include
> your email address, and it will be mandatory in future! See below...
> 
> If using Bio.Entrez, the tool parameter will by default be set to
> Biopython, but the email is omitted. We already encourage the email
> to be included in our documentation but given the new NCBI guidance
> I'd suggest we make omitting the email issue a warning in the next
> release (and an error in the subsequent release of Biopython?).
> 
> Peter
> 
> 
> ---------- Forwarded message ----------
> From:  <utilities-announce at ncbi.nlm.nih.gov>
> Date: Tue, Dec 1, 2009 at 6:59 PM
> Subject: [Utilities-announce] NCBI E-Utility Policy Change
> To: utilities-announce at ncbi.nlm.nih.gov
> 
> 
> As part of an ongoing effort to ensure efficient access to the Entrez
> Utilities (E-utilities) by all users, NCBI has decided to change the
> usage policy for the E-utilities effective June 1, 2010. Effective on
> June 1, 2010, all E-utility requests, either using standard URLs or
> SOAP, must contain non-null values for both the &tool and &email
> parameters. Any E-utility request made after June 1, 2010 that does
> not contain values for both parameters will return an error explaining
> that these parameters must be included in E-utility requests.
> 
> 
> 
> The value of the &tool parameter should be a URI-safe string that is
> the name of the software package, script or web page producing the
> E-utility request.
> 
> 
> 
> The value of the &email parameter should be a valid e-mail address for
> the appropriate contact person or group responsible for maintaining
> the tool producing the E-utility request.
> 
> 
> 
> NCBI uses these parameters to contact users whose use of the
> E-utilities violates the standard usage policies described at
> http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements.
> These usage policies are designed to prevent excessive requests from a
> small group of users from reducing or eliminating the wider
> community's access to the E-utilities. NCBI will attempt to contact a
> user at the e-mail address provided in the &email parameter prior to
> blocking access to the E-utilities.
> 
> 
> 
> NCBI realizes that this policy change will require many of our users
> to change their code. Based on past experience, we anticipate that
> most of our users should be able to make the necessary changes before
> the June 1, 2010 deadline. If you have any concerns about making these
> changes by that date, or if you have any questions about these
> policies, please contact eutilities at ncbi.nlm.nih.gov.
> 
> 
> 
> Thank you for your understanding and cooperation in helping us
> continue to deliver a reliable and efficient web service.
> 
> 
> 
> _______________________________________________
> Utilities-announce mailing list
> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce
> <ATT00001.txt>_______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython




From mike.thon at gmail.com  Wed Dec  2 12:31:45 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Wed, 2 Dec 2009 13:31:45 +0100
Subject: [Biopython] Getting the sequence for a SeqFeature
In-Reply-To: <320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
References: <320fb6e00911060422u2d2742d5r7b5b1db98c991df5@mail.gmail.com>
	<320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
Message-ID: <0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>

I was wondering if you have implemented this method yet and if so, is it in a repository somewhere where I can try it?  I was about to post a message on this and I searched the archives first (!) and found this thread.  I have genbank genomic sequences and I need to get the transcript sequences for the CDS features.  

thanks
Mike

On Nov 6, 2009, at 1:47 PM, Peter wrote:

> On Fri, Nov 6, 2009 at 12:22 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> Hi all,
>> 
>> I am planing to add a new method to the SeqFeature object, but
>> would like a little feedback first. This email is really just the
>> background - I'll write up a few examples later to try and make
>> this a bit clearer...
> 
> OK, here is a non-trivial example - the first CDS feature in the
> GenBank file NC_000932.gb (included as a Biopython unit test),
> which is a three part join on the reverse strand. In this case, the
> GenBank file includes the protein translation for the CDS features
> so we can use it to check our results.
> 
> We can parse this GenBank file into a SeqRecord with:
> 
> from Bio import SeqIO
> record = SeqIO.read(open("../biopython/Tests/GenBank/NC_000932.gb"), "gb")
> 
> Let's have a look at the first CDS feature (index 2):
> 
> f = record.features[2]
> print f.type, f.location, f.strand, f.location_operator
> for sub_f in f.sub_features :
>    print " - ", sub_f.location, sub_f.strand
> table = f.qualifiers.get("transl_table",[1])[0] # List of one int
> print "Table", table
> 
> Giving:
> 
> CDS [97998:69724] -1 join
> -  [97998:98024] -1
> -  [98561:98793] -1
> -  [69610:69724] -1
> Table 11
> 
> Looking at the raw GenBank file, this feature has location string:
> 
> complement(join(97999..98024,98562..98793,69611..69724))
> 
> i.e. To get the sequence you need to do this (note zero based
> Python counting as in the output above):
> 
> print (record.seq[97998:98024] + record.seq[98561:98793] +
> record.seq[69610:69724]).reverse_complement()
> 
> And then translate it using NCBI genetic code table 11,
> 
> print "Manual translation:"
> print (record.seq[97998:98024] + record.seq[98561:98793] +
> record.seq[69610:69724]).reverse_complement().translate(table=11,
> cds=True)
> print "Given translation:"
> print f.qualifiers["translation"][0] # List of one string
> print "Biopython translation (with proposed code):"
> print f.extract(record.seq).translate(table, cds=True)
> 
> And the output, together with the provided translation in the
> feature annotation, and the shortcut with the new code I am
> proposing to include in Biopython:
> 
> Manual translation:
> MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK
> Given translation:
> MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK
> Biopython translation:
> MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK
> 
> The point of all this was with the proposed new extract method,
> you just need:
> 
> feature_seq = f.extract(record.seq)
> 
> instead of:
> 
> feature_seq = (record.seq[97998:98024] + record.seq[98561:98793] +
> record.seq[69610:69724]).reverse_complement()
> 
> which is in itself a slight simplification since you'd need to get the
> those coordinates from the sub features, worry about strands, etc.
> 
> Peter
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython




From kellrott at gmail.com  Wed Dec  2 15:12:53 2009
From: kellrott at gmail.com (Kyle Ellrott)
Date: Wed, 2 Dec 2009 07:12:53 -0800
Subject: [Biopython] Getting the sequence for a SeqFeature
In-Reply-To: <0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>
References: <320fb6e00911060422u2d2742d5r7b5b1db98c991df5@mail.gmail.com>
	<320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
	<0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>
Message-ID: <bb02be080912020712w51d3515bk85d0e66d9d9b195f@mail.gmail.com>

On Wed, Dec 2, 2009 at 4:31 AM, Michael Thon <mike.thon at gmail.com> wrote:

> I was wondering if you have implemented this method yet and if so, is it in
> a repository somewhere where I can try it?  I was about to post a message on
> this and I searched the archives first (!) and found this thread.  I have
> genbank genomic sequences and I need to get the transcript sequences for the
> CDS features.
>
>
It should be in the main GIT repository at
http://github.com/biopython/biopython/
It's to new to have made an official release version yet.

Kyle


From biopython at maubp.freeserve.co.uk  Wed Dec  2 22:44:11 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 2 Dec 2009 22:44:11 +0000
Subject: [Biopython] Getting the sequence for a SeqFeature
In-Reply-To: <bb02be080912020712w51d3515bk85d0e66d9d9b195f@mail.gmail.com>
References: <320fb6e00911060422u2d2742d5r7b5b1db98c991df5@mail.gmail.com>
	<320fb6e00911060447g779f2ac2i7739a28c3f4a4077@mail.gmail.com>
	<0EAFC700-CFDB-4D0B-882A-B9D0EF492172@gmail.com>
	<bb02be080912020712w51d3515bk85d0e66d9d9b195f@mail.gmail.com>
Message-ID: <320fb6e00912021444g11b27f81k8a3c8675ddc25169@mail.gmail.com>

On Wed, Dec 2, 2009 at 3:12 PM, Kyle Ellrott <kellrott at gmail.com> wrote:
> On Wed, Dec 2, 2009 at 4:31 AM, Michael Thon <mike.thon at gmail.com> wrote:
>
>> I was wondering if you have implemented this method yet and if so, is it in
>> a repository somewhere where I can try it? ?I was about to post a message on
>> this and I searched the archives first (!) and found this thread. ?I have
>> genbank genomic sequences and I need to get the transcript sequences for the
>> CDS features.
>>
>
> It should be in the main GIT repository at
> http://github.com/biopython/biopython/
> It's to new to have made an official release version yet.
>
> Kyle

Kyle has also been following the dicussion on the dev mailing
list, where it was mentioned this was now "on the trunk". See
also: http://www.biopython.org/wiki/SourceCode

Getting people using and testing the code now would be nice,
especially if we hope to get a release out before too long.

Peter



From richard_w_g_price at academia.edu  Thu Dec  3 01:21:26 2009
From: richard_w_g_price at academia.edu (Richard Price)
Date: Wed, 2 Dec 2009 17:21:26 -0800
Subject: [Biopython] New Academia.edu feature for Biopython
Message-ID: <cc0d7cc0912021721g660b39a2ga13c8213ec701454@mail.gmail.com>

Dear Biopython members,


I wanted to tell the list about a new feature on Academia.edu.
Academia.edu launched 12 months ago and now helps 300,000 academics a
month answer the question 'who's researching what?'


We have built a dedicated page on Academia.edu for the Biopython mailing list:


http://lists.academia.edu/See-members-of-Biopython


This page will show you fellow members already on Academia.edu.  You
can see their papers, research interests, and other information.


Visit the link below, sign up with Academia.edu, and see who else from
Biopython is on Academia.edu.



http://lists.academia.edu/See-members-of-Biopython


Richard


Dr. Richard Price, post-doc, Philosophy Dept, Oxford University.
Founder of Academia.edu


From mike.thon at gmail.com  Thu Dec  3 05:20:12 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 3 Dec 2009 06:20:12 +0100
Subject: [Biopython] can't compile version from github
Message-ID: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>

Don't know if this belongs on the dev mailing list or here...

I just checked out a copy of biopython from the github repo and I tried to install it in an non-root directory to try out a new feature.  

here is the command I ran on the command line:
python setup.py install --prefix=/Users/mike/biopython_dev

Here is the offending part of the compile:

gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype

The installer did not find the numpy that I installed using easy_install so I continued without it and without Reportlab.  (Mac OS 10.6)

Mike







From biopython at maubp.freeserve.co.uk  Thu Dec  3 10:19:32 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 3 Dec 2009 10:19:32 +0000
Subject: [Biopython] can't compile version from github
In-Reply-To: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
Message-ID: <320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>

On Thu, Dec 3, 2009 at 5:20 AM, Michael Thon <mike.thon at gmail.com> wrote:
> Don't know if this belongs on the dev mailing list or here...

Tricky - I might have picked the dev list, but this is fine.

> I just checked out a copy of biopython from the github repo and I
> tried to install it in an non-root directory to try out a new feature.
>
> here is the command I ran on the command line:
> python setup.py install --prefix=/Users/mike/biopython_dev
>
> Here is the offending part of the compile:
>
> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
> In file included from Bio/triemodule.c:3:
> Bio/trie.h:12: warning: function declaration isn?t a prototype
>
> The installer did not find the numpy that I installed using easy_install
> so I continued without it and without Reportlab. ?(Mac OS 10.6)
>
> Mike

Ah - Snow Leopard. Are you using the Apple provided Python with Mac OS 10.6?
Apple have as usual done odd things with Python, but people have
reported getting
it to work.

Looking at the compiler flags I am puzzled about the inclusion of
"-arch ppc" since
Snow Leopard is x86 only. Could you give us the whole of the compile log? What
you have shown just has a warning - no actual error. Also, doing it in
stages would
be wiser:

#First remove old build files:
python setup clean

#Do the compile:
python setup build

#Run the unit tests:
python setup test

#To install under your home directory I'd use:
python steup install --prefix=/Users/mike/

Peter



From mike.thon at gmail.com  Thu Dec  3 12:17:17 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 3 Dec 2009 13:17:17 +0100
Subject: [Biopython] can't compile version from github
In-Reply-To: <320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
	<320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
Message-ID: <EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>


On Dec 3, 2009, at 11:19 AM, Peter wrote:

> On Thu, Dec 3, 2009 at 5:20 AM, Michael Thon <mike.thon at gmail.com> wrote:
>> Don't know if this belongs on the dev mailing list or here...
> 
> Tricky - I might have picked the dev list, but this is fine.
> 
>> I just checked out a copy of biopython from the github repo and I
>> tried to install it in an non-root directory to try out a new feature.
>> 
>> here is the command I ran on the command line:
>> python setup.py install --prefix=/Users/mike/biopython_dev
>> 
>> Here is the offending part of the compile:
>> 
>> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
>> In file included from Bio/triemodule.c:3:
>> Bio/trie.h:12: warning: function declaration isn?t a prototype
>> 
>> The installer did not find the numpy that I installed using easy_install
>> so I continued without it and without Reportlab.  (Mac OS 10.6)
>> 
>> Mike
> 
> Ah - Snow Leopard. Are you using the Apple provided Python with Mac OS 10.6?
> Apple have as usual done odd things with Python, but people have
> reported getting
> it to work.

 
Yup, I'm using the Apple-provided python.  Below is the full output of the build phase.  

...so, as usual, I am off on a tangent instead of working on the stuff that actually needs to get done.  I don't really need to get this installed.  I just wanted to try the SeqFeature.extract method that you mentioned in a previous thread.  I realized that I probably don't need to compile all the C extensions to get that to work so I opened up SeqFeature.py to see what this method looks like.  I couldn't find it so I suppose this method has not made its way into the main git repo on github.  In the end, I wrote one myself but it would still be good to compare its output to what you have in biopython.

...but I still have this biopython from github that won't compile and it probably should.  So, if you have any ideas what might be wrong and how to fix it I can try it and report back.
-Mike

python setup.py build
running build
running build_py
*** Numerical Python *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Numerical Python at http://numpy.sourceforge.net/.

Do you want to continue this installation? (Y/n)  Y
*** Reportlab *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Reportlab at http://www.reportlab.org/downloads.html.

Do you want to continue this installation? (Y/n)  Y
running build_ext
building 'Bio.trie' extension
creating build/temp.macosx-10.6-universal-2.6
creating build/temp.macosx-10.6-universal-2.6/Bio
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ?_write_value_to_handle?:
Bio/triemodule.c:480: error: too few arguments to function ?PyMarshal_WriteObjectToString?
Bio/triemodule.c:482: warning: passing argument 3 of ?PyString_AsStringAndSize? from incompatible pointer type
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ?_write_value_to_handle?:
Bio/triemodule.c:480: error: too few arguments to function ?PyMarshal_WriteObjectToString?
Bio/triemodule.c:482: warning: passing argument 3 of ?PyString_AsStringAndSize? from incompatible pointer type
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn?t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ?_write_value_to_handle?:
Bio/triemodule.c:480: error: too few arguments to function ?PyMarshal_WriteObjectToString?
Bio/triemodule.c:482: warning: passing argument 3 of ?PyString_AsStringAndSize? from incompatible pointer type
lipo: can't open input file: /var/folders/wI/wIckOkhJHe0hxBDeAEI1VE+++TI/-Tmp-//ccemhRHR.out (No such file or directory)
error: command 'gcc-4.2' failed with exit status 1




From biopython at maubp.freeserve.co.uk  Thu Dec  3 12:26:12 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 3 Dec 2009 12:26:12 +0000
Subject: [Biopython] can't compile version from github
In-Reply-To: <EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
	<320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
	<EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>
Message-ID: <320fb6e00912030426gc84e3f5w6e238638e9b40b2e@mail.gmail.com>

On Thu, Dec 3, 2009 at 12:17 PM, Michael Thon <mike.thon at gmail.com> wrote:
>
> Yup, I'm using the Apple-provided python. ?Below is the full output of the build phase.

I'll take a look at it, but until I have a machine with Snow Leopard,
solving this will be tricky. Any other Snow Leopard users please
speak up.

> ...so, as usual, I am off on a tangent instead of working on the stuff that
> actually needs to get done. ?I don't really need to get this installed. ?I just
> wanted to try the SeqFeature.extract method that you mentioned in a
> previous thread. ?I realized that I probably don't need to compile all the
> C extensions to get that to work so I opened up SeqFeature.py to see
> what this method looks like. ?I couldn't find it so I suppose this method
> has not made its way into the main git repo on github. ?In the end, I
> wrote one myself but it would still be good to compare its output to
> what you have in biopython.

I'm not sure why you couldn't find this in the latest code from git.
The method is in Bio/SeqFeature.py, search for "def extract":
http://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py

You can probably take a working Biopython 1.52 install, and manually
update just the Bio/SeqFeature.py file if you really need to.

You could also try installing just the "pure Python" part of Biopython
by hacking setup.py to set EXTENSIONS = [], as done for Jython.

> ...but I still have this biopython from github that won't compile and it
> probably should. ?So, if you have any ideas what might be wrong and
> how to fix it I can try it and report back.

I'll try to get back to you on this shortly.

Peter



From johncumbers at gmail.com  Fri Dec  4 07:50:43 2009
From: johncumbers at gmail.com (John Cumbers)
Date: Thu, 3 Dec 2009 23:50:43 -0800
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
	<320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
	<320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>
Message-ID: <cfd758050912032350w61e2fc82v6c674834765e3c32@mail.gmail.com>

Many thanks Peter,
Sorry for delayed reply, I filter this list and forgot to check the folder
:)
Best wishes,
John

John Cumbers, Ph.D Candidate
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.
cell +1 (401) 523 8190, office +1 (650) 604-1914, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA


On Tue, Dec 1, 2009 at 11:19 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Tue, Dec 1, 2009 at 9:52 AM, Peter <biopython at maubp.freeserve.co.uk>
> wrote:
> >
> > It looks like an undocumented option, much like -phyi (which I guessed)
> > for PHYLIP interlaced and -phys for PHYLIP sequential. These match
> > the documented format options (e.g. -msf, -html, -clw and -clwstrict).
> > i.e. You can use this:
> >
> > "muscle -in myinputfile -phyi -out myoutputfile"
> >
> > I think we should ask the MUSCLE author which of these
> > undocumented arguments are actually supported rather than
> > adding them all.
>
> Robert Edgar agreed the documentation was out of sync, and has
> confirmed these are safe arguments to include in our wrapper.
>
> Peter
>


From biopython at maubp.freeserve.co.uk  Fri Dec  4 12:32:23 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 4 Dec 2009 12:32:23 +0000
Subject: [Biopython] MuscleCommandline and phyiout
In-Reply-To: <cfd758050912032350w61e2fc82v6c674834765e3c32@mail.gmail.com>
References: <cfd758050911302310m483226d0r324587344daecde5@mail.gmail.com>
	<320fb6e00912010123j984fcc2s34499263295164dc@mail.gmail.com>
	<320fb6e00912010152r6e2f50e4v90091a98524481ed@mail.gmail.com>
	<320fb6e00912011119o62d5ef51t1f27f7a4c310a026@mail.gmail.com>
	<cfd758050912032350w61e2fc82v6c674834765e3c32@mail.gmail.com>
Message-ID: <320fb6e00912040432k628392c5n57fc79a3b68a88eb@mail.gmail.com>

On Fri, Dec 4, 2009 at 7:50 AM, John Cumbers <johncumbers at gmail.com> wrote:
> Many thanks Peter,
> Sorry for delayed reply, I filter this list and forgot to check the folder
> :)
> Best wishes,
> John

Bug filed,
http://bugzilla.open-bio.org/show_bug.cgi?id=2961


From brynedal at gmail.com  Fri Dec  4 19:01:49 2009
From: brynedal at gmail.com (Boel Brynedal)
Date: Fri, 4 Dec 2009 14:01:49 -0500
Subject: [Biopython] Problems installing Biopython
Message-ID: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>

Dear List,

I am trying to install Biopython from source on my Mac OS X v.10.6.1. I ran
into some problems when building Biopython, thought that it might be due to
the fact that I am missing xcore tools (gcc-4.0 was missing) so I installed
version 2.5 of xcore. This is however the output as I try to build biopython
after installing xcore:

$ python setup.py install
running install
running build
running build_py
creating build
a lot of creating, copying etc etc...
running build_ext
building 'Bio.clistfns' extension
creating build/temp.macosx-10.3-fat-2.6
creating build/temp.macosx-10.3-fat-2.
6/Bio
gcc-4.0 -arch ppc -arch i386 -fno-strict-aliasing -fno-common -dynamic
-DNDEBUG -g -O3
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
Bio/clistfnsmodule.c -o build/temp.macosx-10.3-fat-2.6/Bio/clistfnsmodule.o
In file included from /usr/include/architecture/i386/math.h:626,
                 from /usr/include/math.h:28,
                 from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/pyport.h:235,
                 from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:58,
                 from Bio/clistfnsmodule.c:10:
/usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
Intel with Mac OS X Deployment Target < 10.4 is invalid.
Compiling with an SDK that doesn't seem to exist:
/Developer/SDKs/MacOSX10.4u.sdk
Please check your Xcode installation
gcc-4.0 -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g
-bundle -undefined dynamic_lookup
build/temp.macosx-10.3-fat-2.6/Bio/clistfnsmodule.o -o
build/lib.macosx-10.3-fat-2.6/Bio/clistfns.so
ld: library not found for -lbundle1.o
collect2: ld returned 1 exit status
ld: library not found for -lbundle1.o
collect2: ld returned 1 exit status
lipo: can't open input file:
/var/folders/fy/fySdohlPEBSVFU-YIflSGk+++TI/-Tmp-//cc1Cm89x.out (No such
file or directory)
error: command 'gcc-4.0' failed with exit status 1


I am new to using Mac, and not the most talented computer nerd, but it seems
like we have two problems here:
the systems seems to be looking for MacOSX10.4u.sdk, when the xcore tools
I've installed contain MacOSX10.5.sdk and MacOSX10.6.sdk. Why does it look
for the earlier version, and what can I do about it?
#warning Building for Intel with Mac OS X Deployment Target < 10.4 is
invalid - this I do not understand at all.

I'm using Python 2.6.4 and I'm trying to install biopython-1.52.

Any tips, comments or ideas would be greatly appreciated!
Thank you,
Boel


From mike.thon at gmail.com  Fri Dec  4 20:27:41 2009
From: mike.thon at gmail.com (Michael Thon)
Date: Fri, 4 Dec 2009 21:27:41 +0100
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
Message-ID: <6D780E44-39B7-4CFF-975B-D72722A5E5B2@gmail.com>

Hi Boel - I installed biopython using easy_install on Mac OS 10.6.2 and didn't have any problems.  I don't know what xcore is.  Do you mean Xcode?  the version I have is 3.2.1 and I downloaded it from developer.apple.com

-Mike




From p.j.a.cock at googlemail.com  Fri Dec  4 20:52:46 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 4 Dec 2009 20:52:46 +0000
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
Message-ID: <320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>

On Fri, Dec 4, 2009 at 7:01 PM, Boel Brynedal wrote:
> Dear List,
>
> I am new to using Mac, and not the most talented computer
> nerd, but it seems like we have two problems here:
> the systems seems to be looking for MacOSX10.4u.sdk,
> when the xcore tools I've installed contain MacOSX10.5.sdk
> and MacOSX10.6.sdk. Why does it look
> for the earlier version, and what can I do about it?
> #warning Building for Intel with Mac OS X Deployment Target < 10.4 is
> invalid - this I do not understand at all.

Sadly there are some general issues with Python on
Snow Leopard (this isn't just a Biopython issue). Right
now as far as I know none of our core developers have
Snow Leopard (10.6) so it is hard to help.

However, with Leopard (10.4), when installing XCode I
had the option of installing the 10.3 headers too. Could
you re-install XCode and check this time for an option
to include the headers for 10.4 (and/or 10.3)?

Peter


From mjldehoon at yahoo.com  Sat Dec  5 15:59:41 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 5 Dec 2009 07:59:41 -0800 (PST)
Subject: [Biopython] CompareAce parser
Message-ID: <613008.1949.qm@web62407.mail.re1.yahoo.com>

Hi everybody,

In Bio.Motif, there is a nominal parser for CompareAce files. However, this parser has almost no functionality. Would anybody mind if we deprecate this module for the next release? Whereas we usually might declare the module obsolete before deprecating it, in this case I think we can deprecate it straightaway since currently this parser does very little.

--Michiel.


      


From bartek at rezolwenta.eu.org  Sun Dec  6 00:58:41 2009
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Sun, 6 Dec 2009 01:58:41 +0100
Subject: [Biopython] CompareAce parser
In-Reply-To: <613008.1949.qm@web62407.mail.re1.yahoo.com>
References: <613008.1949.qm@web62407.mail.re1.yahoo.com>
Message-ID: <8b34ec180912051658s2acb9da1na03a8b0577fa6a8d@mail.gmail.com>

Hi,

I don't have anything against deprecating, even though I don't the
advantages of doing so. (the module is trivial, but so is the output
of compareACE: a number giving a score between motifs. The score,
however is not trivial and I wouldn't want to reimplement it.)

cheers
  Bartek

On Sat, Dec 5, 2009 at 4:59 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi everybody,
>
> In Bio.Motif, there is a nominal parser for CompareAce files. However, this parser has almost no functionality. Would anybody mind if we deprecate this module for the next release? Whereas we usually might declare the module obsolete before deprecating it, in this case I think we can deprecate it straightaway since currently this parser does very little.
>
> --Michiel.
>
>
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>



-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433



From biopython at maubp.freeserve.co.uk  Sun Dec  6 14:10:22 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 6 Dec 2009 14:10:22 +0000
Subject: [Biopython] CompareAce parser
In-Reply-To: <8b34ec180912051658s2acb9da1na03a8b0577fa6a8d@mail.gmail.com>
References: <613008.1949.qm@web62407.mail.re1.yahoo.com>
	<8b34ec180912051658s2acb9da1na03a8b0577fa6a8d@mail.gmail.com>
Message-ID: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>

On Sun, Dec 6, 2009 at 12:58 AM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> Hi,
>
> I don't have anything against deprecating, even though I don't the
> advantages of doing so. (the module is trivial, but so is the output
> of compareACE: a number giving a score between motifs. The score,
> however is not trivial and I wouldn't want to reimplement it.)
>
> cheers
> ?Bartek

So the reason this parser is so simple and has almost no functionality
is just a reflection of the simplicity of the CompareAce files? If so, I'd
say leave the parser in.

Peter



From mjldehoon at yahoo.com  Sun Dec  6 14:31:47 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sun, 6 Dec 2009 06:31:47 -0800 (PST)
Subject: [Biopython] CompareAce parser
In-Reply-To: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
Message-ID: <889087.95522.qm@web62406.mail.re1.yahoo.com>

> So the reason this parser is so simple and has almost no
> functionality is just a reflection of the simplicity of
> the CompareAce files?

Not exactly. CompareAce files can have different outputs, depending on the query given to CompareAce. The simplest query returns only one number. The current CompareAce parser can only parse this output. In other words,

>>> input = open("test.out")
>>> from Bio.Motif.Parsers import AlignAce
>>> AlignAce.CompareAceParser().parse(input)
0.92130000000000001

is equivalent to

>>> input = open("test.out")
>>> float(input.read())
0.92130000000000001

I am not against having a CompareAce parser in Biopython, but if we have such a parser it should be able to handle more output formats than just the trivial output format.

With this in mind, I think we should either extend the CompareAce parser to handle cases that cannot be trivially handled by a simple Python command, or remove it altogether. If we do keep it in Biopython, there should also be some documentation to cover it, and perhaps a unit test.

--Michiel

--- On Sun, 12/6/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] CompareAce parser
> To: "Bartek Wilczynski" <bartek at rezolwenta.eu.org>
> Cc: "Michiel de Hoon" <mjldehoon at yahoo.com>, biopython at biopython.org
> Date: Sunday, December 6, 2009, 9:10 AM
> On Sun, Dec 6, 2009 at 12:58 AM,
> Bartek Wilczynski
> <bartek at rezolwenta.eu.org>
> wrote:
> > Hi,
> >
> > I don't have anything against deprecating, even though
> I don't the
> > advantages of doing so. (the module is trivial, but so
> is the output
> > of compareACE: a number giving a score between motifs.
> The score,
> > however is not trivial and I wouldn't want to
> reimplement it.)
> >
> > cheers
> > ?Bartek
> 
> So the reason this parser is so simple and has almost no
> functionality
> is just a reflection of the simplicity of the CompareAce
> files? If so, I'd
> say leave the parser in.
> 
> Peter
> 


      



From brynedal at gmail.com  Sun Dec  6 21:38:55 2009
From: brynedal at gmail.com (Boel Brynedal)
Date: Sun, 6 Dec 2009 16:38:55 -0500
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
	<320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>
Message-ID: <2167c9200912061338g164a8f61x25df698cab5c0548@mail.gmail.com>

Hi Peter,

I downloaded XCode again and included the 10.4 support - this seem to have
fixed it.
Thank you very much!

Boel

2009/12/4 Peter Cock <p.j.a.cock at googlemail.com>

> On Fri, Dec 4, 2009 at 7:01 PM, Boel Brynedal wrote:
> > Dear List,
> >
> > I am new to using Mac, and not the most talented computer
> > nerd, but it seems like we have two problems here:
> > the systems seems to be looking for MacOSX10.4u.sdk,
> > when the xcore tools I've installed contain MacOSX10.5.sdk
> > and MacOSX10.6.sdk. Why does it look
> > for the earlier version, and what can I do about it?
> > #warning Building for Intel with Mac OS X Deployment Target < 10.4 is
> > invalid - this I do not understand at all.
>
> Sadly there are some general issues with Python on
> Snow Leopard (this isn't just a Biopython issue). Right
> now as far as I know none of our core developers have
> Snow Leopard (10.6) so it is hard to help.
>
> However, with Leopard (10.4), when installing XCode I
> had the option of installing the 10.3 headers too. Could
> you re-install XCode and check this time for an option
> to include the headers for 10.4 (and/or 10.3)?
>
> Peter
>


From biopython at maubp.freeserve.co.uk  Sun Dec  6 21:49:28 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 6 Dec 2009 21:49:28 +0000
Subject: [Biopython] Problems installing Biopython
In-Reply-To: <2167c9200912061338g164a8f61x25df698cab5c0548@mail.gmail.com>
References: <2167c9200912041101m5df4d144n8cdff208e8dc3b1c@mail.gmail.com>
	<320fb6e00912041252u705058c2ue06c4b88d4e34059@mail.gmail.com>
	<2167c9200912061338g164a8f61x25df698cab5c0548@mail.gmail.com>
Message-ID: <320fb6e00912061349v2dbc3586g185701894e8e7c05@mail.gmail.com>

> 2009/12/4 Peter Cock <p.j.a.cock at googlemail.com>
>> However, with Leopard (10.4), when installing XCode I
>> had the option of installing the 10.3 headers too. Could
>> you re-install XCode and check this time for an option
>> to include the headers for 10.4 (and/or 10.3)?

Minor typo - Leopard is Mac OS 10.5 of course ;)

On Sun, Dec 6, 2009 at 9:38 PM, Boel Brynedal wrote:
> Hi Peter,
>
> I downloaded XCode again and included the 10.4 support - this
> seem to have fixed it.
> Thank you very much!
>
> Boel

Excellent - thanks for letting us know.

Peter


From biopython at maubp.freeserve.co.uk  Mon Dec  7 12:14:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Dec 2009 12:14:35 +0000
Subject: [Biopython] Deprecating old Bio.GFF module in preparation for new
	code?
Message-ID: <320fb6e00912070414i3e4503dt311953b99d2efeb5@mail.gmail.com>

Dear all,

Is anyone using the "old" Bio.GFF module in Biopython?

This was written by Michael Hoffman back 2002, and allowed
access to a General Feature Format (GFF) MySQL database
created with BioPerl's Bio::DB:GFF.  It may need updating to
work with the latest BioPerl, or GFF3 files (I don't know). This
old code did not include any GFF parser of its own.

As those on the dev mailing list will know, Brad Chapman
has been working on a GFF parser (covering GFF3, and
the older GFF2 and GTF files). The obvious place to put
this is under Bio.GFF.

I would therefore like to propose deprecating the current
Bio.GFF code in the next release of Biopython (hopefully
this month), which will allow us to replace it with Brad's
new parser in the subsequent release.

If anyone is using the old module, please let us know now.

Thank you,

Peter


From biopython at maubp.freeserve.co.uk  Mon Dec  7 14:02:51 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Dec 2009 14:02:51 +0000
Subject: [Biopython] can't compile version from github
In-Reply-To: <320fb6e00912030426gc84e3f5w6e238638e9b40b2e@mail.gmail.com>
References: <909D70B5-2F42-46A8-9F57-407CA362E4EB@gmail.com>
	<320fb6e00912030219j42948b7fue5a3fd8610d66641@mail.gmail.com>
	<EE85D7C2-5794-4F68-8A05-9C2B01E6064F@gmail.com>
	<320fb6e00912030426gc84e3f5w6e238638e9b40b2e@mail.gmail.com>
Message-ID: <320fb6e00912070602i3a881fd7nd758d71ce0d1a3f4@mail.gmail.com>

On Thu, Dec 3, 2009 at 12:26 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Dec 3, 2009 at 12:17 PM, Michael Thon <mike.thon at gmail.com> wrote:
>
>> ...but I still have this biopython from github that won't compile and it
>> probably should. ?So, if you have any ideas what might be wrong and
>> how to fix it I can try it and report back.
>
> I'll try to get back to you on this shortly.
>

Hi Michael,

As discussed on the other thread, could you try reinstalling XCode on
Snow Leopard (Mac OS X 10.6), but this time tick the option to include
the older headers (Tiger 10.4 SDK - not sure exactly what it is called).

http://lists.open-bio.org/pipermail/biopython/2009-December/005906.html

Peter



From iwan.grin at googlemail.com  Tue Dec  8 18:52:13 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Tue, 8 Dec 2009 19:52:13 +0100
Subject: [Biopython] Parsing problem
Message-ID: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>

Hi all,

I am having a little problem while trying to parse a GenBank (or rather
GenProt) file using BioPython. I am trying to extract the position on the
genome from the "coded_by" qualifier of the CDS feature of a protein.

The "coded_by" string in this specific case looks like this:

'complement(NC_012967.1:
3622110..3624728)'

Now, when I run

Bio.GFF.easy.LocationFromString('complement(NC_012967.1:3622110..3624728)' )

I get

File "/usr/lib/pymodules/python2.6/Bio/GFF/easy.py", line 419, in __init__
   list.__init__(self, [int(location_str)-1]) # zero based, nip it in the
bud
ValueError: invalid literal for int() with base 10:
'NC_012967.1:3622110..3624728'

Is there another way to parse this location string or do I have to cook up
some kind of custom RegExp?

Iwan

P.S.: Code snippet:

from Bio import Entrez
from Bio import SeqIO
from Bio import GFF
gi = 254163455
handle = Entrez.efetch(db="protein", id=gi, rettype="gb")
record= SeqIO.read(handle,"genbank")
handle.close()
for feature in record.features:
   if(feature.type=="CDS" and feature.qualifiers.has_key("coded_by")):
       print feature.qualifiers["coded_by"][0],
       loc=GFF.easy.LocationFromString(feature.qualifiers["coded_by"][0])
       print loc.start(),loc.end(), loc.complement


From biopython at maubp.freeserve.co.uk  Tue Dec  8 22:43:29 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 8 Dec 2009 22:43:29 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
Message-ID: <320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>

On Tue, Dec 8, 2009 at 6:52 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
> Hi all,
>
> I am having a little problem while trying to parse a GenBank (or rather
> GenProt) file using BioPython. I am trying to extract the position on the
> genome from the "coded_by" qualifier of the CDS feature of a protein.
>
> The "coded_by" string in this specific case looks like this:
>
> 'complement(NC_012967.1:
> 3622110..3624728)'

Oh, one of those tricky cross references to another file :(

> Now, when I run
>
> Bio.GFF.easy.LocationFromString('complement(NC_012967.1:3622110..3624728)' )
>

This is interesting timing - Bio.GFF.easy has a lot of
code which duplicated the EMBL/GenBank parsing,
and I'm actually suggesting we deprecate it in the
next release (!). What made you use Bio.GFF in the
first place? It has never been documented. That said,
it does look like you found a bug in Bio.GFF.easy ...

In the long term, I think Bio.GenBank would be a
better place to put this functionality (and reworking
the location parsing is on the todo list, partly as it
is currently a speed bottleneck).

Peter


From biopython at maubp.freeserve.co.uk  Tue Dec  8 23:53:29 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 8 Dec 2009 23:53:29 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
Message-ID: <320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>

On Tue, Dec 8, 2009 at 10:43 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Dec 8, 2009 at 6:52 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
>> Hi all,
>>
>> I am having a little problem while trying to parse a GenBank (or rather
>> GenProt) file using BioPython. I am trying to extract the position on the
>> genome from the "coded_by" qualifier of the CDS feature of a protein.
>>
>> The "coded_by" string in this specific case looks like this:
>>
>> 'complement(NC_012967.1:
>> 3622110..3624728)'
>
> Oh, one of those tricky cross references to another file :(

It looks like the Bio.GFF.easy code expects that to be formatted
as NC_012967.1:complement(3622110..3624728) and not as
complement(NC_012967.1:3622110..3624728)

Peter


From iwan.grin at googlemail.com  Wed Dec  9 12:33:09 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Wed, 9 Dec 2009 13:33:09 +0100
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
Message-ID: <b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>

Hi Peter, Thank you for your reply.

I am new to BioPython and stumbled upon GFF.easy while searching through the
API docs. Actually, What I wanted was a way to parse that location string
into an SeqFeature-like thing from which I could get start, end and
strand.Unfortunately I could not find the correct parser in Bio.Genbank -
any suggestions are welcome.

I agree with you that Bio.GFF.easy expects the Accession number before the
complement. (Actually for my purpose I do not need the accession number at
all.)

Iwan

2009/12/9 Peter <biopython at maubp.freeserve.co.uk>

> On Tue, Dec 8, 2009 at 10:43 PM, Peter <biopython at maubp.freeserve.co.uk>
> wrote:
> > On Tue, Dec 8, 2009 at 6:52 PM, Iwan Grin <iwan.grin at googlemail.com>
> wrote:
> >> Hi all,
> >>
> >> I am having a little problem while trying to parse a GenBank (or rather
> >> GenProt) file using BioPython. I am trying to extract the position on
> the
> >> genome from the "coded_by" qualifier of the CDS feature of a protein.
> >>
> >> The "coded_by" string in this specific case looks like this:
> >>
> >> 'complement(NC_012967.1:
> >> 3622110..3624728)'
> >
> > Oh, one of those tricky cross references to another file :(
>
> It looks like the Bio.GFF.easy code expects that to be formatted
> as NC_012967.1:complement(3622110..3624728) and not as
> complement(NC_012967.1:3622110..3624728)
>
> Peter
>


From biopython at maubp.freeserve.co.uk  Wed Dec  9 13:25:44 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Dec 2009 13:25:44 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
Message-ID: <320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>

On Wed, Dec 9, 2009 at 12:33 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
> Hi Peter, Thank you for your reply.
>
> I am new to BioPython and stumbled upon GFF.easy while searching through the
> API docs. Actually, What I wanted was a way to parse that location string
> into an SeqFeature-like thing from which I could get start, end and
> strand.Unfortunately I could not find the correct parser in Bio.Genbank -
> any suggestions are welcome.

Right now Bio.GenBank doesn't really expose the location parsing in an
easy to use way like Bio.GFF.easy does.

> I agree with you that Bio.GFF.easy expects the Accession number before the
> complement. (Actually for my purpose I do not need the accession number at
> all.)

The pragmatic solution is to write your own quick parser to pull out the
coordinates (if that is all you need).

We'll have to look at this as part of the discussion of what to do with the
old Bio.GFF (as part of planning for Brad's new GFF parsing code).

Peter


From chapmanb at 50mail.com  Wed Dec  9 13:38:02 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Wed, 9 Dec 2009 08:38:02 -0500
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
Message-ID: <20091209133802.GB79820@sobchak.mgh.harvard.edu>

Iwan and Peter;

> > I am new to BioPython and stumbled upon GFF.easy while searching through the
> > API docs. Actually, What I wanted was a way to parse that location string
> > into an SeqFeature-like thing from which I could get start, end and
> > strand.Unfortunately I could not find the correct parser in Bio.Genbank -
> > any suggestions are welcome.
> 
> Right now Bio.GenBank doesn't really expose the location parsing in an
> easy to use way like Bio.GFF.easy does.

If you don't like ugly code, please avert your eyes now. This will
work with the standard GenBank parsing and is definitely not future
proof since it involves using private members. However, it'll work
for something quick n' dirty:

from Bio.GenBank import _FeatureConsumer
from Bio.SeqFeature import SeqFeature

def gb_string_to_feature(content, use_fuzziness=True):
    """Convert a GenBank location string into a SeqFeature.
    """
    consumer = _FeatureConsumer(use_fuzziness)
    consumer._cur_feature = SeqFeature()
    consumer.location(content)
    return consumer._cur_feature

print gb_string_to_feature('complement(NC_012967.1:3622110..3624728)')

Hope this helps,
Brad


From bartek at rezolwenta.eu.org  Wed Dec  9 14:43:23 2009
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Wed, 9 Dec 2009 15:43:23 +0100
Subject: [Biopython] CompareAce parser
In-Reply-To: <889087.95522.qm@web62406.mail.re1.yahoo.com>
References: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
	<889087.95522.qm@web62406.mail.re1.yahoo.com>
Message-ID: <8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>

Hi Michiel,

I haven't given enough consideration to the maintenance costs of
having parsers like this one in biopython. I think you are right that
it's not  useful in its current state, and I don't think it's worth
putting efforts into improving it. There are already other methods of
motif comparison implemented in bio.Motif and if I was to choose an
external motif comparison software to support in biopython, I would
vote for the STAMP tool from Benos lab. So, in conclusion, I think it
would make sense to deprecate the CompareAce parser.


cheers
Bartek


On Sun, Dec 6, 2009 at 3:31 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> So the reason this parser is so simple and has almost no
>> functionality is just a reflection of the simplicity of
>> the CompareAce files?
>
> Not exactly. CompareAce files can have different outputs, depending on the query given to CompareAce. The simplest query returns only one number. The current CompareAce parser can only parse this output. In other words,
>
>>>> input = open("test.out")
>>>> from Bio.Motif.Parsers import AlignAce
>>>> AlignAce.CompareAceParser().parse(input)
> 0.92130000000000001
>
> is equivalent to
>
>>>> input = open("test.out")
>>>> float(input.read())
> 0.92130000000000001
>
> I am not against having a CompareAce parser in Biopython, but if we have such a parser it should be able to handle more output formats than just the trivial output format.
>
> With this in mind, I think we should either extend the CompareAce parser to handle cases that cannot be trivially handled by a simple Python command, or remove it altogether. If we do keep it in Biopython, there should also be some documentation to cover it, and perhaps a unit test.
>
> --Michiel
>
> --- On Sun, 12/6/09, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
>> From: Peter <biopython at maubp.freeserve.co.uk>
>> Subject: Re: [Biopython] CompareAce parser
>> To: "Bartek Wilczynski" <bartek at rezolwenta.eu.org>
>> Cc: "Michiel de Hoon" <mjldehoon at yahoo.com>, biopython at biopython.org
>> Date: Sunday, December 6, 2009, 9:10 AM
>> On Sun, Dec 6, 2009 at 12:58 AM,
>> Bartek Wilczynski
>> <bartek at rezolwenta.eu.org>
>> wrote:
>> > Hi,
>> >
>> > I don't have anything against deprecating, even though
>> I don't the
>> > advantages of doing so. (the module is trivial, but so
>> is the output
>> > of compareACE: a number giving a score between motifs.
>> The score,
>> > however is not trivial and I wouldn't want to
>> reimplement it.)
>> >
>> > cheers
>> > ?Bartek
>>
>> So the reason this parser is so simple and has almost no
>> functionality
>> is just a reflection of the simplicity of the CompareAce
>> files? If so, I'd
>> say leave the parser in.
>>
>> Peter
>>
>
>
>
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>



-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433



From iwan.grin at googlemail.com  Wed Dec  9 14:51:20 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Wed, 9 Dec 2009 15:51:20 +0100
Subject: [Biopython] Parsing problem
In-Reply-To: <20091209133802.GB79820@sobchak.mgh.harvard.edu>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
	<20091209133802.GB79820@sobchak.mgh.harvard.edu>
Message-ID: <b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>

2009/12/9 Brad Chapman <chapmanb at 50mail.com>

> Iwan and Peter;
>
> > > I am new to BioPython and stumbled upon GFF.easy while searching
> through the
> > > API docs. Actually, What I wanted was a way to parse that location
> string
> > > into an SeqFeature-like thing from which I could get start, end and
> > > strand.Unfortunately I could not find the correct parser in Bio.Genbank
> -
> > > any suggestions are welcome.
> >
> > Right now Bio.GenBank doesn't really expose the location parsing in an
> > easy to use way like Bio.GFF.easy does.
>
> If you don't like ugly code, please avert your eyes now. This will
> work with the standard GenBank parsing and is definitely not future
> proof since it involves using private members. However, it'll work
> for something quick n' dirty:
>
> from Bio.GenBank import _FeatureConsumer
> from Bio.SeqFeature import SeqFeature
>
> def gb_string_to_feature(content, use_fuzziness=True):
>    """Convert a GenBank location string into a SeqFeature.
>    """
>    consumer = _FeatureConsumer(use_fuzziness)
>    consumer._cur_feature = SeqFeature()
>    consumer.location(content)
>    return consumer._cur_feature
>
> print gb_string_to_feature('complement(NC_012967.1:3622110..3624728)')
>
> Hope this helps,
> Brad
>

Brad, Thank you very much!

as much as this is a hack, it works for what I want to have. I guess for
future proofness, either the parsers from Bio.GenBank should be exposed, or
the coded_by qualifier should be parsed as location by default, although I
am not sure how well the latter idea fits into the present data structure.

Iwan


From biopython at maubp.freeserve.co.uk  Wed Dec  9 15:05:39 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Dec 2009 15:05:39 +0000
Subject: [Biopython] CompareAce parser
In-Reply-To: <8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>
References: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
	<889087.95522.qm@web62406.mail.re1.yahoo.com>
	<8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>
Message-ID: <320fb6e00912090705h691dd0a3u32b6e8760570d3e1@mail.gmail.com>

On Wed, Dec 9, 2009 at 2:43 PM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> Hi Michiel,
>
> I haven't given enough consideration to the maintenance costs of
> having parsers like this one in biopython. I think you are right that
> it's not ?useful in its current state, and I don't think it's worth
> putting efforts into improving it. There are already other methods of
> motif comparison implemented in bio.Motif and if I was to choose an
> external motif comparison software to support in biopython, I would
> vote for the STAMP tool from Benos lab. So, in conclusion, I think it
> would make sense to deprecate the CompareAce parser.
>
> cheers
> Bartek

I hadn't looked to see just how simple the files and parser were ;)

Do you want to go ahead and make the deprecation Bartek?

Thanks,

Peter



From biopython at maubp.freeserve.co.uk  Wed Dec  9 15:26:18 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Dec 2009 15:26:18 +0000
Subject: [Biopython] Parsing problem
In-Reply-To: <b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
	<20091209133802.GB79820@sobchak.mgh.harvard.edu>
	<b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>
Message-ID: <320fb6e00912090726w95cfa8bi542f6227f84c888b@mail.gmail.com>

On Wed, Dec 9, 2009 at 2:51 PM, Iwan Grin <iwan.grin at googlemail.com> wrote:
> Brad, Thank you very much!
>
> as much as this is a hack, it works for what I want to have. I guess for
> future proofness, either the parsers from Bio.GenBank should be exposed, or
> the coded_by qualifier should be parsed as location by default, although I
> am not sure how well the latter idea fits into the present data structure.

Brad's trick still work in Biopython 1.53 at the very least. I think we'll
try and make the location parser more accessible in future, but
changing the parsing of "coded_by" qualifiers would risk breaking
existing user scripts.

Peter


From iwan.grin at googlemail.com  Wed Dec  9 15:55:21 2009
From: iwan.grin at googlemail.com (Iwan Grin)
Date: Wed, 9 Dec 2009 16:55:21 +0100
Subject: [Biopython] Parsing problem
In-Reply-To: <320fb6e00912090726w95cfa8bi542f6227f84c888b@mail.gmail.com>
References: <b3475c600912081052q417c0392h1ae624acd59c222f@mail.gmail.com>
	<320fb6e00912081443u478afa02pc290c19ae14e21cb@mail.gmail.com>
	<320fb6e00912081553h5091715dpb0c345bf4f8c3dfb@mail.gmail.com>
	<b3475c600912090433p154752abt564f8b9f16dffae9@mail.gmail.com>
	<320fb6e00912090525j399c28e8w15e6fdea61b14133@mail.gmail.com>
	<20091209133802.GB79820@sobchak.mgh.harvard.edu>
	<b3475c600912090651x6e916947t163444d7a2fec054@mail.gmail.com>
	<320fb6e00912090726w95cfa8bi542f6227f84c888b@mail.gmail.com>
Message-ID: <b3475c600912090755l49ea6035ja0c34d40a7bfa9b4@mail.gmail.com>

2009/12/9 Peter <biopython at maubp.freeserve.co.uk>

> On Wed, Dec 9, 2009 at 2:51 PM, Iwan Grin <iwan.grin at googlemail.com>
> wrote:
> > Brad, Thank you very much!
> >
> > as much as this is a hack, it works for what I want to have. I guess for
> > future proofness, either the parsers from Bio.GenBank should be exposed,
> or
> > the coded_by qualifier should be parsed as location by default, although
> I
> > am not sure how well the latter idea fits into the present data
> structure.
>
> Brad's trick still work in Biopython 1.53 at the very least. I think we'll
> try and make the location parser more accessible in future, but
> changing the parsing of "coded_by" qualifiers would risk breaking
> existing user scripts.
>
> Peter
>

I would suggest to add a new "coded_by" feature and leave the qualifier as
it is.
This should minimize the risk of breaking stuff. On the other hand, This
feature would be pretty specific for CDS in Genbank Protein files.

Iwan


From bartek at rezolwenta.eu.org  Wed Dec  9 16:33:58 2009
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Wed, 9 Dec 2009 17:33:58 +0100
Subject: [Biopython] CompareAce parser
In-Reply-To: <320fb6e00912090705h691dd0a3u32b6e8760570d3e1@mail.gmail.com>
References: <320fb6e00912060610w34ea50b3hc828f7b47909f135@mail.gmail.com>
	<889087.95522.qm@web62406.mail.re1.yahoo.com>
	<8b34ec180912090643m58867d29ha7d9cdd6e59e4bb@mail.gmail.com>
	<320fb6e00912090705h691dd0a3u32b6e8760570d3e1@mail.gmail.com>
Message-ID: <8b34ec180912090833uf9ace0x8f0b76335dbd8143@mail.gmail.com>

On Wed, Dec 9, 2009 at 4:05 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> I hadn't looked to see just how simple the files and parser were ;)
>
> Do you want to go ahead and make the deprecation Bartek?

Yes. It's done and pushed to github now.

cheers
Bartek
-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433


From villahozbale at wisc.edu  Fri Dec 11 18:32:53 2009
From: villahozbale at wisc.edu (ANGEL VILLAHOZ-BALETA)
Date: Fri, 11 Dec 2009 12:32:53 -0600
Subject: [Biopython] A potential printing error in the Biopython Tutorial
	and Cookbook?
Message-ID: <70d0d6f9673f4.4b223bf5@wiscmail.wisc.edu>

Hi to all,

I believe that there is a printing error in the Biopython Tutorial and Cookbook...

Go there:

http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc102

Then check the following source code:

>>> for record in records:
...     print "title:", record["TI"]
...     if "AU" in records:
...         print "authors:", record["AU"]
...     print "source:", record["CO"]
...     print

I believe that the if sentence would have the record instead of the records because it would never print such an information about the authors since the data structure of records does not have this key but always integers as its indices.

Let me know if I am right or not.

Thanks very much,

Angel Villahoz-Baleta
Bioinformatics Programmer
University of Wisconsin-Madison


From biopython at maubp.freeserve.co.uk  Fri Dec 11 19:45:31 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 11 Dec 2009 19:45:31 +0000
Subject: [Biopython] A potential printing error in the Biopython
	Tutorial and Cookbook?
In-Reply-To: <70d0d6f9673f4.4b223bf5@wiscmail.wisc.edu>
References: <70d0d6f9673f4.4b223bf5@wiscmail.wisc.edu>
Message-ID: <320fb6e00912111145w68330b80l8b1091db48fac3fb@mail.gmail.com>

On Fri, Dec 11, 2009 at 6:32 PM, ANGEL VILLAHOZ-BALETA
<villahozbale at wisc.edu> wrote:
> Hi to all,
>
> I believe that there is a printing error in the Biopython Tutorial and Cookbook...
>
> Go there:
>
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc102
>
> Then check the following source code:
>
>>>> for record in records:
> ... ? ? print "title:", record["TI"]
> ... ? ? if "AU" in records:
> ... ? ? ? ? print "authors:", record["AU"]
> ... ? ? print "source:", record["CO"]
> ... ? ? print
>
> I believe that the if sentence would have the record
> instead of the records because it would never print
> such an information about the authors since the data
> structure of records does not have this key but always
> integers as its indices.

What version of Biopython do you have?
Could you show us the actual error message?

I've just been playing with the example, and for some
records certain fields are missing (you get a KeyError),
so this works better:

for record in records:
    print "title:", record.get("TI","?")
    print "author:", record.get("AU","?")
    print "source:", record.get("CO","?")
    print

Does that help?

Peter



From mjldehoon at yahoo.com  Sat Dec 12 01:52:08 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 11 Dec 2009 17:52:08 -0800 (PST)
Subject: [Biopython] A potential printing error in the Biopython
	Tutorial and Cookbook?
In-Reply-To: <320fb6e00912111145w68330b80l8b1091db48fac3fb@mail.gmail.com>
Message-ID: <138660.52957.qm@web62406.mail.re1.yahoo.com>

Dear Angel,

This was indeed a typing error in the tutorial.
It is fixed now as Peter suggested.
Thanks for noticing!

--Michiel.

--- On Fri, 12/11/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] A potential printing error in the Biopython Tutorial and Cookbook?
> To: "ANGEL VILLAHOZ-BALETA" <villahozbale at wisc.edu>
> Cc: biopython at lists.open-bio.org
> Date: Friday, December 11, 2009, 2:45 PM
> On Fri, Dec 11, 2009 at 6:32 PM,
> ANGEL VILLAHOZ-BALETA
> <villahozbale at wisc.edu>
> wrote:
> > Hi to all,
> >
> > I believe that there is a printing error in the
> Biopython Tutorial and Cookbook...
> >
> > Go there:
> >
> > http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc102
> >
> > Then check the following source code:
> >
> >>>> for record in records:
> > ... ? ? print "title:", record["TI"]
> > ... ? ? if "AU" in records:
> > ... ? ? ? ? print "authors:", record["AU"]
> > ... ? ? print "source:", record["CO"]
> > ... ? ? print
> >
> > I believe that the if sentence would have the record
> > instead of the records because it would never print
> > such an information about the authors since the data
> > structure of records does not have this key but
> always
> > integers as its indices.
> 
> What version of Biopython do you have?
> Could you show us the actual error message?
> 
> I've just been playing with the example, and for some
> records certain fields are missing (you get a KeyError),
> so this works better:
> 
> for record in records:
> ? ? print "title:", record.get("TI","?")
> ? ? print "author:", record.get("AU","?")
> ? ? print "source:", record.get("CO","?")
> ? ? print
> 
> Does that help?
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list? -? Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 


      



From aboulia at gmail.com  Tue Dec 15 06:01:47 2009
From: aboulia at gmail.com (Kevin Lam)
Date: Tue, 15 Dec 2009 14:01:47 +0800
Subject: [Biopython] rsync download of biopython problems
Message-ID: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>

Hi
I just tried downloading biopython via rsync

 rsync -av code.open-bio.org::cvsbiopython .

But all the files were appended with a ",v" why did that happen? (i.e. see
below)
Attic  Bio  BioSQL  CONTRIB,v  DEPRECATED,v  Doc  Experimental  LICENSE,v
MANIFEST.in,v  Martel  NEWS,v  README,v  Scripts  setup.py,v  Tests


From biopython at maubp.freeserve.co.uk  Tue Dec 15 10:37:55 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 10:37:55 +0000
Subject: [Biopython] rsync download of biopython problems
In-Reply-To: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>
References: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>
Message-ID: <320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>

On Tue, Dec 15, 2009 at 6:01 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi
> I just tried downloading biopython via rsync
>
> ?rsync -av code.open-bio.org::cvsbiopython .
>
> But all the files were appended with a ",v" why did that happen? (i.e. see
> below)
> Attic ?Bio ?BioSQL ?CONTRIB,v ?DEPRECATED,v ?Doc ?Experimental ?LICENSE,v
> MANIFEST.in,v ?Martel ?NEWS,v ?README,v ?Scripts ?setup.py,v ?Tests

CVS likes to add ",v" to files - if you wanted to download them
from the public CVS server (code.open-bio.org) you would have
had to use the CVS command line tool.

However, we don't use CVS anymore, we use git. See:
http://www.biopython.org/wiki/SourceCode

If you really want to use rsync you *might* be able to point it
at http://biopython.org/SRC/biopython/

Peter

P.S. Why did you try downloading with rsync from the code.open-bio.org?
Is there something confusing in our documentation we can fix? Thanks!



From aboulia at gmail.com  Tue Dec 15 11:39:35 2009
From: aboulia at gmail.com (Kevin Lam)
Date: Tue, 15 Dec 2009 19:39:35 +0800
Subject: [Biopython] rsync download of biopython problems
In-Reply-To: <320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>
References: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com> 
	<320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>
Message-ID: <5b6410e0912150339y296aee41xf2277c8ff582015e@mail.gmail.com>

Hi Peter,
git works fine for me!
ok lemme explain how i got there..

from http://www.biopython.org/wiki/CVS
i followed this link http://cvs.biopython.org/
which redirected me to http://www.open-bio.org/wiki/SourceCode

i was on a fresh install system of CentOS so rsync was avail so i used that.

Cheers
Kevin

On Tue, Dec 15, 2009 at 6:37 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Tue, Dec 15, 2009 at 6:01 AM, Kevin Lam <aboulia at gmail.com> wrote:
> > Hi
> > I just tried downloading biopython via rsync
> >
> >  rsync -av code.open-bio.org::cvsbiopython .
> >
> > But all the files were appended with a ",v" why did that happen? (i.e.
> see
> > below)
> > Attic  Bio  BioSQL  CONTRIB,v  DEPRECATED,v  Doc  Experimental  LICENSE,v
> > MANIFEST.in,v  Martel  NEWS,v  README,v  Scripts  setup.py,v  Tests
>
> CVS likes to add ",v" to files - if you wanted to download them
> from the public CVS server (code.open-bio.org) you would have
> had to use the CVS command line tool.
>
> However, we don't use CVS anymore, we use git. See:
> http://www.biopython.org/wiki/SourceCode
>
> If you really want to use rsync you *might* be able to point it
> at http://biopython.org/SRC/biopython/
>
> Peter
>
> P.S. Why did you try downloading with rsync from the code.open-bio.org?
> Is there something confusing in our documentation we can fix? Thanks!
>


From biopython at maubp.freeserve.co.uk  Tue Dec 15 11:48:22 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 11:48:22 +0000
Subject: [Biopython] rsync download of biopython problems
In-Reply-To: <5b6410e0912150339y296aee41xf2277c8ff582015e@mail.gmail.com>
References: <5b6410e0912142201q1bae57b2ybb34dd453afd6204@mail.gmail.com>
	<320fb6e00912150237i7e627b0x9788bf6b112e5@mail.gmail.com>
	<5b6410e0912150339y296aee41xf2277c8ff582015e@mail.gmail.com>
Message-ID: <320fb6e00912150348y7f074d94u74b3b14cc31d4c6@mail.gmail.com>

On Tue, Dec 15, 2009 at 11:39 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi Peter,
> git works fine for me!
> ok lemme explain how i got there..
>
> from http://www.biopython.org/wiki/CVS

I just the "this page is obsolete" bit at the top needs to be more prominent...

> i followed this link http://cvs.biopython.org/

I can ask the sys admins to redirect that to:
http://www.biopython.org/wiki/SourceCode

> which redirected me to http://www.open-bio.org/wiki/SourceCode

Ah - that does need updating. Thanks!

> i was on a fresh install system of CentOS so rsync was avail so i used that.

Well it "worked" (you got a copy of the CVS repository rather than a
snapshot of the code), but the CVS repository is now out of date.

Peter


From biopython at maubp.freeserve.co.uk  Tue Dec 15 17:01:38 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 17:01:38 +0000
Subject: [Biopython] Biopython 1.53 released
Message-ID: <320fb6e00912150901k138ae04bmc5d5af9c867340ec@mail.gmail.com>

Dear Biopythoneers,

We are pleased to announce the availability of Biopython 1.53, a new
stable release of the Biopython library, three months after the
release of Biopython 1.52. This is our first release since migrating
from CVS to git for source code control.

There have been some additions to our core objects ? the Seq (and
related UnknownSeq) objects gained upper and lower methods (like the
string methods of the same name but alphabet aware) plus a new ungap
method. The SeqFeature object now has an extract method to get the
region of sequence it describes (useful for getting CDS nucleotide
sequences from GenBank files). Also SeqRecord objects now support
addition, giving a new SeqRecord with the combined sequence, all the
SeqFeatures, and any common annotation.

SQLite support (built into Python 2.5+) was added to our BioSQL
interface. This is still a little experimental as we are using a draft
BioSQL SQLite schema, but this should be merged into the next
BioSQL release.

Biopython now includes wrappers for the new NCBI BLAST C++ tools,
which will be replacing the old NCBI ?legacy? BLAST tools written in
C. The plain text BLAST parser has been updated to cope as well.
Nevertheless, we (and the NCBI) still recommend using the XML output
for parsing.

Bio.Entrez includes the new (Jan 2010) DTD files from the NCBI for
parsing MedLine/PubMed data.

The NCBI codon tables have been updated from version 3.4 to 3.9, which
adds a few extra start codons, and a few new tables (Tables 16, 21, 22
and 23).

The restriction enzyme list in Bio.Restriction has been updated to the
Nov 2009 release of REBASE.

The Bio.PDB parser and output code has been updated to understand the
element column in ATOM and HETATM lines, and Bio.PDB.PDBList has been
updated for recent changes to the PDB FTP site.

Finally, support for running Biopython under Jython (using the Java
Virtual Machine) has been much improved. Note that Jython does not
support C code, and currently Jython does not parse DTD files (needed
for the Bio.Entrez XML parser). However, most of the Biopython modules
seem fine from testing Jython 2.5.0 and 2.5.1.

Sources and Windows Installers are available from our downloads page.

Thanks to the Biopython development team and to everyone who has
reported bugs or contributed patches since our last release.

--Peter, on behalf of the Biopython developers

P.S. This news post is online at
http://news.open-bio.org/news/2009/12/biopython-release-153/

You may wish to subscribe to our news feed.  For RSS links etc, see:
http://biopython.org/wiki/News

Biopython news is also on twitter:
http://twitter.com/biopython



From cgohlke at uci.edu  Tue Dec 15 17:17:53 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 09:17:53 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
Message-ID: <4B27C4C1.3090206@uci.edu>

Hello,

I have built biopython 1.53 for 64-bit Python 2.6 for Windows using 
Visual Studio 2008. The test output is attached. The installer is at 
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>

Best,

Christoph Gohlke
Laboratory for Fluorescence Dynamics
University of California, Irvine
http://www.lfd.uci.edu/~gohlke/
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: biopython-1.53.win-amd64-py2.6-test.txt
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091215/ce4a9376/attachment-0002.txt>

From biopython at maubp.freeserve.co.uk  Tue Dec 15 17:49:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 17:49:35 +0000
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <4B27C4C1.3090206@uci.edu>
References: <4B27C4C1.3090206@uci.edu>
Message-ID: <320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>

On Tue, Dec 15, 2009 at 5:17 PM, Christoph Gohlke <cgohlke at uci.edu> wrote:
> Hello,
>
> I have built biopython 1.53 for 64-bit Python 2.6 for Windows using Visual
> Studio 2008. The test output is attached. The installer is at
> <http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>

Nice :)

Was this with NumPy 1.4.0rc2?

The fact that test_GraphicsBitmaps.py failed with a font problem
is indicative of something not quite right in ReportLab and/or PIL.
This is almost certainly not a Biopython problem.

A couple of SCOP tested failed - could you run unix2dos (or
similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
and retest? That "fixes" it on win32.

Also what does this do on your Windows 64bit python?

>>> import sys
>>> sys.platform
'win32'

I've seen threads discussing if it should return "win64" or
"win32", but the simplest way to check is try it and see.

Thanks,

Peter


From cgohlke at uci.edu  Tue Dec 15 18:22:23 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 10:22:23 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
References: <4B27C4C1.3090206@uci.edu>
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
Message-ID: <4B27D3DF.4070006@uci.edu>



On 12/15/2009 9:49 AM, Peter wrote:
> On Tue, Dec 15, 2009 at 5:17 PM, Christoph Gohlke<cgohlke at uci.edu>  wrote:
>> Hello,
>>
>> I have built biopython 1.53 for 64-bit Python 2.6 for Windows using Visual
>> Studio 2008. The test output is attached. The installer is at
>> <http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>
>
> Nice :)
>
> Was this with NumPy 1.4.0rc2?
Yes, numpy-1.4.0rc2.dev7996, also available on the same download page.

>
> The fact that test_GraphicsBitmaps.py failed with a font problem
> is indicative of something not quite right in ReportLab and/or PIL.
> This is almost certainly not a Biopython problem.
>
OK, I will check Reportlab and PIL. I now remember seeing some font 
loading issues with PIL 1.1.7 in other packages even though all internal 
tests pass.

> A couple of SCOP tested failed - could you run unix2dos (or
> similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
> and retest? That "fixes" it on win32.
>
That worked. The font error is now the only failing test.

> Also what does this do on your Windows 64bit python?
>
>>>> import sys
>>>> sys.platform
> 'win32'
'win32' is correct.
I use "'64 bit' in sys.version" to check for a 64 bit version at runtime.

>
> I've seen threads discussing if it should return "win64" or
> "win32", but the simplest way to check is try it and see.
>

Thank you. Feel free to redistribute the installer if you think it is 
good enough.

Christoph



From cgohlke at uci.edu  Tue Dec 15 18:20:07 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 10:20:07 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
References: <4B27C4C1.3090206@uci.edu>
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
Message-ID: <4B27D357.30705@uci.edu>



On 12/15/2009 9:49 AM, Peter wrote:
> On Tue, Dec 15, 2009 at 5:17 PM, Christoph Gohlke<cgohlke at uci.edu>  wrote:
>> Hello,
>>
>> I have built biopython 1.53 for 64-bit Python 2.6 for Windows using Visual
>> Studio 2008. The test output is attached. The installer is at
>> <http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython>
>
> Nice :)
>
> Was this with NumPy 1.4.0rc2?
>
> The fact that test_GraphicsBitmaps.py failed with a font problem
> is indicative of something not quite right in ReportLab and/or PIL.
> This is almost certainly not a Biopython problem.
>
> A couple of SCOP tested failed - could you run unix2dos (or
> similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
> and retest? That "fixes" it on win32.
>
> Also what does this do on your Windows 64bit python?
>
>>>> import sys
>>>> sys.platform
> 'win32'
>
> I've seen threads discussing if it should return "win64" or
> "win32", but the simplest way to check is try it and see.
>
> Thanks,
>
> Peter
>
>


From biopython at maubp.freeserve.co.uk  Tue Dec 15 18:57:09 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Dec 2009 18:57:09 +0000
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <4B27D3DF.4070006@uci.edu>
References: <4B27C4C1.3090206@uci.edu>
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>
	<4B27D3DF.4070006@uci.edu>
Message-ID: <320fb6e00912151057t41a6e889k1df389cbccf1a8cd@mail.gmail.com>

On Tue, Dec 15, 2009 at 6:22 PM, Christoph Gohlke <cgohlke at uci.edu> wrote:
>
>> The fact that test_GraphicsBitmaps.py failed with a font problem
>> is indicative of something not quite right in ReportLab and/or PIL.
>> This is almost certainly not a Biopython problem.
>>
> OK, I will check Reportlab and PIL. I now remember seeing some
> font loading issues with PIL 1.1.7 in other packages even though
> all internal tests pass.

If you are happy to investigate further, that would be great.

>> A couple of SCOP tested failed - could you run unix2dos (or
>> similar) on Tests/SCOP/*.txt and Tests/SCOP/scopseq-test/*.txt
>> and retest? That "fixes" it on win32.
>
> That worked. The font error is now the only failing test.

Good.

>> Also what does this do on your Windows 64bit python?
>>
>>>>> import sys
>>>>> sys.platform
>>
>> 'win32'
>
> 'win32' is correct.
> I use "'64 bit' in sys.version" to check for a 64 bit version at runtime.

Thanks - I just wanted to be sure.

>
> Thank you. Feel free to redistribute the installer if you think it is
> good enough.
>

Given NumPy don't offer their own 64bit installers, and the
possible need for Microsoft Visual C++ 2008 redistributable
package, perhaps linking to your page makes most sense
for now. I'll update our download page if that sounds sensible.

Thank you,

Peter


From cgohlke at uci.edu  Tue Dec 15 19:29:28 2009
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Tue, 15 Dec 2009 11:29:28 -0800
Subject: [Biopython] biopython-1.53.win-amd64-py2.6
In-Reply-To: <320fb6e00912151057t41a6e889k1df389cbccf1a8cd@mail.gmail.com>
References: <4B27C4C1.3090206@uci.edu>	
	<320fb6e00912150949x58594a50sf8d2e60b107f26cf@mail.gmail.com>	
	<4B27D3DF.4070006@uci.edu>
	<320fb6e00912151057t41a6e889k1df389cbccf1a8cd@mail.gmail.com>
Message-ID: <4B27E398.3090600@uci.edu>



On 12/15/2009 10:57 AM, Peter wrote:
> On Tue, Dec 15, 2009 at 6:22 PM, Christoph Gohlke<cgohlke at uci.edu>  wrote:
>>
>>> The fact that test_GraphicsBitmaps.py failed with a font problem
>>> is indicative of something not quite right in ReportLab and/or PIL.
>>> This is almost certainly not a Biopython problem.
>>>
>> OK, I will check Reportlab and PIL. I now remember seeing some
>> font loading issues with PIL 1.1.7 in other packages even though
>> all internal tests pass.
>
> If you are happy to investigate further, that would be great.
>

Turned out that the Times-Roman font is simply missing from the 
reportlab 2.3 source distribution, which I used. The missing fonts can 
be downloaded at <http://www.reportlab.org/ftp/pfbfer.zip> and put in 
the reportlab/fonts directory. I also included these fonts in the 
updated reportlab-2.3.win-amd64-py2.6.exe installer.

All tests pass now. Some tests were skipped due to missing third party 
packages on my computer.

>>
>> Thank you. Feel free to redistribute the installer if you think it is
>> good enough.
>>
>
> Given NumPy don't offer their own 64bit installers, and the
> possible need for Microsoft Visual C++ 2008 redistributable
> package, perhaps linking to your page makes most sense
> for now. I'll update our download page if that sounds sensible.
>
Makes sense. The VC.CRT redistributable is usually installed with Python 
and I compiled with the http://bugs.python.org/issue4120 patch.

Best,

Christoph



From aboulia at gmail.com  Wed Dec 16 03:52:36 2009
From: aboulia at gmail.com (Kevin Lam)
Date: Wed, 16 Dec 2009 11:52:36 +0800
Subject: [Biopython] Entrez.efetch Service unavailable!
Message-ID: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>

Hi I have been trying to use
Entrez.efetch
to download ~1000 bacteria genomes
I read in the docs that biopython will auto take care of the delay and fetch
via the preferred site for download scripts
but I have been getting service unavailable  errors at GMT +8 1100am
is this normal? Or should i edit the source to give a larger delay buffer?
So far I have only managed to get 3 fasta sequences out

Or should I bring this up to NCBI instead?

Traceback (most recent call last):
  File "../retr-fasta.py", line 15, in ?
    handle = Entrez.efetch(db="genome", id=uid, rettype="fasta")
  File
"/home/k/lib/biopython-biopython-9a41381/build/lib.linux-x86_64-2.4/Bio/Entrez/__init__.py",
line 105, in efetch
    return _open(cgi, variables)
  File
"/home/k/lib/biopython-biopython-9a41381/build/lib.linux-x86_64-2.4/Bio/Entrez/__init__.py",
line 343, in _open
    raise IOError("Service unavailable!")
IOError: Service unavailable!


Cheers
Kevin


From biopython at maubp.freeserve.co.uk  Wed Dec 16 08:58:35 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 08:58:35 +0000
Subject: [Biopython] Entrez.efetch Service unavailable!
In-Reply-To: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>
References: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>
Message-ID: <320fb6e00912160058i57acc020nba7c61c53a4ec64b@mail.gmail.com>

On Wed, Dec 16, 2009 at 3:52 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi I have been trying to use
> Entrez.efetch
> to download ~1000 bacteria genomes

Why not use their FTP site? They even make bundles available, e.g.
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.gbk.tar.gz
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.faa.tar.gz
etc. Note the folder is called Bacteria for historical reasons,
it is really Prokaryotes as there are plenty of Archaea in there.

> I read in the docs that biopython will auto take care of the delay and fetch
> via the preferred site for download scripts
> but I have been getting service unavailable ?errors at GMT +8 1100am
> is this normal? Or should i edit the source to give a larger delay buffer?
> So far I have only managed to get 3 fasta sequences out

The NCBI were planning some Entrez work about now (updating
DTD files), so the downtime might be expected. I'd wait a day,
and then if it is still down email them.

Regards,

Peter



From iua1 at psu.edu  Wed Dec 16 16:49:11 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 11:49:11 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
Message-ID: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>

Hello Everyone,

I applaud the move to Github, I think it was a great decision that
will allow more people to contribute to the project.

Yet at the same time a community is built on communication and the
current mailing list feels extremely antiquated. The way of
interaction is tedious: sending emails to an address, then one reads
one message at a time, messages are not displayed in a threaded form
where multiple messages are shown at the same time. There is no of
search,  etc. and it all feels like a throwback to the 90s. Personally
I think a choice of mailman is a choice of deliberately of limiting
access to all but the most hardcore - and for example that's why the
main Python-dev uses it, it is a more of  a mechanism to keep people
away. Of course  python has comp.lang.python and it is a nice and
thriving group.

The alternative such as Google groups would be far superior in
attracting and building a community of developers and users as well.
Is this an idea that  the owners of the list would entertain?

best regards,

Istvan Albert


-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From hlapp at drycafe.net  Wed Dec 16 16:56:57 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 11:56:57 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>

Istvan,

what is your solution to Google all of a sudden deciding to take  
Google Groups down, or to make it a paid subscription service, or if  
Google goes out of business?

All of these things have happened over and over before with commercial  
vendors. Economies do go through cycles. Would it be OK to lose the  
entire archive of the mailing list in such an event?

BTW if you use a threaded email client (such as GMail, or in fact most  
modern email readers), you *will* see threaded messages. Also, the  
Biopython list is indexed in GMane I believe, so you can search there  
pretty conveniently. Finally, have you tried using Google to search  
the Biopython archive? It's not so bad, actually.

Just my $0.02 (and I'm a big fan of Google Groups).

	-hilmar

On Dec 16, 2009, at 11:49 AM, Istvan Albert wrote:

> Hello Everyone,
>
> I applaud the move to Github, I think it was a great decision that
> will allow more people to contribute to the project.
>
> Yet at the same time a community is built on communication and the
> current mailing list feels extremely antiquated. The way of
> interaction is tedious: sending emails to an address, then one reads
> one message at a time, messages are not displayed in a threaded form
> where multiple messages are shown at the same time. There is no of
> search,  etc. and it all feels like a throwback to the 90s. Personally
> I think a choice of mailman is a choice of deliberately of limiting
> access to all but the most hardcore - and for example that's why the
> main Python-dev uses it, it is a more of  a mechanism to keep people
> away. Of course  python has comp.lang.python and it is a nice and
> thriving group.
>
> The alternative such as Google groups would be far superior in
> attracting and building a community of developers and users as well.
> Is this an idea that  the owners of the list would entertain?
>
> best regards,
>
> Istvan Albert
>
>
> -- 
> Istvan Albert
> http://www.personal.psu.edu/iua1
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

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






From carlos.borroto at gmail.com  Wed Dec 16 16:57:05 2009
From: carlos.borroto at gmail.com (Carlos Javier Borroto)
Date: Wed, 16 Dec 2009 11:57:05 -0500
Subject: [Biopython] Is there any in silico PCR tool on biopython?
Message-ID: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>

Hi there,

I'm looking for a way to show some information on the specificity of
sets of primers I'm designing, I'll love to have a way to run an in
silico PCR reaction and parse the results with biopython.

Is there something to use with one of the available PCR simulation tools?

regards,
-- 
Carlos Javier Borroto
Baltimore, MD
Google Voice: (410) 929 4020


From biopython at maubp.freeserve.co.uk  Wed Dec 16 17:07:05 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:07:05 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <320fb6e00912160907m4f201a90xb85851ef9ba43271@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
> Hello Everyone,
>
> I applaud the move to Github, I think it was a great decision that
> will allow more people to contribute to the project.
>
> Yet at the same time a community is built on communication and the
> current mailing list feels extremely antiquated. The way of
> interaction is tedious: sending emails to an address, then one reads
> one message at a time, messages are not displayed in a threaded form
> where multiple messages are shown at the same time. There is no of
> search, ?etc. and it all feels like a throwback to the 90s.

A lot of that is down to your email program - I find none of
those issue apply to how I use the list (in GoogleMail).

You are specifically talking about browsing the mailing list
archive? There yes, things are a bit rudimentary, and search
isn't as good as in GoogleMail. But on the other hand it is
clearly a read only archive.

> Personally I think a choice of mailman is a choice of deliberately of
> limiting access to all but the most hardcore - and for example that's
> why the main Python-dev uses it, it is a more of ?a mechanism to
> keep people away. Of course?python has comp.lang.python and it
> is a nice and thriving group.
>
> The alternative such as Google groups would be far superior in
> attracting and building a community of developers and users as
> well. Is this an idea that ?the owners of the list would entertain?

It is something that the OBF may consider - but there are a
lot of concerns about reliance on third parties, advertising, loss
of brand control etc (see also Hilmar's email).

Peter



From biopython at maubp.freeserve.co.uk  Wed Dec 16 17:08:00 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:08:00 +0000
Subject: [Biopython] Is there any in silico PCR tool on biopython?
In-Reply-To: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
References: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
Message-ID: <320fb6e00912160908r152bbc49o38ea32a33cf6ff89@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:57 PM, Carlos Javier Borroto
<carlos.borroto at gmail.com> wrote:
> Hi there,
>
> I'm looking for a way to show some information on the specificity of
> sets of primers I'm designing, I'll love to have a way to run an in
> silico PCR reaction and parse the results with biopython.
>
> Is there something to use with one of the available PCR simulation tools?
>

I know people use Biopython with primer3 (usually the EMBOSS
wrapped version, eprimer3).

Peter


From biopython at maubp.freeserve.co.uk  Wed Dec 16 17:11:40 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:11:40 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
Message-ID: <320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:56 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>
> Also, the Biopython list is indexed in GMane I believe, so you can
> search there pretty conveniently.

Good point - should we add links to these on the mailing list wiki page?

Main mailing list:
http://dir.gmane.org/gmane.comp.python.bio.general

Dev mailing list:
http://dir.gmane.org/gmane.comp.python.bio.general

Announcement list:
http://dir.gmane.org/gmane.comp.python.bio.general

Peter


From biopython at maubp.freeserve.co.uk  Wed Dec 16 17:14:31 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:14:31 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>
Message-ID: <320fb6e00912160914w12e8ff2eiaa42b7924226eca8@mail.gmail.com>

On Wed, Dec 16, 2009 at 5:11 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Dec 16, 2009 at 4:56 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>
>> Also, the Biopython list is indexed in GMane I believe, so you can
>> search there pretty conveniently.
>
> Good point - should we add links to these on the mailing list wiki page?

Sorry, same link three times, should be:

Main mailing list:
http://dir.gmane.org/gmane.comp.python.bio.general
http://news.gmane.org/gmane.comp.python.bio.general

Dev mailing list:
http://dir.gmane.org/gmane.comp.python.bio.devel
http://news.gmane.org/gmane.comp.python.bio.devel

Announcement list:
http://dir.gmane.org/gmane.comp.python.bio.announce
http://news.gmane.org/gmane.comp.python.bio.announce

Peter


From biopython at maubp.freeserve.co.uk  Wed Dec 16 17:26:01 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 17:26:01 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>

On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
>
> The alternative such as Google groups would be far superior in
> attracting and building a community of developers and users as well.
> Is this an idea that ?the owners of the list would entertain?
>

As far as I can tell from the limited documentation I found on
Google Groups (maybe I was looking in the wrong place?) there
is no way to import our existing decade long mail archives.
That would be a major downside.

Also, using Google Groups would *require* all posters to have
a Google Account - a potential sticking point for some.

Peter



From cjfields at illinois.edu  Wed Dec 16 17:19:52 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 11:19:52 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160907m4f201a90xb85851ef9ba43271@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160907m4f201a90xb85851ef9ba43271@mail.gmail.com>
Message-ID: <52405282-5654-47D8-885F-4733F9A40873@illinois.edu>

On Dec 16, 2009, at 11:07 AM, Peter wrote:

> On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
>> Hello Everyone,
>> 
>> I applaud the move to Github, I think it was a great decision that
>> will allow more people to contribute to the project.
>> 
>> Yet at the same time a community is built on communication and the
>> current mailing list feels extremely antiquated. The way of
>> interaction is tedious: sending emails to an address, then one reads
>> one message at a time, messages are not displayed in a threaded form
>> where multiple messages are shown at the same time. There is no of
>> search,  etc. and it all feels like a throwback to the 90s.
> 
> A lot of that is down to your email program - I find none of
> those issue apply to how I use the list (in GoogleMail).
> 
> You are specifically talking about browsing the mailing list
> archive? There yes, things are a bit rudimentary, and search
> isn't as good as in GoogleMail. But on the other hand it is
> clearly a read only archive.
> 
>> Personally I think a choice of mailman is a choice of deliberately of
>> limiting access to all but the most hardcore - and for example that's
>> why the main Python-dev uses it, it is a more of  a mechanism to
>> keep people away. Of course python has comp.lang.python and it
>> is a nice and thriving group.
>> 
>> The alternative such as Google groups would be far superior in
>> attracting and building a community of developers and users as
>> well. Is this an idea that  the owners of the list would entertain?
> 
> It is something that the OBF may consider - but there are a
> lot of concerns about reliance on third parties, advertising, loss
> of brand control etc (see also Hilmar's email).
> 
> Peter

I agree with peter and hilmar.  Nabble and Gmane both archive the open-bio lists, at least for bioperl, but I would assume biopython as well.  For a painful example of how bad third party mail lists can be (painful at least to me), see the gmod lists at Sourceforge.

chris




From iua1 at psu.edu  Wed Dec 16 17:36:45 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 12:36:45 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
Message-ID: <c878cd560912160936p8224e55yc765ab73ba1999b7@mail.gmail.com>

On Wed, Dec 16, 2009 at 11:56 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Groups down, or to make it a paid subscription service, or if Google goes
> out of business?

>  Economies do go through cycles. Would it be OK to lose the entire
> archive of the mailing list in such an event?

Every choice has two sides. Has a positive and has negative dimension
to it. I am sure one can come up with  unlikely yet equally
pessimistic scenarios for the existing setup as well.

One thing is seems clear to me and I do not think that you are aware
of it. This mailman setup is a throttle - it imposes a negative
feedback on the amount of messages that it can handle.

This system of messages cannot grow over a certain limit. Just imagine
regularly getting a dozen new emails a day plus their followups, yet
you are just a casual user.

This would be unbearable for many people whose inboxes are already
overflowing. So they either don't participate or once they get even a
few of these messages they turn off email delivery at which point you
are left with a rudimentary site where it is hard to contribute so it
drops off their radar.

I can't even imagine what it would look like to have a popular
newsgroup being delivered to my mailbox. In a nutshell you are saying
it already works - but that is only because you get so few messages
... and getting more becomes actually inconvenient to the point at
which it has to decay again to the manageable level

Istvan

-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From hlapp at drycafe.net  Wed Dec 16 17:40:45 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 12:40:45 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
Message-ID: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>


On Dec 16, 2009, at 12:18 PM, Istvan Albert wrote:

> I am sure one can come up with  unlikely yet equally pessimistic  
> scenarios for the existing setup as well.

My point was that this is not unlikely at all. It happened with some  
of Yahoo's services, and it happened with others rather popular ones.

If you own and operate your own brand, your equipment can still go out  
of order. But at least it's under your own control. Do you see that  
difference? Would you argue that that is unimportant?

> This mailman setup is a throttle - it imposes a negative feedback on  
> the amount of messages that it can handle.

I really don't know what you mean by this. I get 200 messages a day  
from various lists. I'd be dead if I had an email client that can't  
thread and can't filter, but I do have one that can (and it's free).  
GMail can do both too, and is free. Have you tried a threading email  
reader? Can you explain how reading newsgroups through a threaded and  
filtering news reader is different and more efficient than reading  
emails through a threaded and filtering email reader?

That all being said, if what's at issue here is to have a Google Group  
interface to the Biopython mailing list, then that's actually easy to  
achieve. Someone (ideally one of the current list or project admins/ 
owners) creates a (presumably identically named) Google Group, and  
sets it to mirror the mailman mailing list.

Guys - I'm happy to help with that if you don't know how to do that.  
Create the group, subscribe drycafe at gmail.com, and make me an admin.  
I'll configure the mirroring.

	-hilmar

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






From sdavis2 at mail.nih.gov  Wed Dec 16 17:48:30 2009
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Wed, 16 Dec 2009 12:48:30 -0500
Subject: [Biopython] Is there any in silico PCR tool on biopython?
In-Reply-To: <320fb6e00912160908r152bbc49o38ea32a33cf6ff89@mail.gmail.com>
References: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
	<320fb6e00912160908r152bbc49o38ea32a33cf6ff89@mail.gmail.com>
Message-ID: <264855a00912160948q538bed21q6dc0d410d468c5c7@mail.gmail.com>

On Wed, Dec 16, 2009 at 12:08 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Dec 16, 2009 at 4:57 PM, Carlos Javier Borroto
> <carlos.borroto at gmail.com> wrote:
>> Hi there,
>>
>> I'm looking for a way to show some information on the specificity of
>> sets of primers I'm designing, I'll love to have a way to run an in
>> silico PCR reaction and parse the results with biopython.
>>
>> Is there something to use with one of the available PCR simulation tools?
>>
>
> I know people use Biopython with primer3 (usually the EMBOSS
> wrapped version, eprimer3).

Carlos,

If it is something like the UCSC genome browser in-silico PCR (for
mapping the putative amplimers from a set of primers), they (UCSC)
have an executable of the software.  I always have trouble finding
their software tools, but they are very responsive to email if you
have problems.  I don't have an example output file, but I bet it is
just tab-delimited text, so parsing is probably not too difficult.

Sean


From lueck at ipk-gatersleben.de  Wed Dec 16 17:31:18 2009
From: lueck at ipk-gatersleben.de (lueck at ipk-gatersleben.de)
Date: Wed, 16 Dec 2009 18:31:18 +0100
Subject: [Biopython] suggestion: moving to the discussion list to	Google
	groups
In-Reply-To: <320fb6e00912160914w12e8ff2eiaa42b7924226eca8@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<320fb6e00912160911tdedfb2ew47a0535379e828b5@mail.gmail.com>
	<320fb6e00912160914w12e8ff2eiaa42b7924226eca8@mail.gmail.com>
Message-ID: <20091216183118.zy9yvhd0hdcs4ggs@webmail.ipk-gatersleben.de>

What about a free forum e.g. smf (http://www.simplemachines.org/) on 
the biopython homepage?

I'm using this too and I'm quite happy. Easy building, maintaining...
Just an idea...

Zitat von Peter <biopython at maubp.freeserve.co.uk>:

> On Wed, Dec 16, 2009 at 5:11 PM, Peter 
> <biopython at maubp.freeserve.co.uk> wrote:
>> On Wed, Dec 16, 2009 at 4:56 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>>
>>> Also, the Biopython list is indexed in GMane I believe, so you can
>>> search there pretty conveniently.
>>
>> Good point - should we add links to these on the mailing list wiki page?
>
> Sorry, same link three times, should be:
>
> Main mailing list:
> http://dir.gmane.org/gmane.comp.python.bio.general
> http://news.gmane.org/gmane.comp.python.bio.general
>
> Dev mailing list:
> http://dir.gmane.org/gmane.comp.python.bio.devel
> http://news.gmane.org/gmane.comp.python.bio.devel
>
> Announcement list:
> http://dir.gmane.org/gmane.comp.python.bio.announce
> http://news.gmane.org/gmane.comp.python.bio.announce
>
> Peter
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>





From iua1 at psu.edu  Wed Dec 16 18:02:26 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:02:26 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
Message-ID: <c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>

Hi Everyone,

> Also, using Google Groups would *require* all posters to have
> a Google Account - a potential sticking point for some.

Right, but even currently one has to make an account on your  site
with email and password. Aren't you  less comfortable signing up with
various third parties than Google?

A response mentioned that Gmail's email threading works just as well
...  well it doesn't help anyone who has not already been subscribed
to the messages to begin with.  If you come to a discussion later you
cannot get that.

My goal is not to argue with each point, I only picked these two
because  both seemed to me like obvious responses yet  they are only
superficially addressing  the issues that  I brought up.

But to step back a second, and maybe I wasn't specific enough. It is
less about me, I can filter and thread my own email, I could download
the email entire archive and search it etc..
I teach an introductory level class that uses Biopython, can I
recommend my class that all go and sign up with you? I cannot really.
Many people are just learning about computing, they will be
overwhelmed with the everything interface, lack of search etc.

All of you who responded - frankly I think you are too close to this
issue to be able judge it correctly. It is like advising a newbie to
use VI, one in a hundred will love it ninety nine will hate it, but
hey who could argue that it is not super awesome? Once you do
something for a bunch of  years, you develop strategies and
everything seems to work just fine, and everything makes sense. Get
someone who is 20 and has never heard of sending emails to an address
then see what they say about it...

You all obviously care about the a community around biopython  so all
I am saying here is this:  when you look around and wish that you
could get a lot more people in - I think the answer is right there.
Make it really easy to ask question,  participate but also easy to
just not participate and just be able to catch up really quickly of
what is going on.

I wish you all the best,

Istvan Albert

-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From lueck at ipk-gatersleben.de  Wed Dec 16 18:04:17 2009
From: lueck at ipk-gatersleben.de (lueck at ipk-gatersleben.de)
Date: Wed, 16 Dec 2009 19:04:17 +0100
Subject: [Biopython] suggestion: moving to the discussion list to	Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <20091216190417.1z9yrs6mn4f4gcsw@webmail.ipk-gatersleben.de>

What about a free forum e.g. smf (http://www.simplemachines.org/) on 
the biopython homepage?

I'm using this too and I'm quite happy. Easy building, maintaining...
Just an idea...

Zitat von Hilmar Lapp <hlapp at drycafe.net>:

>
> On Dec 16, 2009, at 12:18 PM, Istvan Albert wrote:
>
>> I am sure one can come up with  unlikely yet equally pessimistic  
>> scenarios for the existing setup as well.
>
> My point was that this is not unlikely at all. It happened with some  
> of Yahoo's services, and it happened with others rather popular ones.
>
> If you own and operate your own brand, your equipment can still go 
> out  of order. But at least it's under your own control. Do you see 
> that  difference? Would you argue that that is unimportant?
>
>> This mailman setup is a throttle - it imposes a negative feedback on 
>>  the amount of messages that it can handle.
>
> I really don't know what you mean by this. I get 200 messages a day  
> from various lists. I'd be dead if I had an email client that can't  
> thread and can't filter, but I do have one that can (and it's free).  
> GMail can do both too, and is free. Have you tried a threading email  
> reader? Can you explain how reading newsgroups through a threaded and 
>  filtering news reader is different and more efficient than reading  
> emails through a threaded and filtering email reader?
>
> That all being said, if what's at issue here is to have a Google 
> Group  interface to the Biopython mailing list, then that's actually 
> easy to  achieve. Someone (ideally one of the current list or project 
> admins/ owners) creates a (presumably identically named) Google 
> Group, and  sets it to mirror the mailman mailing list.
>
> Guys - I'm happy to help with that if you don't know how to do that.  
> Create the group, subscribe drycafe at gmail.com, and make me an admin.  
> I'll configure the mirroring.
>
> 	-hilmar
>
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>





From iua1 at psu.edu  Wed Dec 16 18:13:45 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:13:45 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>

On Wed, Dec 16, 2009 at 12:40 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> If you own and operate your own brand, your equipment can still go out of
> order. But at least it's under your own control. Do you see that difference?
> Would you argue that that is unimportant?

It is a valid argument. No question about that.

I do have a comeback though, what percent of the past decade's
archive's content do you think is still actually useful? Isn't the
archive's purpose more of a historical one. And type of archiving you
could do for yourself.

But as for useful content that other people want to use - I am
guessing the half life of any particular advice is no more than about
one two two years.

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From hlapp at drycafe.net  Wed Dec 16 18:23:18 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 13:23:18 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
Message-ID: <9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>


On Dec 16, 2009, at 1:13 PM, Istvan Albert wrote:

> what percent of the past decade's archive's content do you think is  
> still actually useful?


Actually I find it very useful. We frequently cite past posts as  
references for explanations, or problems previously reported. It's one  
of the main differences between an archived mailing list and a simple  
alias for a group of people.

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






From cjfields at illinois.edu  Wed Dec 16 18:28:37 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 12:28:37 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
Message-ID: <F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>


On Dec 16, 2009, at 12:23 PM, Hilmar Lapp wrote:

> 
> On Dec 16, 2009, at 1:13 PM, Istvan Albert wrote:
> 
>> what percent of the past decade's archive's content do you think is still actually useful?
> 
> 
> Actually I find it very useful. We frequently cite past posts as references for explanations, or problems previously reported. It's one of the main differences between an archived mailing list and a simple alias for a group of people.
> 
> 	-hilmar

Agreed.  With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.

chris


From iua1 at psu.edu  Wed Dec 16 18:40:27 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:40:27 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
Message-ID: <c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>

On Wed, Dec 16, 2009 at 1:28 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
> Agreed. ?With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.

My fault for being insufficiently clear. I am not saying that having
archives is useless.

It all needs to be framed in the mindset of an unexpected event
causing an archive to be  lost. Is that irreparable harm? For example
would having a hundred more active participants be worth the small
risk of losing the archives?

I am just putting the 100 as a number out there, just to get you to
think. I think you all agree that at some level of extra participation
the risks would be well worth it.

Now I am convinced that a Google group would get more participation.
But is that 10 more people, one hundred, one thousand? That I do not
dare to guesstimate.

(definitely more than 10, ;-) )

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1



From cjfields at illinois.edu  Wed Dec 16 18:34:42 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 12:34:42 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <61CD9E3F-3F1A-4AC0-B863-9A24E7A373EF@illinois.edu>


On Dec 16, 2009, at 11:40 AM, Hilmar Lapp wrote:

> 
> On Dec 16, 2009, at 12:18 PM, Istvan Albert wrote:
> 
>> I am sure one can come up with  unlikely yet equally pessimistic scenarios for the existing setup as well.
> 
> My point was that this is not unlikely at all. It happened with some of Yahoo's services, and it happened with others rather popular ones.
> 
> If you own and operate your own brand, your equipment can still go out of order. But at least it's under your own control. Do you see that difference? Would you argue that that is unimportant?
> 
>> This mailman setup is a throttle - it imposes a negative feedback on the amount of messages that it can handle.
> 
> I really don't know what you mean by this. I get 200 messages a day from various lists. I'd be dead if I had an email client that can't thread and can't filter, but I do have one that can (and it's free). GMail can do both too, and is free. Have you tried a threading email reader? Can you explain how reading newsgroups through a threaded and filtering news reader is different and more efficient than reading emails through a threaded and filtering email reader?
> 
> That all being said, if what's at issue here is to have a Google Group interface to the Biopython mailing list, then that's actually easy to achieve. Someone (ideally one of the current list or project admins/owners) creates a (presumably identically named) Google Group, and sets it to mirror the mailman mailing list.
> 
> Guys - I'm happy to help with that if you don't know how to do that. Create the group, subscribe drycafe at gmail.com, and make me an admin. I'll configure the mirroring.
> 
> 	-hilmar

That would probably be a good idea for all the (most trafficked) open-bio groups.  I'll work on it from the bioperl end.

chris




From tiagoantao at gmail.com  Wed Dec 16 18:52:55 2009
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Wed, 16 Dec 2009 18:52:55 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
Message-ID: <6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>

On Wed, Dec 16, 2009 at 5:40 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> If you own and operate your own brand, your equipment can still go out of
> order. But at least it's under your own control. Do you see that difference?
> Would you argue that that is unimportant?

+1 .

Just to say I fully subscribe to this point of view.

github is _different_ by the very nature of being a distributed
system. If tomorrow github.com disappears, it will be very easy to
recover from it. If google turns bad, we loose a lot of history as
google groups is not inherently distributed and thus neither resilient
nor fail-safe.

I prefer the status quo to the google groups change. From my point of
view the technological autonomy provided by the OBF is a good thing.

My ?0.02,
Tiago



From biopython at maubp.freeserve.co.uk  Wed Dec 16 18:55:16 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Dec 2009 18:55:16 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
	<c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>
Message-ID: <320fb6e00912161055l38b8e27dpbb4c19be7c23b18b@mail.gmail.com>

On Wed, Dec 16, 2009 at 6:02 PM, Istvan Albert <iua1 at psu.edu> wrote:
> A response mentioned that Gmail's email threading works just as well
> ... ?well it doesn't help anyone who has not already been subscribed
> to the messages to begin with. ?If you come to a discussion later you
> cannot get that.

True - but that becomes less and less of an issue once you
have signed up.

> ... Get someone who is 20 and has never heard of sending
> emails to an address then see what they say about it...

Do 20 year olds really not know how to use email these days?
I do talk to graduate students, and hadn't noticed a trend.
I must be getting old(er). Maybe we need a "Dummies
Guide to setting up a GoogleMail/Thunderbird/Outlook
filter"? e.g. I have one to move things from the inbox to a
"Biopython" folder automatically.

I do take you point that making the mailing list more
accessible to novices (especially university students) is a
good idea - and you may be right that *mirroring* it on
GoogleGroups could be a solution. I don't know enough
about how that works to have an informed viewpoint, but
I trust Hilmar to look into it.

Peter



From iua1 at psu.edu  Wed Dec 16 18:57:39 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:57:39 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>
Message-ID: <c878cd560912161057l1fc52636nef4ab79d64cd0643@mail.gmail.com>

2009/12/16 Tiago Ant?o <tiagoantao at gmail.com>:

> If google turns bad, we loose a lot of history as google groups
> is not inherently distributed and thus neither resilient

No, on a second thought it actually is.

Sign up to the group such that is sends an email for every single
message (if you wish so). Google goes under, go back to the site the
way it is right now.

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1



From iua1 at psu.edu  Wed Dec 16 18:59:11 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 13:59:11 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912161055l38b8e27dpbb4c19be7c23b18b@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
	<c878cd560912161002h7d3af725mbb686935e7bf49a4@mail.gmail.com>
	<320fb6e00912161055l38b8e27dpbb4c19be7c23b18b@mail.gmail.com>
Message-ID: <c878cd560912161059s1d06eff1j4cf7eabd23c03c0d@mail.gmail.com>

On Wed, Dec 16, 2009 at 1:55 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> Do 20 year olds really not know how to use email these days?
> I do talk to graduate students, and hadn't noticed a trend.
> I must be getting old(er). Maybe we need a "Dummies

Not email but interacting with a listserver via emails.

Ask your students what a list server is.


-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From iua1 at psu.edu  Wed Dec 16 19:14:21 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 14:14:21 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <c878cd560912161114h391b7673tf9e26ad0d9745705@mail.gmail.com>

On Wed, Dec 16, 2009 at 2:07 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Just curious, but does anyone know whether Google groups are more or less susceptible to spamming?
> The current mailman setup does keep out a vast majority of spam (I can't recall the last instance, actually).


The effective way to deal with it is white listing. There is a setting
that requires that the first message from a given email be approved by
mods.

That being said spam, popularity and ease of access all correlate.



-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From cjfields at illinois.edu  Wed Dec 16 19:05:46 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 13:05:46 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161057l1fc52636nef4ab79d64cd0643@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<6d941f120912161052m4360fe66w2fcff505fa61be3c@mail.gmail.com>
	<c878cd560912161057l1fc52636nef4ab79d64cd0643@mail.gmail.com>
Message-ID: <CE55BF20-B8A3-4BAF-AC72-10A3DB8890C6@illinois.edu>


On Dec 16, 2009, at 12:57 PM, Istvan Albert wrote:

> 2009/12/16 Tiago Ant?o <tiagoantao at gmail.com>:
> 
>> If google turns bad, we loose a lot of history as google groups
>> is not inherently distributed and thus neither resilient
> 
> No, on a second thought it actually is.
> 
> Sign up to the group such that is sends an email for every single
> message (if you wish so). Google goes under, go back to the site the
> way it is right now.
> 
> Istvan

...and in the meantime we lose any content only present on the google group list.  Whereas if the group is a mirror of this list, then nothing is lost.

chris


From hlapp at drycafe.net  Wed Dec 16 19:20:21 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 14:20:21 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <307922E9-8DD9-408F-8D39-D259186B3568@drycafe.net>

It's the mailing list moderator volunteers that keep the spam out,  
actually. It's gotten so bad though that most OBF lists are set to  
reject non-member posts.

What Google might be better at is to reject the spam well enough that  
one could open up the lists again to non-member posting.

-hilmar

Sent from away

On Dec 16, 2009, at 2:07 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Just curious, but does anyone know whether Google groups are more or  
> less susceptible to spamming?  The current mailman setup does keep  
> out a vast majority of spam (I can't recall the last instance,  
> actually).


From cjfields at illinois.edu  Wed Dec 16 19:07:39 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Dec 2009 13:07:39 -0600
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
Message-ID: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>

On Dec 16, 2009, at 12:40 PM, Istvan Albert wrote:

> On Wed, Dec 16, 2009 at 1:28 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>> Agreed.  With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.
> 
> My fault for being insufficiently clear. I am not saying that having
> archives is useless.
> 
> It all needs to be framed in the mindset of an unexpected event
> causing an archive to be  lost. Is that irreparable harm? For example
> would having a hundred more active participants be worth the small
> risk of losing the archives?

Not that I think Google is in any danger of going under, or that Google Groups will cease to exist, but they have discontinued services in the past (notebook was one, and I recall others going away).

> I am just putting the 100 as a number out there, just to get you to
> think. I think you all agree that at some level of extra participation
> the risks would be well worth it.

I understand your point, but I'm not really convinced this is something that can't be accomplished by simply mirroring the group and redirecting new users to sign up on the obf forums.

> Now I am convinced that a Google group would get more participation.
> But is that 10 more people, one hundred, one thousand? That I do not
> dare to guesstimate.
> 
> (definitely more than 10, ;-) )
> 
> Istvan

I think mirroring the list is the best compromise.  I can't envision moving everything wholesale over to Google Groups for the reasons Hilmar has outlined.

Just curious, but does anyone know whether Google groups are more or less susceptible to spamming?  The current mailman setup does keep out a vast majority of spam (I can't recall the last instance, actually).  

chris


From iua1 at psu.edu  Wed Dec 16 19:21:05 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Wed, 16 Dec 2009 14:21:05 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>

On Wed, Dec 16, 2009 at 2:07 PM, Chris Fields <cjfields at illinois.edu> wrote:

> I understand your point, but I'm not really convinced this is something that can't be accomplished by simply mirroring the group and redirecting new users to sign up on the obf forums.

Great idea! While you are at it, why not allow people to post as well?

Sign up the current list so that when someone posts on Google Groups
it also goes to the current biopython list. When people reply-all from
biopython group it will go to both lists.

Maybe it is possible to get both worlds and using them in parallel!

Istvan


-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From hlapp at drycafe.net  Wed Dec 16 19:29:14 2009
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Dec 2009 14:29:14 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
	<c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
Message-ID: <C1D71945-4ACB-450D-9B55-39D5699B3C83@drycafe.net>

That's included in the mirroring. You can post through either  
interface and join at either interface, it's transparent.

-hilmar

Sent from away

On Dec 16, 2009, at 2:21 PM, Istvan Albert <iua1 at psu.edu> wrote:

> Great idea! While you are at it, why not allow people to post as well?


From pingou at pingoured.fr  Wed Dec 16 19:35:07 2009
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 16 Dec 2009 20:35:07 +0100
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
	<c878cd560912161121j24cc63b7m470215c40468d720@mail.gmail.com>
Message-ID: <1260992107.5993.0.camel@localhost.localdomain>

On Wed, 2009-12-16 at 14:21 -0500, Istvan Albert wrote:
> 
> Sign up the current list so that when someone posts on Google Groups
> it also goes to the current biopython list 
that implies that people are suscribed to both list and that won't be
always the case

Pierre



From richard_w_g_price at academia.edu  Wed Dec 16 22:50:05 2009
From: richard_w_g_price at academia.edu (Richard Price)
Date: Wed, 16 Dec 2009 14:50:05 -0800
Subject: [Biopython] New Academia.edu feature for Biopython
In-Reply-To: <cc0d7cc0912021721g660b39a2ga13c8213ec701454@mail.gmail.com>
References: <cc0d7cc0912021721g660b39a2ga13c8213ec701454@mail.gmail.com>
Message-ID: <cc0d7cc0912161450u7e188b9cm6eb85e24afc6458@mail.gmail.com>

Dear Biopython members,

I just wanted to let you know that there are now 5 members of Biopython on
Academia.edu listing their research interests such as Analytical
Chemistry, Computational Biology, and Bioinformatics. They have also
listed contacts, photos and papers.

There are thousands of people listing the same research interests as
the Biopython
members on Academia.edu, so there are lots of researchers for Biopython
members to discover.

To see the 5 members of Biopython on Academia.edu, and their research
interests and papers, follow the link below:

http://lists.academia.edu/See-members-of-Biopython

Richard

Dr. Richard Price, post-doc, Philosophy Dept, Oxford University.
Founder of Academia.edu

On Wed, Dec 2, 2009 at 5:21 PM, Richard Price
<richard_w_g_price at academia.edu> wrote:
> Dear Biopython members,
>
>
> I wanted to tell the list about a new feature on Academia.edu.
> Academia.edu launched 12 months ago and now helps 300,000 academics a
> month answer the question 'who's researching what?'
>
>
> We have built a dedicated page on Academia.edu for the Biopython mailing list:
>
>
> http://lists.academia.edu/See-members-of-Biopython
>
>
> This page will show you fellow members already on Academia.edu. ?You
> can see their papers, research interests, and other information.
>
>
> Visit the link below, sign up with Academia.edu, and see who else from
> Biopython is on Academia.edu.
>
>
>
> http://lists.academia.edu/See-members-of-Biopython
>
>
> Richard
>
>
> Dr. Richard Price, post-doc, Philosophy Dept, Oxford University.
> Founder of Academia.edu
>



From lpritc at scri.ac.uk  Thu Dec 17 09:35:56 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Thu, 17 Dec 2009 09:35:56 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
Message-ID: <C74FABFC.2DBF9%lpritc@scri.ac.uk>

Hi,

On 16/12/2009 16:49, "Istvan Albert" <iua1 at psu.edu> wrote:

> [the mailing list] feels like a throwback to the 90s. [...]
> Of course  python has comp.lang.python and it is a nice and
> thriving group.

<stir>

comp.lang.python is a Usenet group, and Usenet is a throwback to the 70s. ;)

</stir>

> I can't even imagine what it would look like to have a popular
> newsgroup being delivered to my mailbox.

Mailing lists are far more convenient - for me - than having to navigate to
a website especially to check new messages on a particular subject.  Mailing
lists bring new posts and issues to my attention via a single always-on
interface in a timely manner.  The current mailing list also has the
advantage of grabbing the attention, specifically, of many people who might
be able to do something about a query.

As it happens, when I used to still read Usenet groups, I would do so from
my mail client, with exactly the same threaded interface as I used for
mailing lists and all other email.

Biopython is never likely to be more than a niche interest, so I wouldn't
expect it to ever reach the traffic of - say - alt.binaries.  To be honest,
the traffic doesn't even seem to approach that of numpy-discussion.  And
while we're talking about numpy-discussion, it illustrates one of Hilmar's
and Chris' points:

On 16/12/2009 16:56, "Hilmar Lapp" <hlapp at drycafe.net> wrote:

> what is your solution to Google all of a sudden deciding to take
> Google Groups down, or to make it a paid subscription service, or if
> Google goes out of business?

On 16/12/2009 19:07, "Chris Fields" <cjfields at illinois.edu> wrote:

> Not that I think Google is in any danger of going under, or that Google Groups
> will cease to exist, but they have discontinued services in the past (notebook
> was one, and I recall others going away).

http://groups.google.com/group/numpy-discussion/unlock?_done=/group/numpy-di
scussion/

That mailing list was taken down from Google Groups for 'violating terms of
service' - why, I don't know: it's a mailing list for a specialist Python
library.  It does illustrate though, how control can be (irrevocably) lost
over communication via Google Groups.  Notably, the mailing list itself
persists without interruption.

On 16/12/2009 17:36, "Istvan Albert" <iua1 at psu.edu> wrote:

> One thing is seems clear to me and I do not think that you are aware
> of it. This mailman setup is a throttle - it imposes a negative
> feedback on the amount of messages that it can handle.
> 
> This system of messages cannot grow over a certain limit. Just imagine
> regularly getting a dozen new emails a day plus their followups, yet
> you are just a casual user.
> 
> This would be unbearable for many people whose inboxes are already
> overflowing.

This issue - that some people don't like to receive lots of messages at once
- is already solved in mailman.  There is a 'daily digest' option on the
mailing list that collates the messages for a day, and sends them out as a
single email for you.

As a mailing list, mailman is deliberately designed to be relatively low
volume in terms of content, but to reach many readers directly; the idea is
to send relatively few messages to many people - but to push those messages
through to the reader.

Forums, wikis and website-based discussion lists require a deliberate effort
on the part of the reader either to find what they're interested in, or to
visit the site regularly.  Otherwise they just end up signing up to receive
updates by email, much like mailman.

On 16/12/2009 17:40, "Hilmar Lapp" <hlapp at drycafe.net> wrote:

> That all being said, if what's at issue here is to have a Google Group
> interface to the Biopython mailing list, then that's actually easy to
> achieve.

FWIW, I think that archiving the mailing list on Google Groups is not a bad
idea - so long as the current registration scheme continues to prevent the
inevitable waves of spam from Google Groups users.

The Biopython mailing lists appear already to have been archived - with
various degrees of usable interface, and likely intermittent coverage, too -
at sites such as:

http://www.mailinglistarchive.com/biopython at biopython.org/index.html

and

http://osdir.com/ml/search.html?cx=008059810939676512379%3Af5owd_2hq3u&cof=F
ORID%3A10&q=%5Bbiopython%5D&sa=Search

amongst others.

On 16/12/2009 18:02, "Istvan Albert" <iua1 at psu.edu> wrote:

> All of you who responded - frankly I think you are too close to this
> issue to be able judge it correctly. [...] Get
> someone who is 20 and has never heard of sending emails to an address
> then see what they say about it...

<stir>

If they've never heard of emailing an address, and/or can't use a mail
client to filter their email, I'm not sure the immediate problem is
necessarily with the mailing list... ;)

</stir>

I don't think that anyone here wants to restrict access to Biopython, or to
prevent discussion, even inadvertently.  That we've had 28 posts on this
issue in about 12 hours suggests that the list can handle issues of some
interest.  Sure, it would be nice to have a convenient, web-accessible and
searchable archive with a pretty and robust interface (and Google Groups
could give us that).  But I'm not convinced that the current mailing list is
a particular barrier to participation.


+1 for mirroring/archiving on Google Groups:
http://groups.google.com/support/bin/answer.py?hl=en&answer=46387


L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________


From lpritc at scri.ac.uk  Thu Dec 17 10:14:54 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Thu, 17 Dec 2009 10:14:54 +0000
Subject: [Biopython] Is there any in silico PCR tool on biopython?
In-Reply-To: <65d4b7fc0912160857l30796cb4p33b8ff2c8dfac693@mail.gmail.com>
Message-ID: <C74FB51E.2DBFD%lpritc@scri.ac.uk>

Hi Carlos,

There's an interface to the EMBOSS package primersearch, which might be what
you're looking for.

http://embossgui.sourceforge.net/demo/manual/primersearch.html

http://github.com/biopython/biopython/blob/master/Bio/Emboss/Applications.py

Cheers,

L.


On 16/12/2009 16:57, "Carlos Javier Borroto" <carlos.borroto at gmail.com>
wrote:

> Hi there,
> 
> I'm looking for a way to show some information on the specificity of
> sets of primers I'm designing, I'll love to have a way to run an in
> silico PCR reaction and parse the results with biopython.
> 
> Is there something to use with one of the available PCR simulation tools?
> 
> regards,

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________


From biopython at maubp.freeserve.co.uk  Thu Dec 17 10:42:16 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 10:42:16 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <C74FABFC.2DBF9%lpritc@scri.ac.uk>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<C74FABFC.2DBF9%lpritc@scri.ac.uk>
Message-ID: <320fb6e00912170242p7caa551eh91c2aa7beabc00f1@mail.gmail.com>

On Thu, Dec 17, 2009 at 9:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
>
> On 16/12/2009 16:56, "Hilmar Lapp" <hlapp at drycafe.net> wrote:
>
>> what is your solution to Google all of a sudden deciding to take
>> Google Groups down, or to make it a paid subscription service,
>> or if Google goes out of business?
>
> On 16/12/2009 19:07, "Chris Fields" <cjfields at illinois.edu> wrote:
>
>> Not that I think Google is in any danger of going under, or that Google Groups
>> will cease to exist, but they have discontinued services in the past (notebook
>> was one, and I recall others going away).
>
> http://groups.google.com/group/numpy-discussion/unlock?_done=/group/numpy-di
> scussion/
>
> That mailing list was taken down from Google Groups for 'violating terms of
> service' - why, I don't know: it's a mailing list for a specialist Python
> library. ?It does illustrate though, how control can be (irrevocably) lost
> over communication via Google Groups. ?Notably, the mailing list itself
> persists without interruption.

I remembered that example later - if NumPy had *switched*
that would have been a major upset to their community. As it
was, it seems people who were using the Google Groups
interface switched to using plain old email:
http://mail.scipy.org/pipermail/numpy-discussion/2009-October/045855.html

Peter



From biopython at maubp.freeserve.co.uk  Thu Dec 17 10:55:51 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 10:55:51 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <C74FABFC.2DBF9%lpritc@scri.ac.uk>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<C74FABFC.2DBF9%lpritc@scri.ac.uk>
Message-ID: <320fb6e00912170255y3968a6e4s3bd904071910251@mail.gmail.com>

On Wed, Dec 16, 2009 at 6:55 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> I do take you point that making the mailing list more
> accessible to novices (especially university students) is a
> good idea - and you may be right that *mirroring* it on
> GoogleGroups could be a solution. I don't know enough
> about how that works to have an informed viewpoint, but
> I trust Hilmar to look into it.
>

On Thu, Dec 17, 2009 at 9:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
>
> +1 for mirroring/archiving on Google Groups:
> http://groups.google.com/support/bin/answer.py?hl=en&answer=46387
>

It looks like we can see mirroring/archiving on Google Groups in action -
Hilmar and Chris have got this up and running for the main BioPerl list,

http://lists.open-bio.org/pipermail/bioperl-l/2009-December/031789.html
http://groups.google.com/group/bioperl-l

It is a shame there isn't any obvious way to import the existing archive
though.

Peter


From biopython at maubp.freeserve.co.uk  Thu Dec 17 12:27:59 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 12:27:59 +0000
Subject: [Biopython] Entrez.efetch Service unavailable!
In-Reply-To: <5b6410e0912160125j4f034218x263e6ab90b4afd47@mail.gmail.com>
References: <5b6410e0912151952h76787344t18968aba5ab350d8@mail.gmail.com>
	<320fb6e00912160058i57acc020nba7c61c53a4ec64b@mail.gmail.com>
	<5b6410e0912160125j4f034218x263e6ab90b4afd47@mail.gmail.com>
Message-ID: <320fb6e00912170427q6b31ee33x6b161323d24f3027@mail.gmail.com>

On Wed, Dec 16, 2009 at 9:25 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi Peter,
> Thanks for the suggestion. It was also an exercise for me since I am new to
> Biopython and add to the fact that I do not need the Archaea sequences as I
> am looking for pathogenic bacteria. I admit I am lazy ha! All the same,
> thanks for being so helpful to a newbie to biopython.
> Cheers
> Kevin

No problem. I've been trying Entrez EFtech on and off over the last 24
hours, and it has been unavailable for a while. It seems to be back now.

Peter

P.S. Mailing list CC'd


From giles.weaver at googlemail.com  Thu Dec 17 13:25:18 2009
From: giles.weaver at googlemail.com (Giles Weaver)
Date: Thu, 17 Dec 2009 13:25:18 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
Message-ID: <4B2A313E.3050300@googlemail.com>

I urge extreme caution with regards to using Google Groups.
My experiences with Google Groups have been less than satisfactory. I've 
administered several small groups and they have been plagued with 
delivery issues for a small subset of users. I've also known members to 
be unable to access a group that they are a member of, and find that 
Google Groups has "disappeared" their profile - despite having an 
otherwise fully functioning Google account (Gmail etc).

I'm not a fan of mailman, but at least the open-bio administrators have 
full control over the lists. I've known Chris to solve issues with the 
bioperl mailman list within minutes. You won't get that kind of service 
(if any) from Google.

Having looked at alternatives to Google Groups myself, the two things 
that have caught my attention are bbPress (a wordpress derived bulletin 
board) and Google Wave. Both are still under development.
bbPress <http://bbpress.org/> boards can be subscribed to via RSS (and 
possibly email), so users can have messages drop into their mail/news 
reader.
Wave looks promising, but I wouldn't touch it with a barge pole until 
mature Google free implementations take off, and that could be some time 
away.

Mirroring the open-bio mailman lists onto Google Groups seems to me the 
right way to go, but I think there should be a health warning on the 
list home pages!

Giles

On 16/12/2009 19:07, Chris Fields wrote:
> On Dec 16, 2009, at 12:40 PM, Istvan Albert wrote:
>
>    
>> On Wed, Dec 16, 2009 at 1:28 PM, Chris Fields<cjfields at illinois.edu>  wrote:
>>      
>>> Agreed.  With bioperl we generally indicate it's best to search the archives prior to asking a question, just in case the answer is already known or has been worked out.
>>>        
>> My fault for being insufficiently clear. I am not saying that having
>> archives is useless.
>>
>> It all needs to be framed in the mindset of an unexpected event
>> causing an archive to be  lost. Is that irreparable harm? For example
>> would having a hundred more active participants be worth the small
>> risk of losing the archives?
>>      
> Not that I think Google is in any danger of going under, or that Google Groups will cease to exist, but they have discontinued services in the past (notebook was one, and I recall others going away).
>
>    
>> I am just putting the 100 as a number out there, just to get you to
>> think. I think you all agree that at some level of extra participation
>> the risks would be well worth it.
>>      
> I understand your point, but I'm not really convinced this is something that can't be accomplished by simply mirroring the group and redirecting new users to sign up on the obf forums.
>
>    
>> Now I am convinced that a Google group would get more participation.
>> But is that 10 more people, one hundred, one thousand? That I do not
>> dare to guesstimate.
>>
>> (definitely more than 10, ;-) )
>>
>> Istvan
>>      
> I think mirroring the list is the best compromise.  I can't envision moving everything wholesale over to Google Groups for the reasons Hilmar has outlined.
>
> Just curious, but does anyone know whether Google groups are more or less susceptible to spamming?  The current mailman setup does keep out a vast majority of spam (I can't recall the last instance, actually).
>
> chris
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>    


From biopython at maubp.freeserve.co.uk  Thu Dec 17 13:35:25 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 13:35:25 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <4B2A313E.3050300@googlemail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<227F9F99-39F4-4AF1-AEE0-03313D14049F@drycafe.net>
	<c878cd560912160918v3e2d1e89q4bc4b886f1917920@mail.gmail.com>
	<0B35BE99-F267-4A0E-8E86-63EF079167B1@drycafe.net>
	<c878cd560912161013q5463b278uc05be87ca34f00b5@mail.gmail.com>
	<9B112844-2D52-41BF-8D25-83BDD64D2560@drycafe.net>
	<F5E8ED46-9C7F-4D46-975F-6C2C7BE8834F@illinois.edu>
	<c878cd560912161040y685932f9h9e33f0815ba3299a@mail.gmail.com>
	<085CF361-FDAA-414B-BD7A-E249B6E9FC66@illinois.edu>
	<4B2A313E.3050300@googlemail.com>
Message-ID: <320fb6e00912170535r3a6d2a4cv37d852aff3671e6e@mail.gmail.com>

On Thu, Dec 17, 2009 at 1:25 PM, Giles Weaver
<giles.weaver at googlemail.com> wrote:
> I urge extreme caution with regards to using Google Groups.
> My experiences with Google Groups have been less than satisfactory.
> ...
>
> Mirroring the open-bio mailman lists onto Google Groups seems to me the
> right way to go, but I think there should be a health warning on the list
> home pages!

Thanks for the hard earned advice. I absolutely agree that *moving* to
GoogleGroups is a bad idea, and accept that *mirroring* may be worth
a try.

Given the BioPerl list is already trying this out, let's give that a week
or so, and if they think it works nicely then we could do the same for
Biopython.

Peter


From David.Lapointe at umassmed.edu  Thu Dec 17 12:42:15 2009
From: David.Lapointe at umassmed.edu (Lapointe, David)
Date: Thu, 17 Dec 2009 07:42:15 -0500
Subject: [Biopython] EMBOSS and Python
Message-ID: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>

I haven't used EMBOSS though the python module before so this hasn't
been an issue but even though I have  a working install of EMBOSS, all
of the EMBOSS tests seem to fail. I haven't seen any instructions for
this.

David 





From biopython at maubp.freeserve.co.uk  Thu Dec 17 17:04:11 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 17:04:11 +0000
Subject: [Biopython] EMBOSS and Python
In-Reply-To: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
Message-ID: <320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>

On Thu, Dec 17, 2009 at 12:42 PM, Lapointe, David
<David.Lapointe at umassmed.edu> wrote:
> I haven't used EMBOSS though the python module before so this hasn't
> been an issue but even though I have ?a working install of EMBOSS, all
> of the EMBOSS tests seem to fail. I haven't seen any instructions for
> this.

What version of Biopython do you have? And if you are talking about the
Biopython unit tests, could you post the output please?

What version of EMBOSS do you have? Some of the Biopython tests did
flag issues in EMBOSS which are fixed in their latest release.

Thanks,

Peter



From iua1 at psu.edu  Thu Dec 17 17:29:17 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Thu, 17 Dec 2009 12:29:17 -0500
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <C74FABFC.2DBF9%lpritc@scri.ac.uk>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com>
	<C74FABFC.2DBF9%lpritc@scri.ac.uk>
Message-ID: <c878cd560912170929k2dc7fe72sa3de81bc058e00@mail.gmail.com>

On Thu, Dec 17, 2009 at 4:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:

> Mailing lists are far more convenient - for me - than having to navigate to
> a website especially to check new messages on a particular subject.

Just for clarity:  nobody is suggesting to take that away. You can
*always* get the messages delivered via email. I think some of you get
a little bit defensive because you assume that the suggestion is about
messing with your system.

> Biopython is never likely to be more than a niche interest,

You are perfectly right here and that echoes my original sentiment!
What keeps biopython a niche interest is exactly the lack of community
building features. There obstacles in getting into it, so most won't.
It doesn't take much to discourage a newcomer.

best,

Istvan

-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From dalloliogm at gmail.com  Thu Dec 17 17:48:18 2009
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Thu, 17 Dec 2009 18:48:18 +0100
Subject: [Biopython] suggestion: moving to the discussion list to Google
	groups
In-Reply-To: <320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
References: <c878cd560912160849j1c54bc63r8f251f4c718eb23f@mail.gmail.com> 
	<320fb6e00912160926i2d17312br3f6ca730aa42daa1@mail.gmail.com>
Message-ID: <5aa3b3570912170948k1890aa5ft3c30c760718c3cbd@mail.gmail.com>

On Wed, Dec 16, 2009 at 6:26 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Dec 16, 2009 at 4:49 PM, Istvan Albert <iua1 at psu.edu> wrote:
>>
>> The alternative such as Google groups would be far superior in
>> attracting and building a community of developers and users as well.
>> Is this an idea that ?the owners of the list would entertain?
>>
>
> As far as I can tell from the limited documentation I found on
> Google Groups (maybe I was looking in the wrong place?) there
> is no way to import our existing decade long mail archives.
> That would be a major downside.


It seems that you can use a google/group to archive the messages from
a remote mailing list, but you can't import the older messages to the
google group:
- http://groups.google.com/support/bin/answer.py?hl=en&answer=46387

Maybe you can give it a try: just create a group on google and use it
as a mirror for the current mailing list. This way google users will
be able to use the google interface to search and read messages, but
they won't be able to post messages by mail. It won't arm anyone to
have a mirror of the messages in GG, except that it may be a bit
confusing for new users.

About other possibilities, it seems that there is not yet a way to
import a whole archive go GG:
- http://groups.google.com/group/Groups-Suggestions/browse_thread/thread/3eb3ed32dee6b97e

I have tried google/wave (I have invitations if anyone wants) but
please, avoid to switch to it yet because it is still very very buggy
and it will take them at least one year or so to make it useful.


> Also, using Google Groups would *require* all posters to have
> a Google Account - a potential sticking point for some.

I am still not sure about this: it seems that you can subscribe with
another address if you are invited, but you have to create a google
account (not necessarily a google mail) to subscribe to it manually.

It is a nice idea to switch to a fancier program for managing the
list, but maybe it would require too much time to switch to
google/groups.

>
> Peter
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it



From lpritc at scri.ac.uk  Thu Dec 17 17:55:52 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Thu, 17 Dec 2009 17:55:52 +0000
Subject: [Biopython] suggestion: moving to the discussion list to Google
 groups
In-Reply-To: <c878cd560912170929k2dc7fe72sa3de81bc058e00@mail.gmail.com>
Message-ID: <C7502128.2DC9B%lpritc@scri.ac.uk>

Hi,

On 17/12/2009 17:29, "Istvan Albert" <iua1 at psu.edu> wrote:

> On Thu, Dec 17, 2009 at 4:35 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> 
>> Mailing lists are far more convenient - for me - than having to navigate to
>> a website especially to check new messages on a particular subject.
> 
> Just for clarity:  nobody is suggesting to take that away. You can
> *always* get the messages delivered via email.

I wasn't worried that anyone would 'take it away'.  Though it must be said
that not all discussion systems allow email tracking.

> I think some of you get a little bit defensive because you assume that the
> suggestion is about messing with your system.

I don't think that's a fair characterisation.  So far, what I've seen is
open and thoughtful discussion of a comment you've made, and general
agreement that mirroring/archiving on Google Groups is a good idea.  Just
because someone doesn't agree with every point you make, that doesn't make
them defensive.

>> Biopython is never likely to be more than a niche interest,
> 
> You are perfectly right here and that echoes my original sentiment!
> What keeps biopython a niche interest is exactly the lack of community
> building features. There obstacles in getting into it, so most won't.
> It doesn't take much to discourage a newcomer.

That's not what I meant when I wrote that it's a niche interest.

Biopython is a niche interest because a user likely fulfils three - rather
unusual - criteria.  I believe that these are the big obstacles to
participation - not the software used for the mailing list:

- they program in Python
- they have an interest (likely professional or educational - not many
bioinformatics hobbyists out there) in bioinformatics
- they have bothered to investigate an existing general library for
bioinformatics in Python, rather than try to solve their problem from
scratch ;)

Add to that, that the mailing list is a forum for discussion which - along
with all other online fora for discussion, including Google Groups - is
inherently self-selecting for active members.  Taken together, this sets its
own upper limit to the user base, which in turn helps define what is a
sensible system to convey information between, and to, users.

The three criteria listed above do suggest a sufficient level of comfort
with the problem domain, such that Biopython's presence on Google Groups is
- in my opinion - unlikely to be the major draw for new contributors or
users.

I do worry for the future of research if signing up to a mailing list (which
you can do via the website; no subscription email is required) is an
insurmountable hurdle for young, apparently computer-literate scientists.
If that sort of thing really is a problem, it should at least keep
conference attendances down in years to come, as navigating their Byzantine
registration systems must drive them to endless despair...

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________


From iua1 at psu.edu  Thu Dec 17 18:47:23 2009
From: iua1 at psu.edu (Istvan Albert)
Date: Thu, 17 Dec 2009 13:47:23 -0500
Subject: [Biopython] some eye opening stats
Message-ID: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>

Hello Everyone,

So I ran some statistics on this group (see below) that includes the
entire past year. Make you own decisions based on it.

Here is one of my observation:  I find it saddening that I made the
list at number 18!  That's some niche list where one person posting
ten messages in a whole year gets to be at number 18. In fact I only
need three more posts to make myself top ten poster! Would you still
claim this to be a good way to establish, grow and interact with a
community?

I said this many times before, and I'll try for this to be the last
time I bring this up:

I believe biopython is a niche software tool because *YOU* are
limiting its reach *YOURSELVES* by making inappropriate decisions as
far as accessibility and community goes. It will stay so as long as
you don't recognize and act on this.

best regards,

Istvan Albert

=================================

Statistics from 1.12.2008 to 17.12.2009
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
***** People who have written most messages:
+----+-----Author-----------------------------------+--Msg-+-Percent-+
|  1 | biopython at maubp.freeserve.co.uk (Peter)   |  472 | 39.70 % |
|  2 | chapmanb at 50mail.com (Brad Chapman)        |   53 |  4.46 % |
|  3 | p.j.a.cock at googlemail.com (Peter Cock)    |   36 |  3.03 % |
|  4 | lueck at ipk-gatersleben.de (=?iso-8859-1?Q? |   27 |  2.27 % |
|  5 | mjldehoon at yahoo.com (Michiel de Hoon)     |   23 |  1.93 % |
|  6 | cjfields at illinois.edu (Chris Fields)      |   22 |  1.85 % |
|  7 | dalloliogm at gmail.com (Giovanni Marco Dall |   21 |  1.77 % |
|  8 | winda002 at student.otago.ac.nz (David Winte |   15 |  1.26 % |
|  9 | lpritc at scri.ac.uk (Leighton Pritchard)    |   14 |  1.18 % |
| 10 | cmckay at u.washington.edu (Cedar McKay)     |   13 |  1.09 % |
| 11 | italo.maia at gmail.com (Italo Maia)         |   12 |  1.01 % |
| 12 | kellrott at gmail.com (Kyle Ellrott)         |   12 |  1.01 % |
| 13 | rodrigo_faccioli at uol.com.br (Rodrigo facc |   12 |  1.01 % |
| 14 | bartek at rezolwenta.eu.org (Bartek Wilczyns |   12 |  1.01 % |
| 15 | anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Ro |   11 |  0.93 % |
| 16 | bartomas at gmail.com (bar tomas)            |   11 |  0.93 % |
| 17 | pzs at dcs.gla.ac.uk (Peter Saffrey)         |   11 |  0.93 % |
| 18 | iua1 at psu.edu (Istvan Albert)              |   10 |  0.84 % |
| 19 | dejmail at gmail.com (Liam Thompson)         |   10 |  0.84 % |
| 20 | stran104 at chapman.edu (Matthew Strand)     |   10 |  0.84 % |
| 21 | ibdeno at gmail.com (Miguel Ortiz Lombardia) |    9 |  0.76 % |
| 22 | pengyu.ut at gmail.com (Peng Yu)             |    9 |  0.76 % |
| 23 | yvan.strahm at bccs.uib.no (Yvan Strahm)     |    9 |  0.76 % |
| 24 | kelly.oakeson at utah.edu (Kelly F Oakeson)  |    9 |  0.76 % |
| 25 | carlos.borroto at gmail.com (Carlos Javier B |    9 |  0.76 % |
+----+----------------------------------------------+------+---------+
|    | other                                        |  337 | 28.34 % |
+----+----------------------------------------------+------+---------+

***** Best authors, by total size of their messages (w/o quoting):
+----+-----Author-------------------------------------------+-KBytes-+
|  1 | biopython at maubp.freeserve.co.uk (Peter)           |  391.4 |
|  2 | chapmanb at 50mail.com (Brad Chapman)                |   48.1 |
|  3 | lpritc at scri.ac.uk (Leighton Pritchard)            |   39.1 |
|  4 | p.j.a.cock at googlemail.com (Peter Cock)            |   35.7 |
|  5 | lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie |   27.9 |
|  6 | matzke at berkeley.edu (Nick Matzke)                 |   21.2 |
|  7 | animesh.agrawal at anu.edu.au (Animesh Agrawal)      |   21.1 |
|  8 | kelly.oakeson at utah.edu (Kelly F Oakeson)          |   16.7 |
|  9 | pzs at dcs.gla.ac.uk (Peter Saffrey)                 |   15.4 |
| 10 | dalloliogm at gmail.com (Giovanni Marco Dall'Olio)   |   14.7 |
| 11 | natassa_g_2000 at yahoo.com (natassa)                |   12.7 |
| 12 | hlapp at gmx.net (Hilmar Lapp)                       |   12.7 |
| 13 | mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydG |   12.5 |
| 14 | cjfields at illinois.edu (Chris Fields)              |   12.0 |
| 15 | bartek at rezolwenta.eu.org (Bartek Wilczynski)      |   11.6 |
| 16 | winda002 at student.otago.ac.nz (David Winter)       |   11.3 |
| 17 | cmckay at u.washington.edu (Cedar McKay)             |   11.0 |
| 18 | mjldehoon at yahoo.com (Michiel de Hoon)             |   10.9 |
| 19 | dejmail at gmail.com (Liam Thompson)                 |   10.6 |
| 20 | rodrigo_faccioli at uol.com.br (Rodrigo faccioli)    |   10.3 |
| 21 | anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues? |    9.7 |
| 22 | fufezan at uni-muenster.de (Christian Fufezan)       |    9.6 |
| 23 | kellrott at gmail.com (Kyle Ellrott)                 |    9.2 |
| 24 | peter at maubp.freeserve.co.uk (Peter)               |    8.9 |
| 25 | ibdeno at gmail.com (Miguel Ortiz Lombardia)         |    8.3 |
+----+------------------------------------------------------+--------+

***** Best authors, by average size of their message (w/o quoting):
+----+-----Author--------------------------------------------+-bytes-+
|  1 | agarbino at gmail.com (Alex Garbino)                  |  7991 |
|  2 | aduran at fhcrc.org (Duran, Alysha M)                 |  3893 |
|  3 | n.j.loman at bham.ac.uk (Nick Loman)                  |  3877 |
|  4 | mmueller at python-academy.de (=?ISO-8859-15?Q?Mike_M |  3816 |
|  5 | animesh.agrawal at anu.edu.au (Animesh Agrawal)       |  3598 |
|  6 | ivan at biodec.com (Ivan Rossi)                       |  2947 |
|  7 | thomas.e.keller at gmail.com (Thomas Keller)          |  2937 |
|  8 | lpritc at scri.ac.uk (Leighton Pritchard)             |  2860 |
|  9 | matzke at berkeley.edu (Nick Matzke)                  |  2717 |
| 10 | jhcepas at gmail.com (Jaime Huerta Cepas)             |  2705 |
| 11 | fufezan at uni-muenster.de (Christian Fufezan)        |  2447 |
| 12 | natassa_g_2000 at yahoo.com (natassa)                 |  2175 |
| 13 | bav853 at bham.ac.uk (Bhima A van der Molen)          |  1987 |
| 14 | kteague at bcgsc.ca (Kevin Teague)                    |  1932 |
| 15 | danielchubb at gmail.com (Daniel Chubb)               |  1923 |
| 16 | lueck at ipk-gatersleben.de (=?utf-8?Q?Stefanie_L=C3= |  1919 |
| 17 | dalloliogm at fastwebnet.it (Giovanni Marco Dall'Olio |  1915 |
| 18 | kelly.oakeson at utah.edu (Kelly F Oakeson)           |  1895 |
| 19 | bav853 at bham.ac.uk (Bhima Auro van der Molen)       |  1874 |
| 20 | darnells at dnastar.com (Steve Darnell)               |  1768 |
| 21 | gatoygata at hotmail.com (Joaquin Abian Monux)        |  1744 |
| 22 | srini_iyyer_bio at yahoo.com (Srinivas Iyyer)         |  1733 |
| 23 | bassbabyface at yahoo.com (Ben O'Loghlin)             |  1698 |
| 24 | hlapp at gmx.net (Hilmar Lapp)                        |  1624 |
| 25 | mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGl |  1603 |
+----+-------------------------------------------------------+-------+

***** Table showing the most successful subjects:
+----+----Subject-----------------------------------+--Msg-+-Percent-+
|  1 | [Biopython] suggestion: moving to the discus |   33 |  2.78 % |
|  2 | [Biopython] Problems parsing with PSIBlastPa |   32 |  2.69 % |
|  3 | [BioPython] The count method of a Seq (or Mu |   23 |  1.93 % |
|  4 | [Biopython] Biopython and Snow Leopard       |   21 |  1.77 % |
|  5 | [Biopython] Phylogenetic trees with biopytho |   16 |  1.35 % |
|  6 | [Biopython] Indexing large sequence files    |   15 |  1.26 % |
|  7 | [Biopython] SQL Alchemy based BioSQL         |   14 |  1.18 % |
|  8 | [BioPython] AlignIO: Sequences of different  |   13 |  1.09 % |
|  9 | [Biopython] searching for a human chromosome |   13 |  1.09 % |
| 10 | [Biopython] BLAST against mouse genome only  |   12 |  1.01 % |
| 11 | [Biopython] How to get sequences upstream of |   12 |  1.01 % |
| 12 | [Biopython] Parsing large blast files        |   11 |  0.93 % |
| 13 | [Biopython] Additions to the SeqRecord       |   11 |  0.93 % |
| 14 | [Biopython] Biopython & p3d                  |   11 |  0.93 % |
| 15 | [BioPython] Feedback from Biopython 1.50 bet |   10 |  0.84 % |
| 16 | [BioPython] Adding startswith and endswith m |   10 |  0.84 % |
| 17 | [Biopython] Bio.Sequencing.Ace               |   10 |  0.84 % |
| 18 | [Biopython] Entrez.read return value is type |   10 |  0.84 % |
| 19 | [Biopython] SeqIO for fasta conversion of Il |   10 |  0.84 % |
| 20 | [Biopython] Parsing problem                  |    9 |  0.76 % |
| 21 | [Biopython] Fasta.index_file: functionality  |    9 |  0.76 % |
| 22 | [Biopython] Adaptor trimmer and dimers       |    9 |  0.76 % |
| 23 | [BioPython] Is query_length really the lengt |    8 |  0.67 % |
| 24 | [BioPython] Reading Roche 454 binary SFF fil |    8 |  0.67 % |
| 25 | [Biopython] Writing into a PDB file using PD |    8 |  0.67 % |
+----+----------------------------------------------+------+---------+
|    | other                                        |  851 | 71.57 % |
+----+----------------------------------------------+------+---------+

***** Most used email clients:
+----+----Mailer------------------------------------+--Msg-+-Percent-+
|  1 | (unknown)                                    | 1189 |100.00 % |
+----+----------------------------------------------+------+---------+
|    | other                                        |    0 |  0.00 % |
+----+----------------------------------------------+------+---------+

***** Table of maximal quoting:
+----+-----Author------------------------------------------+-Percent-+
|  1 | golubchi at stats.ox.ac.uk (Tanya Golubchik)        | 94.68 % |
|  2 | fredgca at hotmail.com (Frederico Arnoldi)          | 92.56 % |
|  3 | srikrishnamohan at gmail.com (km)                   | 92.28 % |
|  4 | cmckay at u.washington.edu (Cedar Mckay)            | 88.19 % |
|  5 | harekrishna at gmail.com (Austin Davis-Richar       | 87.51 % |
|  6 | biopython.chen at gmail.com (chen Ku)               | 86.14 % |
|  7 | wgheath at gmail.com (William Heath)                | 85.12 % |
|  8 | jkhilmer at gmail.com (Jonathan Hilmer)             | 82.50 % |
|  9 | andrea at biodec.com (Andrea)                       | 80.82 % |
| 10 | nuin at genedrift.org (Paulo Nuin)                  | 79.90 % |
| 11 | lueck at ipk-gatersleben.de (lueck at ipk-gat       | 78.81 % |
| 12 | ibdeno at gmail.com (Miguel Ortiz Lombardia)        | 78.57 % |
| 13 | oda at georgetown.edu (Ogan ABAAN)                  | 75.33 % |
| 14 | sean.maceach at gmail.com (Sean MacEachern)         | 75.09 % |
| 15 | pengyu.ut at gmail.com (Peng Yu)                    | 73.17 % |
| 16 | fungazid at yahoo.com (Fungazid)                    | 71.57 % |
| 17 | yvan.strahm at bccs.uib.no (Yvan Strahm)            | 70.23 % |
| 18 | cjfields at illinois.edu (Chris Fields)             | 70.18 % |
| 19 | sdavis2 at mail.nih.gov (Sean Davis)                | 68.54 % |
| 20 | thomas.hamelryck at gmail.com (Thomas Hamelry       | 68.31 % |
| 21 | mjldehoon at yahoo.com (Michiel de Hoon)            | 66.49 % |
| 22 | mavata at gmail.com (Manu Tamminen)                 | 66.42 % |
| 23 | eric.talevich at gmail.com (Eric Talevich)          | 65.92 % |
| 24 | bsouthey at gmail.com (Bruce Southey)               | 64.70 % |
| 25 | biopythonlist at gmail.com (dr goettel)             | 64.53 % |
+----+-----------------------------------------------------+---------+
|    | average                                             | 44.57 % |
+----+-----------------------------------------------------+---------+

***** Graph showing number of messages written during hours of day:

100% ---------------------#--------------------------- - 146
 90% ---------------------#--------------------------- msgs
 80% ---------------------#---------------------------
 70% ---------------------#-#-------------------------
 60% ---------------------#-#-#-#-#---#---------------
 50% ---------------------#-#-#-#-#-#-#-#-------------
 40% ---------------------#-#-#-#-#-#-#-#-#-----------
 30% -----------------#-#-#-#-#-#-#-#-#-#-#-#---------
 20% -----------------#-#-#-#-#-#-#-#-#-#-#-#---------
 10% ---------------#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-
      * * * * * * * * * * * * * * * * * * * * * * * *
hour  0         5           11          17          23


***** Graph showing number of messages written during days of month:

100% -----------------------------#--------------------------------- - 74
 90% -----------------------------#-#------------------------------- msgs
 80% -----------------#-----------#-#-------------------------------
 70% -#---------------#---------#-#-#---#---------------------------
 60% -#-------#-#-----#---------#-#-#-#-#-#-#-----------------#-----
 50% -#-------#-#-----#-------#-#-#-#-#-#-#-#-----#-#---------#-----
 40% -#-#-----#-#-----#-----#-#-#-#-#-#-#-#-#-#---#-#---#---#-#-----
 30% -#-#-#-#-#-#---#-#-#---#-#-#-#-#-#-#-#-#-#---#-#-#-#-#-#-#-----
 20% -#-#-#-#-#-#-#-#-#-#---#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-
 10% -#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-
      * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 day  1         6           12          18          24            31


***** Graph showing number of messages written during days of week:

100% -------------#--------------- - 262
 90% ---------#---#--------------- msgs
 80% ---------#---#---#-----------
 70% -#---#---#---#---#-----------
 60% -#---#---#---#---#-----------
 50% -#---#---#---#---#-----------
 40% -#---#---#---#---#-----------
 30% -#---#---#---#---#-----------
 20% -#---#---#---#---#-----------
 10% -#---#---#---#---#---#---#---
      *   *   *   *   *   *   *
     Mon Tue Wed Thu Fri Sat Sun


***** Maximal quoting:
      Author     : andrea at biodec.com (Andrea)
      Subject    : [Biopython] Problems parsing with PSIBlastParser
      Date       : Thu, 15 Oct 2009 17:39:48 +0200
      Quote ratio: 98.63% / 15890 bytes

***** Longest message:
      Author     : chapmanb at 50mail.com (Brad Chapman)
      Subject    : [Biopython] Skipping over blank/erroneous Entrez.esummary()
      Date       : Wed, 7 Oct 2009 16:29:11 -0400
      Size       : 18503 bytes

***** Most successful subject:
      Subject    : [Biopython] suggestion: moving to the discussion
list to Google
      No. of msgs: 33
      Total size : 43527 bytes

***** Final summary:
      Total number of messages:             1189
      Total number of different authors:    159
      Total number of different subjects:   332
      Total size of messages (w/o headers): 1992170 bytes
      Average size of a message:            1675 bytes

***** Generated by MailListStat v1.3, (C) 2001-2003 <marki (at) nexin.sk>
***** See http://freshmeat.net/projects/mls for details...

-- 
Istvan Albert
http://www.personal.psu.edu/iua1


From mailinglist.honeypot at gmail.com  Thu Dec 17 19:08:55 2009
From: mailinglist.honeypot at gmail.com (Steve Lianoglou)
Date: Thu, 17 Dec 2009 14:08:55 -0500
Subject: [Biopython] some eye opening stats
In-Reply-To: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
References: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
Message-ID: <6E3B0A7F-476A-4417-A580-0FBCF4512763@gmail.com>

Hi Istvan,

On Dec 17, 2009, at 1:47 PM, Istvan Albert wrote:

> Hello Everyone,
> 
> So I ran some statistics on this group (see below) that includes the
> entire past year. Make you own decisions based on it.
> 
> Here is one of my observation:  I find it saddening that I made the
> list at number 18!  That's some niche list where one person posting
> ten messages in a whole year gets to be at number 18. In fact I only
> need three more posts to make myself top ten poster! Would you still
> claim this to be a good way to establish, grow and interact with a
> community?
> 
> I said this many times before, and I'll try for this to be the last
> time I bring this up:
> 
> I believe biopython is a niche software tool because *YOU* are
> limiting its reach *YOURSELVES* by making inappropriate decisions as
> far as accessibility and community goes. It will stay so as long as
> you don't recognize and act on this.

I haven't said much so far because (1) I'm not really actively using biopython atm, and (2) I'm largely indifferent about the choice of mailing list vs. web interface, but let's be serious here ... how can you be so confident in drawing any causality between your stats and the fact that biopython is using a mailing list?

You're arguing that since you are at # 18 w/ only 10 posts, it must be due to discussion about this project is confined to a mailing-list instead of a more "open" and "accessible" web group and the community needs to "act now" or ignore this at its peril.

Try doing the same experiment with the bioconductor mailing list, or (depending on how bold you're feeling)  the R-user mailing list. Discussion on both groups is via mailing-list only (or through gmane --- same can be said with this list) and come back with that report.

Now, go try your same experiment on the networkx or igraph user group. Both are hosted on google groups. With 10 posts, you'll likely be somewhere in the top 10 posters for the year.

Oh, even better: igraph just set up the mirror-do-hicky-whatever so you can access their mailing list via GG sometime in July:

http://groups.google.com/group/network-analysis-with-igraph/browse_thread/thread/77305d9b6bc6d35/c6a694e287936049?lnk=gst&q=google+groups#c6a694e287936049

Perhaps you'd like to see how traffic has changed on that list before and after that fact. I'm going to guess it wasn't by all that much, but that would at least be a better experiment you can use to base your hunches on.

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact




From cjfields at illinois.edu  Thu Dec 17 19:46:08 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Dec 2009 13:46:08 -0600
Subject: [Biopython] some eye opening stats
In-Reply-To: <6E3B0A7F-476A-4417-A580-0FBCF4512763@gmail.com>
References: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
	<6E3B0A7F-476A-4417-A580-0FBCF4512763@gmail.com>
Message-ID: <1ED2ED4E-F87E-4229-8D6A-8EF56C837D73@illinois.edu>

On Dec 17, 2009, at 1:08 PM, Steve Lianoglou wrote:

> Hi Istvan,
> 
> On Dec 17, 2009, at 1:47 PM, Istvan Albert wrote:
> 
>> Hello Everyone,
>> 
>> So I ran some statistics on this group (see below) that includes the
>> entire past year. Make you own decisions based on it.
>> 
>> Here is one of my observation:  I find it saddening that I made the
>> list at number 18!  That's some niche list where one person posting
>> ten messages in a whole year gets to be at number 18. In fact I only
>> need three more posts to make myself top ten poster! Would you still
>> claim this to be a good way to establish, grow and interact with a
>> community?
>> 
>> I said this many times before, and I'll try for this to be the last
>> time I bring this up:
>> 
>> I believe biopython is a niche software tool because *YOU* are
>> limiting its reach *YOURSELVES* by making inappropriate decisions as
>> far as accessibility and community goes. It will stay so as long as
>> you don't recognize and act on this.
> 
> I haven't said much so far because (1) I'm not really actively using biopython atm, and (2) I'm largely indifferent about the choice of mailing list vs. web interface, but let's be serious here ... how can you be so confident in drawing any causality between your stats and the fact that biopython is using a mailing list?
> 
> You're arguing that since you are at # 18 w/ only 10 posts, it must be due to discussion about this project is confined to a mailing-list instead of a more "open" and "accessible" web group and the community needs to "act now" or ignore this at its peril.
> 
> Try doing the same experiment with the bioconductor mailing list, or (depending on how bold you're feeling)  the R-user mailing list. Discussion on both groups is via mailing-list only (or through gmane --- same can be said with this list) and come back with that report.
> 
> Now, go try your same experiment on the networkx or igraph user group. Both are hosted on google groups. With 10 posts, you'll likely be somewhere in the top 10 posters for the year.
> 
> Oh, even better: igraph just set up the mirror-do-hicky-whatever so you can access their mailing list via GG sometime in July:
> 
> http://groups.google.com/group/network-analysis-with-igraph/browse_thread/thread/77305d9b6bc6d35/c6a694e287936049?lnk=gst&q=google+groups#c6a694e287936049
> 
> Perhaps you'd like to see how traffic has changed on that list before and after that fact. I'm going to guess it wasn't by all that much, but that would at least be a better experiment you can use to base your hunches on.
> 
> -steve
> 
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  |  Memorial Sloan-Kettering Cancer Center
>  |  Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact

This also doesn't factor participation via other means, such as other mail lists, IRC, etc.  As an example, the Perl Moose mail list is fairly low traffic, with a few posts a week, but the IRC channel is much more active.  Conversely, we in BioPerl tend to use the mail list over #bioperl (though I do use both if time permits). 

I think way too much time has been pushed into this topic, considering we've reached a pretty viable option, namely mirroring the list to Google Groups.  That seems satisfactory to everyone.  I fail to see the reason to press the issue (and everyone's ire) more?

chris





From jtomkins at ICR.org  Thu Dec 17 19:43:19 2009
From: jtomkins at ICR.org (Jeff Tomkins)
Date: Thu, 17 Dec 2009 13:43:19 -0600
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
Message-ID: <C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>

I installed biopython 1.52 as directed for OS X leopard.  Everything imports using the python prompt in the terminal, idle, ipython, wing ide, etc.  But when I run a standard python script (#!/usr/bin/python) in the shell it cannot locate Bio.  What setup feature have I missed?

Thanks, Jeff


From villahozbale at wisc.edu  Thu Dec 17 20:23:30 2009
From: villahozbale at wisc.edu (ANGEL VILLAHOZ-BALETA)
Date: Thu, 17 Dec 2009 14:23:30 -0600
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <7065_1261079798_ZZg0M1E7a5Xoa.00_C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<7065_1261079798_ZZg0M1E7a5Xoa.00_C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
Message-ID: <6f80a33d6a3f0.4b2a3ee2@wiscmail.wisc.edu>

Jeff,

Have you added the path of the libraries of Biopython to the shell variable called as PYTHONPATH?

Angel Villahoz-Baleta
Bioinformatics Programmer
University of Wisconsin-Madison

----- Original Message -----
From: Jeff Tomkins <jtomkins at ICR.org>
Date: Thursday, December 17, 2009 1:56 pm
Subject: [Biopython] Bio won't import in *.py scripts
To: "Biopython at lists.open-bio.org" <Biopython at lists.open-bio.org>

> I installed biopython 1.52 as directed for OS X leopard.  Everything 
> imports using the python prompt in the terminal, idle, ipython, wing 
> ide, etc.  But when I run a standard python script (#!/usr/bin/python) 
> in the shell it cannot locate Bio.  What setup feature have I missed?
> 
> Thanks, Jeff
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython


From daniel at dim.fm.usp.br  Thu Dec 17 19:49:28 2009
From: daniel at dim.fm.usp.br (Daniel Silvestre)
Date: Thu, 17 Dec 2009 17:49:28 -0200
Subject: [Biopython] Why so few recipes in the cookbook?
Message-ID: <4B2A8B48.50302@dim.fm.usp.br>

Greeting everybody,

Is there a reason to the existence of so few recipes in Biopython
cookbook? Is there a task force to improve the documentation and related
stuff?

Usually I see perfect reusable and instructional recipes in blogs of
biopython users. But, they simply don't get to the cookbook.

Att.
Daniel


-- 
+---------------------------------------+
Daniel de A. M. M. Silvestre
LIM01 - Laborat?rio de Inform?tica M?dica - HCFMUSP
Sala 1349 - Depto. de Patologia
Faculdade de Medicina
Universidade de S?o Paulo
Av. Dr. Arnaldo, 455                | e-mail:  daniel at dim.fm.usp.br
Cerqueira C?sar                     |    Tel: +55-11-3061-7381
01246-903  -  S?o Paulo  -  SP      |    Cel: +55-11-8042-9369
BRASIL                              |  Skype: jarretinha

---------------------------------------------------------------------
Esta mensagem pode conter informacao confidencial.
Se voce nao for o destinatario ou a pessoa autorizada a receber
esta mensagem, nao podera usar, copiar ou divulgar as informacoes nela
contidas ou tomar qualquer acao baseada nessas informacoes. Se
voce recebeu esta mensagem por engano, favor avisar imediatamente o
remetente, respondendo o e-mail e, em seguida, apague-o.
Agradecemos sua cooperacao.

This message may contain confidential information.
If you are not the addressee or authorized person to receive it for the
addressee, you must not use, copy, disclose or take any action based on
this message or any information herein. If you have received this message
in error, please advise the sender immediately by replying this e-mail 
message and delete it.
Thanks in advance for your cooperation.
----------------------------------------------------------------------
               DIM   Faculdade de Medicina USP
----------------------------------------------------------------------

-------------- next part --------------
A non-text attachment was scrubbed...
Name: daniel.vcf
Type: text/x-vcard
Size: 375 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091217/a6313b8c/attachment-0002.vcf>

From biopython at maubp.freeserve.co.uk  Thu Dec 17 21:16:42 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Dec 2009 21:16:42 +0000
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <4B2A8B48.50302@dim.fm.usp.br>
References: <4B2A8B48.50302@dim.fm.usp.br>
Message-ID: <320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>

2009/12/17 Daniel Silvestre <daniel at dim.fm.usp.br>:
> Greeting everybody,
>
> Is there a reason to the existence of so few recipes in Biopython
> cookbook? Is there a task force to improve the documentation
> and related stuff?

The cookbook wiki is still quite new (6 months or so), but the
idea was to encourage user participation. What would you like
to write about ;)

http://news.open-bio.org/news/2009/04/biopython-cookbook-wiki/

> Usually I see perfect reusable and instructional recipes in blogs of
> biopython users. But, they simply don't get to the cookbook.

Any specific examples? We can ask blog authors to put
some of their finished receipes on the wiki (with a link
back to the original).

Peter

P.S. Your message was delayed for moderation - probably the attachment?


From p.j.a.cock at googlemail.com  Thu Dec 17 22:59:07 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 17 Dec 2009 22:59:07 +0000
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
Message-ID: <320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>

Hi Jeff,

On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins <jtomkins at icr.org> wrote:
> I installed biopython 1.52 as directed for OS X leopard.
> ?Everything imports using the python prompt in the terminal,
> idle, ipython, wing ide, etc.

Good :)

> But when I run a standard python script (#!/usr/bin/python)
> in the shell it cannot locate Bio. ?What setup feature have I missed?

That does seem odd. You didn't call your script Bio.py did you?
Could you show us the error message?

Peter



From mjldehoon at yahoo.com  Fri Dec 18 08:35:40 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Dec 2009 00:35:40 -0800 (PST)
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>
Message-ID: <274100.45967.qm@web62402.mail.re1.yahoo.com>

If you start python in the terminal, does it start /usr/bin/python or a different python?

--- On Thu, 12/17/09, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [Biopython] Bio won't import in *.py scripts
> To: "Jeff Tomkins" <jtomkins at icr.org>
> Cc: "Biopython at lists.open-bio.org" <Biopython at lists.open-bio.org>
> Date: Thursday, December 17, 2009, 5:59 PM
> Hi Jeff,
> 
> On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins <jtomkins at icr.org>
> wrote:
> > I installed biopython 1.52 as directed for OS X
> leopard.
> > ?Everything imports using the python prompt in the
> terminal,
> > idle, ipython, wing ide, etc.
> 
> Good :)
> 
> > But when I run a standard python script
> (#!/usr/bin/python)
> > in the shell it cannot locate Bio. ?What setup
> feature have I missed?
> 
> That does seem odd. You didn't call your script Bio.py did
> you?
> Could you show us the error message?
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list? -? Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 


      



From lpritc at scri.ac.uk  Fri Dec 18 08:49:51 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Fri, 18 Dec 2009 08:49:51 +0000
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>
Message-ID: <C750F2AF.2DD39%lpritc@scri.ac.uk>

Hi,

On 17/12/2009 22:59, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> Hi Jeff,
> 
> On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins <jtomkins at icr.org> wrote:
>> I installed biopython 1.52 as directed for OS X leopard.
>> ?Everything imports using the python prompt in the terminal,
>> idle, ipython, wing ide, etc.
> 
> Good :)
> 
>> But when I run a standard python script (#!/usr/bin/python)
>> in the shell it cannot locate Bio. ?What setup feature have I missed?

It could be a $PATH issue.

On my Mac, /usr/bin/python is where Apple's Python lives.  I leave that
installation alone, and don't replace it to avoid problems with the OS's
potential use of Python (I had horrors with it back at 10.2).  My 'working'
version of Python is installed as /usr/local/bin/python.

lpmacpro:scripts lpritc$ /usr/bin/python
Python 2.5.1 (r251:54863, Feb  6 2009, 19:02:12)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
lpmacpro:scripts lpritc$ which python
/usr/local/bin/python
lpmacpro:scripts lpritc$ python
Python 2.6 (trunk:66714:66715M, Oct  1 2008, 18:36:04)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 
lpmacpro:scripts lpritc$ /usr/local/bin/python
Python 2.6 (trunk:66714:66715M, Oct  1 2008, 18:36:04)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 

You could check to see if your setup is similar.

What this means is that, as I have /usr/local/bin ahead of /usr/bin in my
$PATH (don't shout at me, everyone!), command-line invocation and module
installations with 'python setup.py' use the 'working' version, so install
modules under that version of Python only.  This would mean that if I had
#!/usr/bin/python at the head of my script, it would use Apple's Python, and
not see modules installed under my 'working' Python.  This would give the
same error you seem to describe:

lpmacpro:scripts lpritc$ python
Python 2.6 (trunk:66714:66715M, Oct  1 2008, 18:36:04)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> 
lpmacpro:scripts lpritc$ /usr/bin/python
Python 2.5.1 (r251:54863, Feb  6 2009, 19:02:12)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named Bio
>>> 

If this is the issue, then one way to get around the problem is to use
#!/usr/bin/env python at the top of your script so that it uses the Python
you would get from the command-line.  This is better in some ways, as you
don't have to make guesses about where the Python executable is installed
when you move the script to another machine, though it probably won't matter
on Windows, and there may be security issues that arise from this shortcut
under some circumstances.  If you're at all worried about those, just try
'which python' at the command-line, and substitute that location for
/usr/bin/python.

Cheers,

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________



From lpritc at scri.ac.uk  Fri Dec 18 10:16:42 2009
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Fri, 18 Dec 2009 10:16:42 +0000
Subject: [Biopython] some eye opening stats
In-Reply-To: <c878cd560912171047u2e8092bev377be19a9ecab8d2@mail.gmail.com>
Message-ID: <C751070A.2DD4E%lpritc@scri.ac.uk>

On 17/12/2009 18:47, "Istvan Albert" <iua1 at psu.edu> wrote:
 
> Statistics from 1.12.2008 to 17.12.2009
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ***** People who have written most messages:
> +----+-----Author-----------------------------------+--Msg-+-Percent-+
[...]
> |  9 | lpritc at scri.ac.uk (Leighton Pritchard)    |   14 |  1.18 % |

> 
> ***** Best authors, by total size of their messages (w/o quoting):
> +----+-----Author-------------------------------------------+-KBytes-+
[...]
> |  3 | lpritc at scri.ac.uk (Leighton Pritchard)            |   39.1 |

Hmm... Peter has suggested privately that I do have a somewhat prolix and
flowery writing style - I guess he's right... ;)

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that
addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________


From daniel at dim.fm.usp.br  Fri Dec 18 12:55:15 2009
From: daniel at dim.fm.usp.br (Daniel Silvestre)
Date: Fri, 18 Dec 2009 10:55:15 -0200
Subject: [Biopython] [Fwd: Re:  Why so few recipes in the cookbook?]
Message-ID: <4B2B7BB3.6090505@dim.fm.usp.br>


-- 
+---------------------------------------+
Daniel de A. M. M. Silvestre
LIM01 - Laborat?rio de Inform?tica M?dica - HCFMUSP
Sala 1349 - Depto. de Patologia
Faculdade de Medicina
Universidade de S?o Paulo
Av. Dr. Arnaldo, 455                | e-mail:  daniel at dim.fm.usp.br
Cerqueira C?sar                     |    Tel: +55-11-3061-7381
01246-903  -  S?o Paulo  -  SP      |    Cel: +55-11-8042-9369
BRASIL                              |  Skype: jarretinha

---------------------------------------------------------------------
Esta mensagem pode conter informacao confidencial.
Se voce nao for o destinatario ou a pessoa autorizada a receber
esta mensagem, nao podera usar, copiar ou divulgar as informacoes nela
contidas ou tomar qualquer acao baseada nessas informacoes. Se
voce recebeu esta mensagem por engano, favor avisar imediatamente o
remetente, respondendo o e-mail e, em seguida, apague-o.
Agradecemos sua cooperacao.

This message may contain confidential information.
If you are not the addressee or authorized person to receive it for the
addressee, you must not use, copy, disclose or take any action based on
this message or any information herein. If you have received this message
in error, please advise the sender immediately by replying this e-mail 
message and delete it.
Thanks in advance for your cooperation.
----------------------------------------------------------------------
               DIM   Faculdade de Medicina USP
----------------------------------------------------------------------

-------------- next part --------------
An embedded message was scrubbed...
From: unknown sender
Subject: no subject
Date: no date
Size: 6202
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091218/cd8bf70b/attachment-0002.eml>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: daniel.vcf
Type: text/x-vcard
Size: 375 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20091218/cd8bf70b/attachment-0002.vcf>

From biopython at maubp.freeserve.co.uk  Fri Dec 18 12:57:30 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 12:57:30 +0000
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <4B2B6DE2.3080500@dim.fm.usp.br>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<sfid-+20091217-191648-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
Message-ID: <320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>

2009/12/18 Daniel Silvestre <daniel at dim.fm.usp.br>:
> Greetings again,
>
> There are some blogs like Programming for Scientists and Yokofakun with
> some usable code and tips.
>
> I do want to contribute, but there are no clear objectives stated to the
> cookbook writing process. What's the gist? Just some code snippets?
> Complete examples?

I would personally prefer concrete examples. The name "cookbook"
suggests a collection of complete recipes (rather than snippets).

> My teaching experience says that complete (and real) examples are the
> most wanted. For instance, even in the bioperl community only code
> snippets are available. So, the first question students ask me after a
> brief looking at the tutorials is smth like "Well, how do I use this in
> a directory tree?".
>
> What about a bioinformatics recipes in (bio)python?

Yes please :)

Are there any examples in the main "Biopython Tutorial and
Cookbook" which would in your opinion be better in the wiki?

> Att,
> Daniel
>
> P.S.:Is there a problem with my vcard? I can use a different sig.

Could you try no vcard attachment at all?

Peter


From biopython at maubp.freeserve.co.uk  Fri Dec 18 15:00:13 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 15:00:13 +0000
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <4B2B8CC3.3090307@dim.fm.usp.br>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
	<sfid-+20091218-105736-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>
	<4B2B8CC3.3090307@dim.fm.usp.br>
Message-ID: <320fb6e00912180700w49d3be87r53b1a5201c84461b@mail.gmail.com>

2009/12/18 Daniel Silvestre <daniel at dim.fm.usp.br>:
> Hi people,
>
> Actually, even the tutorial is a collection of snippets. I do consider
> and regard the effort. But, in order to attract biologists like myself
> and my colleagues we need something more pragmatic, problem
> driven.

Most of the tutorial is by its nature "snippets" but the Cookbook
chapter examples are more self standing. I suspect you are
looking for even more self contained things - complete examples
with a motivating rational, sample input data, etc.

> The prototipical workflow of a molecular biologist is:
>
> ?- Select a bunch of interesting genes in Entrez by clicking buttons and
> boxes;
>
> ?- BLAST some sequences and save the results in separated directories,
> normally one for each gene;
>
> ?- Struggle to extract useful statistics from the results, wich usually
> end in sorting and selecting the first few results;
>
> ?- Apply some analytical method (phylogeny reconstruction, mutation
> analysis, etc.) over the "filtered" results;
>
> ?- Restart the cycle until get satisfied or bored;
>
> By the way, in one of my classes I just taught the students (which can
> be grad students and professors) to use the fields of Entrez (molecular
> weight, range search, organism name, etc.) and they felt really powerful
> after that. For instance, they used to retrieve sequence lists of papers
> ?by hand !!!

I confess I don't know or use the full power of the Entrez website,
although that is in part since I can do clever stuff via their API ;)

> On the other hand, the ones who dare to use biopython tipically don't
> know how to glob things and other administrivia. So, without a real
> example only biology geeks like me get to the next step.
>
> There is a list of good recipes to start the cookbook:
>
> ?- How to retrieve and organize sequences and annotations from online
> databases using you own custom command line tool;

We touch on some of this already, e.g. search and retrieve examples
in the Bio.Entrez chapter of the tutorial. Are you looking for something
more in depth? Or using other databases?

> ?- How to setup/insert/retrieve a bunch of results into a local
> (personal) database (SQL);

Done, although not tagged as a cookbook specifically:
http://www.biopython.org/wiki/BioSQL

(The tutorial also points to this page)

> ?- How to annotate retrieved results with your own results;

Now here I'd like a little clarification about what you want to do.

My guess would be something I have considered working up
into a cookbook recipe, based one stuff I have already done:
Taking a small genome (viral or prokaryote), doing simple
gene predictions (e.g. ORF finding, pick first start codon,
or maybe calling a command line tool to do it for us), then
taking the predicted peptides and BLASTing them, then
making a GenBank file with these predicted features and
stick a summary of the BLAST results in their annotation.

However, while this is a reasonable first step, there are
downsides to encouraging this sort of naive approach to
annotation - the example would ideally have "Further
Reading" section, see for example Schnoes et al 2009.
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000605

> These are real problems faced by the common biologist. The proposed
> snippets in the tutorial and the cookbook is already dealt by a lot of
> web tools. It's absolutely necessary to show that biopython can increase
> the power and range of a biologist everyday work, and can possibly be
> automated.
>
> I have some examples to obtain statistics over genome sequences which
> address complete examples (including globbing filelists, retrieving from
> online databases, etc.) and can prepare them as a recipe. But, I could
> use some help . . .

If you start a cookbook entry on the wiki, and some outline
code, I'm sure we can as a group contribute ideas and tips
(particularly in the code, but maybe in the approach too). Or,
if you would rather, discuss some specific ideas here on the
mailing list first.

Note that some of these topics would be ideal for an OBF
project wide set of examples, with reference solutions in
Biopython, BioPerl, BioJava, BioRuby, etc. That is however
a much much bigger task.

Peter



From rjalves at igc.gulbenkian.pt  Fri Dec 18 17:17:44 2009
From: rjalves at igc.gulbenkian.pt (Renato Alves)
Date: Fri, 18 Dec 2009 17:17:44 +0000
Subject: [Biopython] SeqIO.index improvement suggestions
Message-ID: <4B2BB938.5030709@igc.gulbenkian.pt>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

[I tried submitting this message to the dev mailing list, but got
rejected since I'm not yet authorized to post there, so here it goes]

Hi everyone,

I'm working on changes to the Bio.SeqIO.index() function to make it more
consistent with the .read and .parse i.e. accept a filehandle instead of
a filename and also to include a way to cache the index into a file to
speed up the process.

The reason why we are implementing these two is because we were going to
implement our own index solution until we realized this was added to 1.52.

However the implementation in 1.52 has a few limitations.

One limitation is that we are using a gzipped database for the sake of
space and using gzip.open() to create the file-handle that would then be
passed to .parse(). The same was not doable with .index().
This is already implemented in
http://github.com/Unode/biopython/commit/6fc390151452e3ddf26a117269132125a3ffb3fe

The second is that we are going to use this feature to quick search the
database in a web application. Here we have the limitation that we don't
have persistence across web requests, which means that we would need to
recalculate the index on every web request.

The details of how we plan to implement this are the following:

cPickle the internal dictionary of offsets and save it on the database
folder with the same name as the database + .index. The consistency
check on whether the file has changed will be performed based on name
and timestamp. By default .index() will search for this file, check the
timestamp and use the cache if they match, otherwise they will be
recalculated. The save function will be available like:

>>> >>> d = SeqIO.index(...)
>>> >>> d.save(filename)

where filename is optional and defaults to "%s.index" % _handle.name

We already have a solution like this implemented with subclasses of
SeqIO._index, it's just a matter of reworking that and merge it into
BioPython if you consider a good addition to the code.

I would like to hear your comments and suggestions on this.

Regards,
Renato
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iEYEARECAAYFAksruTIACgkQYh11EUYTX9TymgCeL6hu3Uz//itSHx38k9KjfZJg
dGUAmwVCgaI9G/19VKiUolrXogelgrPs
=M+xw
-----END PGP SIGNATURE-----


From biopython at maubp.freeserve.co.uk  Fri Dec 18 21:39:11 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 21:39:11 +0000
Subject: [Biopython] SeqIO.index improvement suggestions
In-Reply-To: <4B2BB938.5030709@igc.gulbenkian.pt>
References: <4B2BB938.5030709@igc.gulbenkian.pt>
Message-ID: <320fb6e00912181339o1a5c4100w6f1957fd4d78d20d@mail.gmail.com>

Hi Renato,

I'm cooking dinner while writing this, so it won't be as in depth as
usual...

On Fri, Dec 18, 2009 at 5:17 PM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
>
> [I tried submitting this message to the dev mailing list, but got
> rejected since I'm not yet authorized to post there, so here it goes]

Have you definitely subscribed to the dev list? That should be all that
is required to post there, and this discussion would be better suited
there.

> Hi everyone,
>
> I'm working on changes to the Bio.SeqIO.index() function to make it more
> consistent with the .read and .parse i.e. accept a filehandle instead of
> a filename and also to include a way to cache the index into a file to
> speed up the process.
>
> The reason why we are implementing these two is because we were going to
> implement our own index solution until we realized this was added to 1.52.
>
> However the implementation in 1.52 has a few limitations.

Yes, this was designed to cover basic use cases in a general way,
but with the option in future to do other things - and in particular
saving the index to disk was kept in mind.

> One limitation is that we are using a gzipped database for the sake of
> space and using gzip.open() to create the file-handle that would then be
> passed to .parse(). The same was not doable with .index().
> This is already implemented in
> http://github.com/Unode/biopython/commit/6fc390151452e3ddf26a117269132125a3ffb3fe

That was a deliberate choice in that the index code wants to "own"
the handle. If other code has access to the handle, there is a risky
of different bits of code moving the handle pointer etc. But, if you
are careful it could be done.

There are also issues here in combination with saving the index.
With a filename, the code can easily reopen the file in the same
mode. With a handle, things are more tricky. You have non-file
handles to consider - such as the gzip example. There is also the
problem of recording the file mode (normal text, universal text,
or binary - which we will need for SFF files - code already written).

If we do change the code to allow handles, it would have to be
to allow handles OR filenames to be compatible with Biopython
1.52 and 1.53 (which take just filenames). This could be handled
as in Bio.SeqIO.convert(), which also allows both (which was the
subject of some discussion!).

> The second is that we are going to use this feature to quick search the
> database in a web application. Here we have the limitation that we don't
> have persistence across web requests, which means that we would need to
> recalculate the index on every web request.
>
> The details of how we plan to implement this are the following:
>
> cPickle the internal dictionary of offsets and save it on the database
> folder with the same name as the database + .index. The consistency
> check on whether the file has changed will be performed based on name
> and timestamp. By default .index() will search for this file, check the
> timestamp and use the cache if they match, otherwise they will be
> recalculated. The save function will be available like:
>
>>>> >>> d = SeqIO.index(...)
>>>> >>> d.save(filename)
>
> where filename is optional and defaults to "%s.index" % _handle.name
>
> We already have a solution like this implemented with subclasses of
> SeqIO._index, it's just a matter of reworking that and merge it into
> BioPython if you consider a good addition to the code.
>
> I would like to hear your comments and suggestions on this.

Yes, saving indexes is an obvious addition. I have explored
using pickle via shelve, and also SQLite - there are
implementations of this on my github respository, plus
begun to look into the existing OBF Open Biological
Database Access (OBDA) specification for cross project
compatibility. Other potential benefits here are reduced
memory usage if we don't keep the dictionary
of offsets in RAM.

http://github.com/peterjc/biopython/tree/index-shelve
http://github.com/peterjc/biopython/tree/index-sqlite

There is a potential complication with index sub-classes
which do more specialised indexing (e.g. GenBank files,
and for a more extreme case, SFF files). See:
http://github.com/peterjc/biopython/tree/sff-seqio

Anyway - great to see you are finding the code useful,
and have some quite similar ideas for how to extend
it further.

Peter


From biopython at maubp.freeserve.co.uk  Fri Dec 18 22:26:43 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Dec 2009 22:26:43 +0000
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <F10A5C1D-E3EF-48FF-BA43-715161600296@ICR.org>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<C5096CF9-B649-4D98-BAF7-DFB9A0AC74D4@icr.org>
	<320fb6e00912171459m14462f0eq9d95f0dcdc039e8e@mail.gmail.com>
	<F10A5C1D-E3EF-48FF-BA43-715161600296@ICR.org>
Message-ID: <320fb6e00912181426i44b93b2co96a1a171a404dc5f@mail.gmail.com>

On Fri, Dec 18, 2009 at 6:25 PM, Jeff Tomkins <jtomkins at icr.org> wrote:
> I got some advice from Angel V. and added the following lines to my
> profile and the scripts now import Bio - it looks like ?it worked and
> fixed the issue. ?Thanks for getting back with me!
> -jeff
>
> PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/biopython-1.52-py2.5-macosx-10.3-fat.egg:${PYTHONPATH}"
> export PYTHONPATH
>

Excellent - and well done Angel for coming up with a working solution.

Peter



From pedro.al at fenhi.uh.cu  Fri Dec 18 22:25:29 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Fri, 18 Dec 2009 17:25:29 -0500
Subject: [Biopython] Superpose structures
Message-ID: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>

Hi all!!

I want to superpose some structures on a reference one.
The fixed selection is the backbone atoms of two residues and i want  
to superpose the rest of structures based in this atoms (for the same  
residues in the others structures, of course)

Reference selection:
[[<Atom O>, <Atom C>, <Atom CA>, <Atom N>], [<Atom O>, <Atom C>, <Atom  
CA>, <Atom N>]]

The moving selection is a similar nested list, with the list of the  
residues backbone atoms to move in the query structures....

How can i superpose these structures based in the backbone atoms of  
two residues?

Please help me...
Thanks




-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI






From p.j.a.cock at googlemail.com  Fri Dec 18 22:55:44 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 18 Dec 2009 22:55:44 +0000
Subject: [Biopython] Superpose structures
In-Reply-To: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
References: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
Message-ID: <320fb6e00912181455g680a8dbmdfa166bd820f06ed@mail.gmail.com>

2009/12/18 Yasser Almeida Hern?ndez <pedro.al at fenhi.uh.cu>:
> Hi all!!
>
> I want to superpose some structures on a reference one.
> The fixed selection is the backbone atoms of two residues and i want to
> superpose the rest of structures based in this atoms (for the same residues
> in the others structures, of course)
>
> Reference selection:
> [[<Atom O>, <Atom C>, <Atom CA>, <Atom N>], [<Atom O>, <Atom C>, <Atom CA>,
> <Atom N>]]
>
> The moving selection is a similar nested list, with the list of the residues
> backbone atoms to move in the query structures....
>
> How can i superpose these structures based in the backbone atoms of two
> residues?
>
> Please help me...
> Thanks

Does this example help?
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/

Peter



From mjldehoon at yahoo.com  Fri Dec 18 23:54:52 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Dec 2009 15:54:52 -0800 (PST)
Subject: [Biopython] Bio won't import in *.py scripts
In-Reply-To: <1D3CBE1D-A7A9-4337-BE0A-E073C2B9A3CC@ICR.org>
Message-ID: <138394.60837.qm@web62408.mail.re1.yahoo.com>

Good to hear you found a solution.
Just for some background information:
The reason /usr/bin/python couldn't find Biopython is that you have Biopython installed with the python in /Library/Frameworks/Python.framework/Versions/2.5/bin/python. These two pythons don't know about each other, so anything you install for one python is not seen by the other python. If you want to use /usr/bin/python in your scripts, another solution would have been to install Biopython for that python using /usr/bin/python setup.py build followed by /usr/bin/python setup.py install. But usually it's better to leave the Apple-installed python in /usr/bin/python alone, and to install modules for /Library/Frameworks/Python.framework/Versions/2.5/bin/python, and use that python.

--Michiel. 


--- On Fri, 12/18/09, Jeff Tomkins <jtomkins at ICR.org> wrote:

> From: Jeff Tomkins <jtomkins at ICR.org>
> Subject: Re: [Biopython] Bio won't import in *.py scripts
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Date: Friday, December 18, 2009, 1:27 PM
> I got some advice from Angel V. and
> added the following lines to my .profile and the scripts now
> import Bio - it looks like? it worked and fixed the
> issue.? Thanks for getting back with me! 
> -jeff
> 
> PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/biopython-1.52-py2.5-macosx-10.3-fat.egg:${PYTHONPATH}"
> export PYTHONPATH
> 
> 
> On Dec 18, 2009, at 2:35 AM, Michiel de Hoon wrote:
> 
> > If you start python in the terminal, does it start
> /usr/bin/python or a different python?
> > 
> > --- On Thu, 12/17/09, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > 
> >> From: Peter Cock <p.j.a.cock at googlemail.com>
> >> Subject: Re: [Biopython] Bio won't import in *.py
> scripts
> >> To: "Jeff Tomkins" <jtomkins at icr.org>
> >> Cc: "Biopython at lists.open-bio.org"
> <Biopython at lists.open-bio.org>
> >> Date: Thursday, December 17, 2009, 5:59 PM
> >> Hi Jeff,
> >> 
> >> On Thu, Dec 17, 2009 at 7:43 PM, Jeff Tomkins
> <jtomkins at icr.org>
> >> wrote:
> >>> I installed biopython 1.52 as directed for OS
> X
> >> leopard.
> >>>? Everything imports using the python
> prompt in the
> >> terminal,
> >>> idle, ipython, wing ide, etc.
> >> 
> >> Good :)
> >> 
> >>> But when I run a standard python script
> >> (#!/usr/bin/python)
> >>> in the shell it cannot locate Bio.? What
> setup
> >> feature have I missed?
> >> 
> >> That does seem odd. You didn't call your script
> Bio.py did
> >> you?
> >> Could you show us the error message?
> >> 
> >> Peter
> >> 
> >> _______________________________________________
> >> Biopython mailing list? -? Biopython at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biopython
> >> 
> > 
> > 
> > 
> 
> 


      



From schafer at rostlab.org  Fri Dec 18 23:57:52 2009
From: schafer at rostlab.org (=?ISO-8859-1?Q?Christian_Sch=E4fer?=)
Date: Fri, 18 Dec 2009 18:57:52 -0500
Subject: [Biopython] Superpose structures
In-Reply-To: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
References: <20091218172529.jfg6oapzgoccsocs@correo.fenhi.uh.cu>
Message-ID: <4B2C1700.6080704@rostlab.org>

Hey,

an alternative would be to use the program ProFit 
(http://www.bioinf.org.uk/software/profit/index.html), which does a 
least-square fitting based on aligned residues of one reference and one 
or more mobile structures. It comes with an extensive yet easy 
comprehensible set of commands.
I'm currently using it myself within my Python code.

Chris

On 12/18/2009 05:25 PM, Yasser Almeida Hern?ndez wrote:
> Hi all!!
>
> I want to superpose some structures on a reference one.
> The fixed selection is the backbone atoms of two residues and i want to
> superpose the rest of structures based in this atoms (for the same
> residues in the others structures, of course)
>
> Reference selection:
> [[<Atom O>, <Atom C>, <Atom CA>, <Atom N>], [<Atom O>, <Atom C>, <Atom
> CA>, <Atom N>]]
>
> The moving selection is a similar nested list, with the list of the
> residues backbone atoms to move in the query structures....
>
> How can i superpose these structures based in the backbone atoms of two
> residues?
>
> Please help me...
> Thanks
>
>
>
>


From bjorn_johansson at bio.uminho.pt  Sat Dec 19 11:00:19 2009
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Sat, 19 Dec 2009 11:00:19 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
Message-ID: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>

Hi,

I am trying to get a restriction batch tha is limited to some enzymes with a
certain size.
I think that the lambdasplit might be used for this.

I have not found any examples of the use of the restrictionbatch.lambdasplit

rb = RestrictionBatch(first=[],suppliers=['F','R'])

rb2= rb.lambdasplit(lambda x: x.size==6)

this code does not work. Could someone give me an example on how to use
this?
I have tried to see docs on the lambda function in python, but I still could
not solve this.
grateful for any answer!
/bjorn


From biopython at maubp.freeserve.co.uk  Sat Dec 19 11:17:33 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 19 Dec 2009 11:17:33 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
Message-ID: <320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>

2009/12/19 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Hi,
>
> I am trying to get a restriction batch tha is limited to some enzymes with a
> certain size.
> I think that the lambdasplit might be used for this.
>
> I have not found any examples of the use of the restrictionbatch.lambdasplit
>
> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>
> rb2= rb.lambdasplit(lambda x: x.size==6)
>
> this code does not work. Could someone give me an example on how to use
> this?
> I have tried to see docs on the lambda function in python, but I still could
> not solve this.
> grateful for any answer!
> /bjorn

Hmm, no mention of lambdasplit in this doc:
http://biopython.org/DIST/docs/cookbook/Restriction.html

Also no mention in Tests/test_Restriction.py

Looking at the code, you need a function (which could
be defined with a python lambda but need not be)
which will be given as single argument and must
return a boolean (or rather, something which will be
evaluated as a boolean). You code looks fine:

>>> from Bio.Restriction import *
>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>> len(rb)
228
>>> len([x for x in rb if x.size==6])
128
>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>> len(rb2)
0

Either we have both misunderstood the point of
this function, or there is a bug in lambdasplit.

Please file a bug report:
http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython

Thanks,

Peter



From sohm at inaf.cnrs-gif.fr  Sat Dec 19 17:53:35 2009
From: sohm at inaf.cnrs-gif.fr (=?ISO-8859-1?Q?Fr=E9d=E9ric_Sohm?=)
Date: Sat, 19 Dec 2009 18:53:35 +0100
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
Message-ID: <4B2D131F.1080302@inaf.cnrs-gif.fr>

Hi Bj?rn, Peter,

The code is working for me.
I can't reproduce the bug.


 >>> from Bio.Restriction import *
 >>> rb = RestrictionBatch(first=[], suppliers=['F','R'])
 >>> len(rb)
228
 >>> len([x for x in rb if x.size == 6])
128
 >>> rb2 = rb.lambdasplit(lambda x : x.size == 6)
 >>> len(rb2)
128
 >>> len([x for x in rb if len(x) == 6])
128
 >>> rb3 = rb.lambdasplit(lambda x : len(x) == 6)
 >>> len(rb3)
128
 >>> rb2 == rb3
True
 >>> EcoRI in rb
True
 >>> EcoRI in rb2 and EcoRI in rb3
True
 >>> EcoRI.size == len(EcoRI) == 6
True
 >>>


I am a bit puzzled there, Peter's code should work (and is effectively 
working on my machine) ...

My setup is :

Debian Lenny
python 2.5.2 or python 2.4.6 (both tested)
Biopython : 1.45

What about yours ?


Best regards

Fred



Peter wrote:
> 2009/12/19 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
>> Hi,
>>
>> I am trying to get a restriction batch tha is limited to some enzymes with a
>> certain size.
>> I think that the lambdasplit might be used for this.
>>
>> I have not found any examples of the use of the restrictionbatch.lambdasplit
>>
>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>
>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>
>> this code does not work. Could someone give me an example on how to use
>> this?
>> I have tried to see docs on the lambda function in python, but I still could
>> not solve this.
>> grateful for any answer!
>> /bjorn
> 
> Hmm, no mention of lambdasplit in this doc:
> http://biopython.org/DIST/docs/cookbook/Restriction.html
> 
> Also no mention in Tests/test_Restriction.py
> 
> Looking at the code, you need a function (which could
> be defined with a python lambda but need not be)
> which will be given as single argument and must
> return a boolean (or rather, something which will be
> evaluated as a boolean). You code looks fine:
> 
>>>> from Bio.Restriction import *
>>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>>> len(rb)
> 228
>>>> len([x for x in rb if x.size==6])
> 128
>>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>>> len(rb2)
> 0
> 
> Either we have both misunderstood the point of
> this function, or there is a bug in lambdasplit.
> 
> Please file a bug report:
> http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython
> 
> Thanks,
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 

-- 
Fr?d?ric Sohm
GIS AMAGEN CNRS INRA
Equipe INRA U1126 "Morphogen?se du syst?me nerveux des Chord?s"
UPR 2197 DEPSN, CNRS
Institut de Neurobiologie A. Fessard
1 Avenue de la Terrasse
91 198 GIF-SUR -YVETTE
FRANCE
Phone: 33 1 69 82 34 12
Fax: 33 1 69 82 41 67
email: sohm at inaf.cnrs-gif.fr


From bjorn_johansson at bio.uminho.pt  Sun Dec 20 06:58:43 2009
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Sun, 20 Dec 2009 06:58:43 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <4B2D131F.1080302@inaf.cnrs-gif.fr>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
	<4B2D131F.1080302@inaf.cnrs-gif.fr>
Message-ID: <c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>

Hi,
I copied the output from running Frederics example on my machine below:

bjorn at bjorn-laptop:~/wikidpad/user_extensions/SeqTools$ python
Python 2.6.4 (r264:75706, Dec  7 2009, 18:45:15)
[GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.Restriction import *
>>> rb = RestrictionBatch(first=[], suppliers=['F','R'])
>>> len(rb)
228
>>> len([x for x in rb if x.size == 6])
128
>>> rb2 = rb.lambdasplit(lambda x : x.size == 6)
>>> len(rb2)
0
>>> len([x for x in rb if len(x) == 6])
128
>>> len([x for x in rb if len(x) == 6])
128
>>> rb3 = rb.lambdasplit(lambda x : len(x) == 6)
>>> len(rb3)
0
>>> rb2 == rb3
True
>>> EcoRI in rb
True
>>> EcoRI in rb2 and EcoRI in rb3
False
>>> EcoRI.size == len(EcoRI) == 6
True
>>>

The lambdasplit does not seem to be working for me. I use python 2.6.4 on
ubuntu karmic
How can I print the biooython version?
thansk for your help!
/bjorn


2009/12/19 Fr?d?ric Sohm <sohm at inaf.cnrs-gif.fr>

> Hi Bj?rn, Peter,
>
> The code is working for me.
> I can't reproduce the bug.
>
>
>
> >>> from Bio.Restriction import *
> >>> rb = RestrictionBatch(first=[], suppliers=['F','R'])
> >>> len(rb)
> 228
> >>> len([x for x in rb if x.size == 6])
> 128
> >>> rb2 = rb.lambdasplit(lambda x : x.size == 6)
> >>> len(rb2)
> 128
> >>> len([x for x in rb if len(x) == 6])
> 128
> >>> rb3 = rb.lambdasplit(lambda x : len(x) == 6)
> >>> len(rb3)
> 128
> >>> rb2 == rb3
> True
> >>> EcoRI in rb
> True
> >>> EcoRI in rb2 and EcoRI in rb3
> True
> >>> EcoRI.size == len(EcoRI) == 6
> True
> >>>
>
>
> I am a bit puzzled there, Peter's code should work (and is effectively
> working on my machine) ...
>
> My setup is :
>
> Debian Lenny
> python 2.5.2 or python 2.4.6 (both tested)
> Biopython : 1.45
>
> What about yours ?
>
>
> Best regards
>
> Fred
>
>
>
> Peter wrote:
>
>> 2009/12/19 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
>>
>>> Hi,
>>>
>>> I am trying to get a restriction batch tha is limited to some enzymes
>>> with a
>>> certain size.
>>> I think that the lambdasplit might be used for this.
>>>
>>> I have not found any examples of the use of the
>>> restrictionbatch.lambdasplit
>>>
>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>>
>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>>
>>> this code does not work. Could someone give me an example on how to use
>>> this?
>>> I have tried to see docs on the lambda function in python, but I still
>>> could
>>> not solve this.
>>> grateful for any answer!
>>> /bjorn
>>>
>>
>> Hmm, no mention of lambdasplit in this doc:
>> http://biopython.org/DIST/docs/cookbook/Restriction.html
>>
>> Also no mention in Tests/test_Restriction.py
>>
>> Looking at the code, you need a function (which could
>> be defined with a python lambda but need not be)
>> which will be given as single argument and must
>> return a boolean (or rather, something which will be
>> evaluated as a boolean). You code looks fine:
>>
>>  from Bio.Restriction import *
>>>>> rb = RestrictionBatch(first=[],suppliers=['F','R'])
>>>>> len(rb)
>>>>>
>>>> 228
>>
>>> len([x for x in rb if x.size==6])
>>>>>
>>>> 128
>>
>>> rb2= rb.lambdasplit(lambda x: x.size==6)
>>>>> len(rb2)
>>>>>
>>>> 0
>>
>> Either we have both misunderstood the point of
>> this function, or there is a bug in lambdasplit.
>>
>> Please file a bug report:
>> http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython
>>
>> Thanks,
>>
>> Peter
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>>
> --
> Fr?d?ric Sohm
> GIS AMAGEN CNRS INRA
> Equipe INRA U1126 "Morphogen?se du syst?me nerveux des Chord?s"
> UPR 2197 DEPSN, CNRS
> Institut de Neurobiologie A. Fessard
> 1 Avenue de la Terrasse
> 91 198 GIF-SUR -YVETTE
> FRANCE
> Phone: 33 1 69 82 34 12
> Fax: 33 1 69 82 41 67
> email: sohm at inaf.cnrs-gif.fr
>



-- 
______O_________oO________oO______o_______oO__
Bj?rn Johansson
Assistant Professor
Departament of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL
http://www.bio.uminho.pt
http://sites.google.com/site/bjornhome
Work (direct) +351-253 601517
Private mob. +351-967 147 704
Dept of Biology (secretariate) +351-253 60 4310
Dept of Biology (fax) +351-253 678980



From biopython at maubp.freeserve.co.uk  Sun Dec 20 18:01:56 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 20 Dec 2009 18:01:56 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
	<4B2D131F.1080302@inaf.cnrs-gif.fr>
	<c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>
Message-ID: <320fb6e00912201001j24acc005uf7ad6d88f25bbf3d@mail.gmail.com>

2009/12/20 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Hi,
> I copied the output from running Frederics example on my machine below:
>
> bjorn at bjorn-laptop:~/wikidpad/user_extensions/SeqTools$ python
> Python 2.6.4 (r264:75706, Dec ?7 2009, 18:45:15)
> [GCC 4.4.1] on linux2
> ...
> The lambdasplit does not seem to be working for me. I use python
> 2.6.4 on ubuntu karmic

I was using the same version of Python (also on Linux Ubuntu Karmic).
This looks like it could be a Python 2.6 specific problem.

> How can I print the biooython version?
> thansk for your help!
> /bjorn

Its in the FAQ in the Tutorial, at the Python prompt just do:

import Bio
print Bio.__version__

Peter



From biopython at maubp.freeserve.co.uk  Mon Dec 21 12:03:34 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 21 Dec 2009 12:03:34 +0000
Subject: [Biopython] Fwd:  Why so few recipes in the cookbook?
In-Reply-To: <320fb6e00912181442r60348fcwf15776a0451bc6a1@mail.gmail.com>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
	<320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>
	<4B2B8CC3.3090307@dim.fm.usp.br>
	<sfid-+20091218-130021-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912180700w49d3be87r53b1a5201c84461b@mail.gmail.com>
	<4B2BAE35.2070404@dim.fm.usp.br>
	<320fb6e00912181442r60348fcwf15776a0451bc6a1@mail.gmail.com>
Message-ID: <320fb6e00912210403q5dd4c0d7xf06c9a850ecde9db@mail.gmail.com>

I just checked with Daniel to make sure he was happy for me to
forward this back to the mailing list.

Peter
---------- Forwarded message ----------
From: Peter <biopython at maubp.freeserve.co.uk>
Date: Fri, Dec 18, 2009 at 10:42 PM
Subject: Re: [Biopython] Why so few recipes in the cookbook?
To: Daniel Silvestre <daniel at dim.fm.usp.br>


Hi Daniel,

Do you mind if I send this to the list too?

2009/12/18 Daniel Silvestre <daniel at dim.fm.usp.br>:
>>
>> I confess I don't know or use the full power of the Entrez website,
>> although that is in part since I can do clever stuff via their API ;)
>
> This is exactly what we want to do when get to the Entrez interface.
> But, the information "How to submit complex query" is hidden (and
> scattered) under many layers of web pages.
>
> The ability to do such things in a more customized way is the dream of
> all life science guy.

This is partly down to the NCBI's Entrez documentation - a lots of
the examples in the Biopython tutorial took some serious exploration
to get working, including trawling the net for other Entrez users (in
other languages). I hope that we've managed to make things clearer.

> While this tutorial is enough to CS-oriented guys, it's a really big
> step to grasp such information for people from other communities.
> That's why I'm always a little confused about the idea behind bio
> projects. If the idea is programming of scientists, the approach is
> way too CS.

You are probably right in that the Bio* projects do cater more to a
programming scientist than a wet biologist - not that there aren't
people that can and do both. You have to be able to program to
take full advantage of any of the Bio* kits. However, there are a
number of front ends, webpages, etc which use them internally.

>> Now here I'd like a little clarification about what you want to do.
>>
>> My guess would be something I have considered working up
>> into a cookbook recipe, based one stuff I have already done:
>> Taking a small genome (viral or prokaryote), doing simple
>> gene predictions (e.g. ORF finding, pick first start codon,
>> or maybe calling a command line tool to do it for us), then
>> taking the predicted peptides and BLASTing them, then
>> making a GenBank file with these predicted features and
>> stick a summary of the BLAST results in their annotation.
>>
>> However, while this is a reasonable first step, there are
>> downsides to encouraging this sort of naive approach to
>> annotation - the example would ideally have "Further
>> Reading" section, see for example Schnoes et al 2009.
>> http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000605
>>
>
> That's exactly my point. Without a complete recipe with a
> specific motivation and a clear stated problem behinf it,
> people will continue with this kind of behavior.

We agree here.

> And I don't see why one need to start simple. The first time I've
> entered in a molbio lab was to carry on a old fashioned gene cloning
> procedure. This is a simple procedure. How do this compares to the
> simple examples we see on bio project tutorials?

I see the tutorial as a teaching aid, and many of the cookbook
examples also. For someone learning to program, an overly
complicated example is intimidating. This is not to say we can't
have some complex cookbook entries too.

i.e. I thank for learning to program, you need to start simple,
and build up the complexity gradually.

>>> These are real problems faced by the common biologist. The proposed
>>> snippets in the tutorial and the cookbook is already dealt by a lot of
>>> web tools. It's absolutely necessary to show that biopython can increase
>>> the power and range of a biologist everyday work, and can possibly be
>>> automated.
>>>
>>> I have some examples to obtain statistics over genome sequences which
>>> address complete examples (including globbing filelists, retrieving from
>>> online databases, etc.) and can prepare them as a recipe. But, I could
>>> use some help . . .
>>
>> If you start a cookbook entry on the wiki, and some outline
>> code, I'm sure we can as a group contribute ideas and tips
>> (particularly in the code, but maybe in the approach too). Or,
>> if you would rather, discuss some specific ideas here on the
>> mailing list first.
>>
>> Note that some of these topics would be ideal for an OBF
>> project wide set of examples, with reference solutions in
>> Biopython, BioPerl, BioJava, BioRuby, etc. That is however
>> a much much bigger task.
>
> I think that there is no need to worry about big things right now. By
> the very nature of programming, people will mirror ideas from one
> another. I've tried a similar approach in the bioperl community. But,
> for the pragmatic life scientist, perl is over expressive while python
> has a much higher first encounter acceptance rate (I'm not sure why,
> tough...).
>
> My idea is not a master blaster cookbook, just to assemble simple ideas
> that work for the everyday user, be this guy a CS or a life scientist.
>
> How do this sound to you?

Wonderful :)

(And I would agree with you that Python is probably easier to teach
to beginners than Perl)

Peter


From chapmanb at 50mail.com  Mon Dec 21 13:11:48 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 21 Dec 2009 08:11:48 -0500
Subject: [Biopython] Why so few recipes in the cookbook?
In-Reply-To: <320fb6e00912210403q5dd4c0d7xf06c9a850ecde9db@mail.gmail.com>
References: <4B2A8B48.50302@dim.fm.usp.br>
	<320fb6e00912171316y5e514052sabaf2a0104a558ac@mail.gmail.com>
	<4B2B6DE2.3080500@dim.fm.usp.br>
	<320fb6e00912180457x31b3c48bl680d48d6b95fdab0@mail.gmail.com>
	<4B2B8CC3.3090307@dim.fm.usp.br>
	<sfid-+20091218-130021-+000.00-1@spamfilter.osbf.lua>
	<320fb6e00912180700w49d3be87r53b1a5201c84461b@mail.gmail.com>
	<4B2BAE35.2070404@dim.fm.usp.br>
	<320fb6e00912181442r60348fcwf15776a0451bc6a1@mail.gmail.com>
	<320fb6e00912210403q5dd4c0d7xf06c9a850ecde9db@mail.gmail.com>
Message-ID: <20091221131148.GB21580@sobchak.mgh.harvard.edu>

Peter and Daniel;
Really interesting discussion. Documentation is an area that can
always use more work to appeal to a wider audience.

Daniel:
> > While this tutorial is enough to CS-oriented guys, it's a really big
> > step to grasp such information for people from other communities.
> > That's why I'm always a little confused about the idea behind bio
> > projects. If the idea is programming of scientists, the approach is
> > way too CS.

This stresses why we actively encourage contributions from biologists
as well. Many of the contributors to Biopython tend more towards the
programming/bioinformatics side, since that experience helps in building
up and appreciating a re-usable toolkit. When those same people write
documentation, it is going to be naturally biased towards the sort of
work they do.

I'd definitely encourage you, and anyone else who might be
interested, to build up examples that are more intuitive to those
coming at the work from a different starting point. This is exactly
the idea behind starting up the cookbook on the wiki; it's all
freely editable, so dig right in.

Brad


From biopython at maubp.freeserve.co.uk  Tue Dec 22 16:22:24 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 22 Dec 2009 16:22:24 +0000
Subject: [Biopython] EMBOSS and Python
In-Reply-To: <5ECA525B88314B48870E4AC72E3B9AF2045A70FE@EDUNIVMAIL05.ad.umassmed.edu>
References: <5ECA525B88314B48870E4AC72E3B9AF2045A70EC@EDUNIVMAIL05.ad.umassmed.edu>
	<320fb6e00912170904x52b8a894s9a0f76ed1c26512c@mail.gmail.com>
	<5ECA525B88314B48870E4AC72E3B9AF2045A70FE@EDUNIVMAIL05.ad.umassmed.edu>
Message-ID: <320fb6e00912220822m7e1c81c5h113a642f1336b328@mail.gmail.com>

Hi David,

I cc'd the mailing list again.

On Tue, Dec 22, 2009 at 4:02 PM, Lapointe, David
<David.Lapointe at umassmed.edu> wrote:
>
> Hi Peter,
>
> I have current version for both EMBOSS (6.1.0) and BioPython (1.53).

Do you have the original unpatched EMBOSS 6.1.0, or the latest
patched version, currently EMBOSS 6.1.0 patch 3? See:
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch

> I looked at the
> code for the unit tests (asis) and the problem might be there, as I could run the
> test fine by hand.

Could you clarify what you meant by "I could run the test fine by hand"?

> Shouldn't there be a '-' in front of asequence?
>
> ? ?def test_water_file(self):
> ? ? ? ?"""water with the asis trick, output to a file."""
> ? ? ? ?#Setup, try a mixture of keyword arguments and later additions:
> ? ? ? ?cline = WaterCommandline(cmd=exes["water"],
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? gapopen="10", gapextend="0.5")
> ? ? ? ?#Try using both human readable names, and the literal ones:
> ? ? ? ?cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
> ? ? ? ?cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
>
> David

Good question, but no. The test is confirming the set_parameter method
supports both these ways of setting the parameters. This is now a semi-
obsolete method - the preferred way would be to use bsequence in the
constructor arguments, or the bsequence property.

Interestingly the test output also indicates issues calling dnal (which
is nothing to do with EMBOSS), yet at least one other command line
tool test seem to be running OK (Clustalw).

Peter



From silvio.tschapke at googlemail.com  Wed Dec 23 10:57:58 2009
From: silvio.tschapke at googlemail.com (Silvio Tschapke)
Date: Wed, 23 Dec 2009 11:57:58 +0100
Subject: [Biopython] cannot find elink_090910.dtd
Message-ID: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>

Hi all,

I am using ubuntu 9.10, python 2.6 and biopython 1.53
But while running these two lines of code

pmid = "14630660"
results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid)

I get the following error message posted at the bottom.
So I searched at the proposed websites and in the web for
"elink_090910.dtd" without success.
I only found the files for elink_020511.dtd and something for 2010. But
nothing related to elink_090910.dtd.
Could you please help me how I can solve this problem?

Cheers and merry christmas,
Silvio


Traceback (most recent call last):
  File "/home/silvio/programming/python/first steps/biopythonTutorial.py",
line 17, in <module>
    results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid))
  File
"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/__init__.py",
line 258, in read
    record = handler.read(handle)
  File
"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
line 108, in read
    self.parser.ParseFile(handle)
  File
"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
line 377, in externalEntityRefHandler
    raise RuntimeError(message)
RuntimeError: Unable to load DTD file eLink_090910.dtd.


From biopython at maubp.freeserve.co.uk  Wed Dec 23 12:10:17 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 12:10:17 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
Message-ID: <320fb6e00912230410hf895e3sa999b0489e0b9e5e@mail.gmail.com>

On Wed, Dec 23, 2009 at 10:57 AM, Silvio Tschapke
<silvio.tschapke at googlemail.com> wrote:
> Hi all,
>
> I am using ubuntu 9.10, python 2.6 and biopython 1.53
> But while running these two lines of code
>
> pmid = "14630660"
> results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid)
>
> I get the following error message posted at the bottom.
> So I searched at the proposed websites and in the web for
> "elink_090910.dtd" without success.
> I only found the files for elink_020511.dtd and something for 2010. But
> nothing related to elink_090910.dtd.
> Could you please help me how I can solve this problem?
>
> Cheers and merry christmas,
> Silvio

Hi Silvio,

Yep, I don't have that file either, it looks like we missed it :(
The NCBI website don't make it easy to find (as far as I could
tell, none of the DTD pages list this file). However, the XML
tells us where to try:
http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/eLink_090910.dtd

I've added this to our repository, and it will be in the next release.

You'll need to download that DTD file. How did you install Biopython?
It looks like the file would need to go inside the egg - so it might
be easier to (re)install from source with this extra file in the source
code subdirectory Bio/Entrez/DTDs. Or start by grabbing the latest
Biopython code from git. Does that make sense?

However, even with the DTD file, I'm getting "Error 111
(Connection refused)" for your example. Maybe the NCBI are
doing some maintenance work at the moment?

Merry Christmas,

Peter


From konrad.koehler at mac.com  Wed Dec 23 11:22:32 2009
From: konrad.koehler at mac.com (Konrad Koehler)
Date: Wed, 23 Dec 2009 12:22:32 +0100
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
Message-ID: <11374559688483741089292458484266867741-Webmail@me.com>

Hi  Silvio,

This appears to be a temporary glitch with the Entrez database and not biopython.  For example, the following link should display the abstract, but current does not:

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=14630660&dopt=Abstract

A lot of other things in Entrez appear to be broken. For example internal links to RefSeq records from EntrezGene do not currently work.  For example, the RefSeq link from here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2645

to here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2645

doesn't work either.

Hopefully the problems in the Entrez database will be sorted out shortly.  Cheers,

Konrad

On Wednesday, December 23, 2009, at 11:57AM, "Silvio Tschapke" <silvio.tschapke at googlemail.com> wrote:
>Hi all,
>
>I am using ubuntu 9.10, python 2.6 and biopython 1.53
>But while running these two lines of code
>
>pmid = "14630660"
>results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid)
>
>I get the following error message posted at the bottom.
>So I searched at the proposed websites and in the web for
>"elink_090910.dtd" without success.
>I only found the files for elink_020511.dtd and something for 2010. But
>nothing related to elink_090910.dtd.
>Could you please help me how I can solve this problem?
>
>Cheers and merry christmas,
>Silvio
>
>
>Traceback (most recent call last):
>  File "/home/silvio/programming/python/first steps/biopythonTutorial.py",
>line 17, in <module>
>    results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid))
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/__init__.py",
>line 258, in read
>    record = handler.read(handle)
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
>line 108, in read
>    self.parser.ParseFile(handle)
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
>line 377, in externalEntityRefHandler
>    raise RuntimeError(message)
>RuntimeError: Unable to load DTD file eLink_090910.dtd.
>_______________________________________________
>Biopython mailing list  -  Biopython at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biopython
>
>


From biopython at maubp.freeserve.co.uk  Wed Dec 23 12:28:37 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 12:28:37 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <11374559688483741089292458484266867741-Webmail@me.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
Message-ID: <320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>

On Wed, Dec 23, 2009 at 11:22 AM, Konrad Koehler wrote:
> Hi ?Silvio,
>
> This appears to be a temporary glitch with the Entrez database and not biopython.
>

Your URLs seem to be working now :)

On Wed, Dec 23, 2009 at 12:10 PM, Peter wrote:
>
> However, even with the DTD file, I'm getting "Error 111
> (Connection refused)" for your example. Maybe the NCBI are
> doing some maintenance work at the moment?

This is also working now. Its looks like both a temporary glitch at the
NCBI, and the problem with Biopython missing eLink_090910.dtd

Peter



From biopython at maubp.freeserve.co.uk  Wed Dec 23 14:03:04 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 14:03:04 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
	<320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>
	<d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
Message-ID: <320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>

On Wed, Dec 23, 2009 at 1:29 PM, Silvio Tschapke
<silvio.tschapke at googlemail.com> wrote:
>
> I have copied the DTD file in
> /usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/DTDs/
> now and it seems to work. Great! I have installed Biopython with
>
> python setup.py build
> python setup.py test
> sudo python setup.py install

OK - good :)

> But will I have the same problems when I use eSearch, or eQuery and so
> on? Because all of the DTD will not be up to date. So far I only
> copied this DTD for eLink you posted.

I *hope* that this was the only DTD file we were missing. If
not, please do let us know so we can fix this for other users.

In the short term, you would again need to download and fetch
other missing DTD files in the same way. You can generally look
at the start of the XML file to see where the DTD can be found, e.g.

>>> from Bio import Entrez
>>> Entrez.email = "your.name.here at example.com"
>>> print Entrez.elink(dbfrom="pubmed", id="12345678").read(300)
<?xml version="1.0"?>
<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 10 August
2009//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_090910.dtd">
<eLinkResult>
...

Thanks,

Peter


From bjorn_johansson at bio.uminho.pt  Wed Dec 23 14:42:37 2009
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Wed, 23 Dec 2009 14:42:37 +0000
Subject: [Biopython] question about RestrictionBatch.lambdasplit
In-Reply-To: <320fb6e00912201001j24acc005uf7ad6d88f25bbf3d@mail.gmail.com>
References: <c3ee7c590912190300s750d99d1g91f7261b7f893cd4@mail.gmail.com>
	<320fb6e00912190317t60c9fe7ai5c7e388849c72b4c@mail.gmail.com>
	<4B2D131F.1080302@inaf.cnrs-gif.fr>
	<c3ee7c590912192258m275bdf22s6b7813c5adbea88b@mail.gmail.com>
	<320fb6e00912201001j24acc005uf7ad6d88f25bbf3d@mail.gmail.com>
Message-ID: <c3ee7c590912230642v6efddad2laf766de37071ee0a@mail.gmail.com>

Hi, my Biopython version seems to be 1.52
bjorn at bjorn-laptop:~$ python
Python 2.6.4 (r264:75706, Dec  7 2009, 18:45:15)
[GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> Bio.__version__
'1.52'

This works really well to get only five cutters and above (rb is a
restriction batch):

rb = [x for x in rb if len(x) > 4]

which was what I wanted initially.
Thanks for all help!
Happy hollidays!
/bjorn


2009/12/20 Peter <biopython at maubp.freeserve.co.uk>

> 2009/12/20 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> > Hi,
> > I copied the output from running Frederics example on my machine below:
> >
> > bjorn at bjorn-laptop:~/wikidpad/user_extensions/SeqTools$ python
> > Python 2.6.4 (r264:75706, Dec  7 2009, 18:45:15)
> > [GCC 4.4.1] on linux2
> > ...
> > The lambdasplit does not seem to be working for me. I use python
> > 2.6.4 on ubuntu karmic
>
> I was using the same version of Python (also on Linux Ubuntu Karmic).
> This looks like it could be a Python 2.6 specific problem.
>
> > How can I print the biooython version?
> > thansk for your help!
> > /bjorn
>
> Its in the FAQ in the Tutorial, at the Python prompt just do:
>
> import Bio
> print Bio.__version__
>
> Peter
>



-- 
______O_________oO________oO______o_______oO__
Bj?rn Johansson
Assistant Professor
Departament of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL
http://www.bio.uminho.pt
http://sites.google.com/site/bjornhome
Work (direct) +351-253 601517
Private mob. +351-967 147 704
Dept of Biology (secretariate) +351-253 60 4310
Dept of Biology (fax) +351-253 678980



From cjfields at illinois.edu  Wed Dec 23 15:08:31 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 23 Dec 2009 09:08:31 -0600
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
	<320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>
	<d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
	<320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>
Message-ID: <9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>

On Dec 23, 2009, at 8:03 AM, Peter wrote:

> On Wed, Dec 23, 2009 at 1:29 PM, Silvio Tschapke
> <silvio.tschapke at googlemail.com> wrote:
>> 
>> I have copied the DTD file in
>> /usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/DTDs/
>> now and it seems to work. Great! I have installed Biopython with
>> 
>> python setup.py build
>> python setup.py test
>> sudo python setup.py install
> 
> OK - good :)
> 
>> But will I have the same problems when I use eSearch, or eQuery and so
>> on? Because all of the DTD will not be up to date. So far I only
>> copied this DTD for eLink you posted.
> 
> I *hope* that this was the only DTD file we were missing. If
> not, please do let us know so we can fix this for other users.
> 
> In the short term, you would again need to download and fetch
> other missing DTD files in the same way. You can generally look
> at the start of the XML file to see where the DTD can be found, e.g.
> 
>>>> from Bio import Entrez
>>>> Entrez.email = "your.name.here at example.com"
>>>> print Entrez.elink(dbfrom="pubmed", id="12345678").read(300)
> <?xml version="1.0"?>
> <!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 10 August
> 2009//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_090910.dtd">
> <eLinkResult>
> ...
> 
> Thanks,
> 
> Peter

Just a quick question: is there any particular reason you need the DTDs?  The BioPerl eutils interface doesn't use them at all, primarily b/c they aren't required on our end.

chris





From biopython at maubp.freeserve.co.uk  Wed Dec 23 15:14:06 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Dec 2009 15:14:06 +0000
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>
References: <d3ddc94e0912230257j31cabb1ena93ee4c8534593c6@mail.gmail.com>
	<11374559688483741089292458484266867741-Webmail@me.com>
	<320fb6e00912230428y3788591at9848206afa2bb8e0@mail.gmail.com>
	<d3ddc94e0912230529w1fb76ac6p77c9defdf291bdb0@mail.gmail.com>
	<320fb6e00912230603o23b93c21v36890dc53617b597@mail.gmail.com>
	<9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>
Message-ID: <320fb6e00912230714y5893143dhd262a6732536c87@mail.gmail.com>

On Wed, Dec 23, 2009 at 3:08 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
> Just a quick question: is there any particular reason you need the DTDs?
> The BioPerl eutils interface doesn't use them at all, primarily b/c they
> aren't required on our end.

Our parser uses the DTDs (local copies) to know the expected data
structure, which gets turned into Python lists, dicts, strings etc using
that information. I don't know too much about the implementation details,
but this doesn't work on Jython (Python under Java) since they haven't
implemented the DTD parsing support we expect.

Peter


From mjldehoon at yahoo.com  Thu Dec 24 15:11:48 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 24 Dec 2009 07:11:48 -0800 (PST)
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <9E777B2B-51F8-407F-B035-B8E34B1BB73F@illinois.edu>
Message-ID: <439227.21985.qm@web62403.mail.re1.yahoo.com>

--- On Wed, 12/23/09, Chris Fields <cjfields at illinois.edu> wrote:
> Just a quick question: is there any particular reason you
> need the DTDs?? The BioPerl eutils interface doesn't
> use them at all, primarily b/c they aren't required on our
> end.
> 
The DTDs are needed to figure out the data structure of the XML file. In other words, what is a list, what is a dictionary, what is plain data, etcetera. How does the BioPerl eutils interface know how to store the information in the XML file?

--Michiel.


      



From cjfields at illinois.edu  Thu Dec 24 18:54:14 2009
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 24 Dec 2009 12:54:14 -0600
Subject: [Biopython] cannot find elink_090910.dtd
In-Reply-To: <439227.21985.qm@web62403.mail.re1.yahoo.com>
References: <439227.21985.qm@web62403.mail.re1.yahoo.com>
Message-ID: <5569562A-372E-414C-889A-9E75B344BA21@illinois.edu>


On Dec 24, 2009, at 9:11 AM, Michiel de Hoon wrote:

> --- On Wed, 12/23/09, Chris Fields <cjfields at illinois.edu> wrote:
>> Just a quick question: is there any particular reason you
>> need the DTDs?  The BioPerl eutils interface doesn't
>> use them at all, primarily b/c they aren't required on our
>> end.
>> 
> The DTDs are needed to figure out the data structure of the XML file. In other words, what is a list, what is a dictionary, what is plain data, etcetera. How does the BioPerl eutils interface know how to store the information in the XML file?
> 
> --Michiel.

We have classes designed to hold the information generically; docsums has docsum items, elink has linkouts, einfo has field/link information, so on.  Has worked fairly well with eutils changes over the last four yeqrs w/o directly relying on the DTDs in a release.

chris




From pedro.al at fenhi.uh.cu  Thu Dec 24 21:05:41 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Thu, 24 Dec 2009 16:05:41 -0500
Subject: [Biopython] Superpose structures...
Message-ID: <20091224160541.4d9f8d4so4g4gcss@correo.fenhi.uh.cu>

Hi all...
I've superpose two structures.. Now i want to compute the RMSD between  
2 residues after the superposition (with the transformed coordinates  
of the moving structure)
How can i do that...?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI






From pedro.al at fenhi.uh.cu  Thu Dec 24 21:37:12 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Thu, 24 Dec 2009 16:37:12 -0500
Subject: [Biopython] Superpose structures...
Message-ID: <20091224163712.mg5fgthu04gcgcgk@correo.fenhi.uh.cu>

I know i made that question already but this time is a quite  
different. I already superpose the structures (Profit isn't so  
suitable for my project), but now i want to compute the RMSD betweeen  
2 residues in the superposed position. When i do that, the RMSD that i  
get is the same that if i superpose the structures according to that  
residue, and what i really want is the "deviation of 2 residues when  
its structures are superposed according to its binding sites  
residues", and i want to know how to do that in Biopython...

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI






From schafer at rostlab.org  Thu Dec 24 22:11:10 2009
From: schafer at rostlab.org (=?ISO-8859-1?Q?Christian_Sch=E4fer?=)
Date: Thu, 24 Dec 2009 17:11:10 -0500
Subject: [Biopython] Superpose structures...
In-Reply-To: <20091224163712.mg5fgthu04gcgcgk@correo.fenhi.uh.cu>
References: <20091224163712.mg5fgthu04gcgcgk@correo.fenhi.uh.cu>
Message-ID: <4B33E6FE.3090709@rostlab.org>

So, what you want to do is to superpose two structures by minimizing the 
RMSD between aligned residues and after that calculating the RMSD 
between two residues? Is that right? If so, ProFit is able to do that. 
Superimpostion is done by the ZONE command (which then returns the 
overall RMSD over the aligned regions after superimpostion); and 
calculating the RMSD between specific residues (after superimposition) 
is done via the RZONE command. You can even chose which kind of atoms to 
consider for RMSD calculation with the ATOMS and RATOMS commands.
I'm not sure if something that specific could be done with plain 
BioPython. But again, you can always write a wrapper for the ProFit part 
in Python.

Chris

On 12/24/2009 04:37 PM, Yasser Almeida Hern?ndez wrote:
> I know i made that question already but this time is a quite different.
> I already superpose the structures (Profit isn't so suitable for my
> project), but now i want to compute the RMSD betweeen 2 residues in the
> superposed position. When i do that, the RMSD that i get is the same
> that if i superpose the structures according to that residue, and what i
> really want is the "deviation of 2 residues when its structures are
> superposed according to its binding sites residues", and i want to know
> how to do that in Biopython...
>
> Thanks
>


From bioinformaticsing at gmail.com  Sat Dec 26 14:37:31 2009
From: bioinformaticsing at gmail.com (ning luwen)
Date: Sat, 26 Dec 2009 22:37:31 +0800
Subject: [Biopython] need help! how to retrieve full text from Pubmed
	central ?
Message-ID: <90247fbe0912260637n7553bdf7wbce10a627c0a124c@mail.gmail.com>

Dear everyone,
?? I need to download full text from Pubmed central. After see the
Entrez manual, maybe Entrez(not the web interface) doesn't give a way
to?download .pdf full text file, is this true?




--
regards,
ningluwen



From bioinformaticsing at gmail.com  Sat Dec 26 14:54:23 2009
From: bioinformaticsing at gmail.com (ning luwen)
Date: Sat, 26 Dec 2009 22:54:23 +0800
Subject: [Biopython] need help! how to retrieve full text from Pubmed
	central ?
In-Reply-To: <90247fbe0912260637n7553bdf7wbce10a627c0a124c@mail.gmail.com>
References: <90247fbe0912260637n7553bdf7wbce10a627c0a124c@mail.gmail.com>
Message-ID: <90247fbe0912260654scd2b0ceyb37d54f36a3531fa@mail.gmail.com>

more about the problem.

     From http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html,
I can learn:
      PubMed Central contains a number of articles classified as "open
access" for which you may download the full text as XML. For the
remaining articles in PMC you may download only the abstracts as XML.

but when try to
handle=Entrez.efetch(db='pmc',id=idlist,rettype='full',retmode='xml')
record=Entrez.read(handle)

got following errors:
    Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.6/dist-packages/Bio/Entrez/__init__.py",
line 258, in read
    record = handler.read(handle)
  File "/usr/local/lib/python2.6/dist-packages/Bio/Entrez/Parser.py",
line 114, in read
    raise CorruptedXMLError
Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data.
Please make sure that the input data are in XML format, and that the
data are not corrupted.

the python version is 1.53 and my system is ubuntu 9.10.

On Sat, Dec 26, 2009 at 10:37 PM, ning luwen
<bioinformaticsing at gmail.com> wrote:
> Dear everyone,
> ?? I need to download full text from Pubmed central. After see the
> Entrez manual, maybe Entrez(not the web interface) doesn't give a way
> to?download .pdf full text file, is this true?
>
>
>
>
> --
> regards,
> ningluwen
>



-- 
regards,
luwening,bioinformatics center in uestc:
www.bioinformaticsinuestc.cz.cc



From pedro.al at fenhi.uh.cu  Mon Dec 28 14:06:38 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Mon, 28 Dec 2009 09:06:38 -0500
Subject: [Biopython] Superpose structures... DONE
Message-ID: <20091228090638.y05tos1p8g0gk08c@correo.fenhi.uh.cu>

The problem with the calculus of the RMSD after the superposition is  
solved. This is done with the class SVDSuperimposer (Bio >  
SVDSuperimposer > SVDSuperimposer.py). This class has the method  
get_init_rms() that compute the structures RMSD after the  
superposition...
Now i have another question. It is possible in Biopython read gziped  
pdb files (.pdb.gz)?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI






From mjldehoon at yahoo.com  Mon Dec 28 17:27:23 2009
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Mon, 28 Dec 2009 09:27:23 -0800 (PST)
Subject: [Biopython] Superpose structures... DONE
In-Reply-To: <20091228090638.y05tos1p8g0gk08c@correo.fenhi.uh.cu>
Message-ID: <363342.11278.qm@web62406.mail.re1.yahoo.com>

--- On Mon, 12/28/09, Yasser Almeida Hern?ndez <pedro.al at fenhi.uh.cu> wrote:
> Now i have another question. It is possible in Biopython
> read gziped pdb files (.pdb.gz)?

I am not a Bio.PDB user, but from its documentation it looks like it uses the file name to open a PDB file instead of a handle. Thomas, how do you feel about modifying Bio.PDB so it uses a file handle instead of a file name? Then Bio.PDB can parse gzipped and bzipped files.

--Michiel.


      



From pedro.al at fenhi.uh.cu  Tue Dec 29 14:18:38 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Tue, 29 Dec 2009 09:18:38 -0500
Subject: [Biopython] Remove hydrogens...
Message-ID: <20091229091838.fnyk66sayos8swww@correo.fenhi.uh.cu>

Hi all...
How can i remove hydrogens atoms from the structures objects?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI






From pengyu.ut at gmail.com  Tue Dec 29 16:08:09 2009
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 29 Dec 2009 10:08:09 -0600
Subject: [Biopython] Comparison between bioperl and biopython?
Message-ID: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>

May I ask somebody who are versitile in both bioperl and biopython
comment on the pros and cons of bioperl and biopython? I'm sending
this email to both bioperl and biopython mailing lists. But I hope
that it will not result in any contention.

I assume that the functionality between bioperl or biopython is the
same, i.e., tasks can be done in bioperl can be done biopython and
vice versa, as both libraries have been out there over 10 years.
Please correct me if my understanding is not true.

Given that a task that can be done with either bioperl or biopython,
I, in particularly, want to know how long it will take to write the
code for the task in bioperl and biopython, with the same readability
requirement (see below) and the assumption that users have the same
fluency in perl and python.

python is claimed to be good for maintainability. But perl is
criticized for there-are-many-ways-for-a-given-task. Since there are
multiple ways in perl, let us assume that we always use perl in a
readable way.


From jason at bioperl.org  Tue Dec 29 16:49:20 2009
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 29 Dec 2009 08:49:20 -0800
Subject: [Biopython] [Bioperl-l] Comparison between bioperl and
	biopython?
In-Reply-To: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
Message-ID: <2B85EF86-8A84-491B-8C33-7EC16CCB8CBC@bioperl.org>

Are you asking for the purposes of choosing a toolkit for your work or  
just curious about the advantages/disadvantages of language choice?

-jason
On Dec 29, 2009, at 8:08 AM, Peng Yu wrote:

> May I ask somebody who are versitile in both bioperl and biopython
> comment on the pros and cons of bioperl and biopython? I'm sending
> this email to both bioperl and biopython mailing lists. But I hope
> that it will not result in any contention.
>
> I assume that the functionality between bioperl or biopython is the
> same, i.e., tasks can be done in bioperl can be done biopython and
> vice versa, as both libraries have been out there over 10 years.
> Please correct me if my understanding is not true.
>
> Given that a task that can be done with either bioperl or biopython,
> I, in particularly, want to know how long it will take to write the
> code for the task in bioperl and biopython, with the same readability
> requirement (see below) and the assumption that users have the same
> fluency in perl and python.
>
> python is claimed to be good for maintainability. But perl is
> criticized for there-are-many-ways-for-a-given-task. Since there are
> multiple ways in perl, let us assume that we always use perl in a
> readable way.
> _______________________________________________
> 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
http://fungalgenomes.org/



From sdavis2 at mail.nih.gov  Tue Dec 29 17:03:40 2009
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Tue, 29 Dec 2009 12:03:40 -0500
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
Message-ID: <264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>

On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> May I ask somebody who are versitile in both bioperl and biopython
> comment on the pros and cons of bioperl and biopython? I'm sending
> this email to both bioperl and biopython mailing lists. But I hope
> that it will not result in any contention.
>
> I assume that the functionality between bioperl or biopython is the
> same, i.e., tasks can be done in bioperl can be done biopython and
> vice versa, as both libraries have been out there over 10 years.
> Please correct me if my understanding is not true.

The two projects have similar goals, but saying that the functionality
is the same would be an extreme oversimplification.  You will need to
define what you want to do and then check to see what the two projects
have to offer.  This will, in general, require perusing the websites
for both projects as well as the relevant documentation.

> Given that a task that can be done with either bioperl or biopython,
> I, in particularly, want to know how long it will take to write the
> code for the task in bioperl and biopython, with the same readability
> requirement (see below) and the assumption that users have the same
> fluency in perl and python.

Again, you will want to define the task(s) to be accomplished and then
weigh the pros and cons of each project combined with local expertise.
 If you don't know what you want to do, then you can certainly read
some examples on the websites and see which project strikes you as a
"winner" for you.

> python is claimed to be good for maintainability. But perl is
> criticized for there-are-many-ways-for-a-given-task. Since there are
> multiple ways in perl, let us assume that we always use perl in a
> readable way.

These two statements are generalizations that provide little insight
into the strengths or weaknesses of the languages.  In other words,
one can write good or bad code in both languages.

Hope that helps.

Sean


From eric.talevich at gmail.com  Tue Dec 29 18:37:43 2009
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 29 Dec 2009 10:37:43 -0800
Subject: [Biopython] Superpose structures... DONE
Message-ID: <3f6baf360912291037o5313b9f0s2acdc481c9989ce1@mail.gmail.com>

On Mon, 28 Dec 2009, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

>
> I am not a Bio.PDB user, but from its documentation it looks like it uses
> the file name to open a PDB file instead of a handle. Thomas, how do you
> feel about modifying Bio.PDB so it uses a file handle instead of a file
> name? Then Bio.PDB can parse gzipped and bzipped files.
>
> --Michiel.
>
>
I guess PDB requires a file name because it wants full control over the file
handle -- the handle is passed between PDBParser and parse_pdb_header, for
instance. But control still isn't as crucial as in SeqIO.index (for
example), so I don't think using a handle directly would lead to catastrophe
in general.

In addition, do you think a StructIO module would be worthwhile?

Benefits:
- Accept either a file name or file handle
- Wouldn't necessarily need to specify the structure object's name as a
separate argument (as PDBParser requires)
- No need to instantiate a Parser object before parsing
- PDB, PDBXML and mmCIF parsing would be called the same way

Drawbacks:
- Integrating parse_pdb_headers would become more important/tricky
- Thin wrappers still require effort, and I'm currently tied up with TreeIO
-- I'd get to it some months from now

Cheers,
Eric


From pengyu.ut at gmail.com  Tue Dec 29 18:58:59 2009
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 29 Dec 2009 12:58:59 -0600
Subject: [Biopython] [Bioperl-l] Comparison between bioperl and
	biopython?
In-Reply-To: <2B85EF86-8A84-491B-8C33-7EC16CCB8CBC@bioperl.org>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<2B85EF86-8A84-491B-8C33-7EC16CCB8CBC@bioperl.org>
Message-ID: <366c6f340912291058t6c601e57re0c35e69fe81e09d@mail.gmail.com>

To choose a toolkit for my work.

On Tue, Dec 29, 2009 at 10:49 AM, Jason Stajich <jason at bioperl.org> wrote:
> Are you asking for the purposes of choosing a toolkit for your work or just
> curious about the advantages/disadvantages of language choice?
>
> -jason
> On Dec 29, 2009, at 8:08 AM, Peng Yu wrote:
>
>> May I ask somebody who are versitile in both bioperl and biopython
>> comment on the pros and cons of bioperl and biopython? I'm sending
>> this email to both bioperl and biopython mailing lists. But I hope
>> that it will not result in any contention.
>>
>> I assume that the functionality between bioperl or biopython is the
>> same, i.e., tasks can be done in bioperl can be done biopython and
>> vice versa, as both libraries have been out there over 10 years.
>> Please correct me if my understanding is not true.
>>
>> Given that a task that can be done with either bioperl or biopython,
>> I, in particularly, want to know how long it will take to write the
>> code for the task in bioperl and biopython, with the same readability
>> requirement (see below) and the assumption that users have the same
>> fluency in perl and python.
>>
>> python is claimed to be good for maintainability. But perl is
>> criticized for there-are-many-ways-for-a-given-task. Since there are
>> multiple ways in perl, let us assume that we always use perl in a
>> readable way.
>> _______________________________________________
>> 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
> http://fungalgenomes.org/
>
>


From pengyu.ut at gmail.com  Tue Dec 29 19:15:14 2009
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 29 Dec 2009 13:15:14 -0600
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
Message-ID: <366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>

On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
>> May I ask somebody who are versitile in both bioperl and biopython
>> comment on the pros and cons of bioperl and biopython? I'm sending
>> this email to both bioperl and biopython mailing lists. But I hope
>> that it will not result in any contention.
>>
>> I assume that the functionality between bioperl or biopython is the
>> same, i.e., tasks can be done in bioperl can be done biopython and
>> vice versa, as both libraries have been out there over 10 years.
>> Please correct me if my understanding is not true.
>
> The two projects have similar goals, but saying that the functionality
> is the same would be an extreme oversimplification. ?You will need to
> define what you want to do and then check to see what the two projects
> have to offer. ?This will, in general, require perusing the websites
> for both projects as well as the relevant documentation.

According to your experience, are there some tasks that are easier
with one than with another?

>> Given that a task that can be done with either bioperl or biopython,
>> I, in particularly, want to know how long it will take to write the
>> code for the task in bioperl and biopython, with the same readability
>> requirement (see below) and the assumption that users have the same
>> fluency in perl and python.
>
> Again, you will want to define the task(s) to be accomplished and then
> weigh the pros and cons of each project combined with local expertise.
> ?If you don't know what you want to do, then you can certainly read
> some examples on the websites and see which project strikes you as a
> "winner" for you.
>
>> python is claimed to be good for maintainability. But perl is
>> criticized for there-are-many-ways-for-a-given-task. Since there are
>> multiple ways in perl, let us assume that we always use perl in a
>> readable way.
>
> These two statements are generalizations that provide little insight
> into the strengths or weaknesses of the languages. ?In other words,
> one can write good or bad code in both languages.
>
> Hope that helps.
>
> Sean
>



From jkhilmer at gmail.com  Tue Dec 29 19:55:18 2009
From: jkhilmer at gmail.com (Jonathan Hilmer)
Date: Tue, 29 Dec 2009 12:55:18 -0700
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
	<366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
Message-ID: <81277ce10912291155x6dde10ewe2055b9692d077c1@mail.gmail.com>

Personally, I think that the differences between Python and Perl
(although substantial) are not large enough to make the language
itself the deciding factor.

Instead, consider the larger community of software.  I haven't yet
found a situation in which Python cannot be applied: it can be used
with R (statistics); lower-level code C or fortran; visualization
software such as PyMol, Chimera, Blender, VTK; plotting with
matplotlib; and scipy/numpy or sage, which provide innumerable
benefits for computation, data-processing, etc.

Although I don't claim to have a great deal of experience with Perl, I
haven't seen the same integration with that language: I'm assuming it
can be used with R and VTK (not sure about C or fortran?).  For this
reason, unless your work is highly targeted and you have no use
programming language integration with other software, I would
recommend Python.

For perl experts, I would truly appreciate any corrections you could
offer to these observations of mine, since I wouldn't mind using perl
if it offers benefits either in general or for specific applications.


Jonathan

On Tue, Dec 29, 2009 at 12:15 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
>>> May I ask somebody who are versitile in both bioperl and biopython
>>> comment on the pros and cons of bioperl and biopython? I'm sending
>>> this email to both bioperl and biopython mailing lists. But I hope
>>> that it will not result in any contention.
>>>
>>> I assume that the functionality between bioperl or biopython is the
>>> same, i.e., tasks can be done in bioperl can be done biopython and
>>> vice versa, as both libraries have been out there over 10 years.
>>> Please correct me if my understanding is not true.
>>
>> The two projects have similar goals, but saying that the functionality
>> is the same would be an extreme oversimplification. ?You will need to
>> define what you want to do and then check to see what the two projects
>> have to offer. ?This will, in general, require perusing the websites
>> for both projects as well as the relevant documentation.
>
> According to your experience, are there some tasks that are easier
> with one than with another?
>
>>> Given that a task that can be done with either bioperl or biopython,
>>> I, in particularly, want to know how long it will take to write the
>>> code for the task in bioperl and biopython, with the same readability
>>> requirement (see below) and the assumption that users have the same
>>> fluency in perl and python.
>>
>> Again, you will want to define the task(s) to be accomplished and then
>> weigh the pros and cons of each project combined with local expertise.
>> ?If you don't know what you want to do, then you can certainly read
>> some examples on the websites and see which project strikes you as a
>> "winner" for you.
>>
>>> python is claimed to be good for maintainability. But perl is
>>> criticized for there-are-many-ways-for-a-given-task. Since there are
>>> multiple ways in perl, let us assume that we always use perl in a
>>> readable way.
>>
>> These two statements are generalizations that provide little insight
>> into the strengths or weaknesses of the languages. ?In other words,
>> one can write good or bad code in both languages.
>>
>> Hope that helps.
>>
>> Sean
>>
>
> _______________________________________________
> Biopython mailing list ?- ?Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From wgheath at gmail.com  Tue Dec 29 20:16:39 2009
From: wgheath at gmail.com (William Heath)
Date: Tue, 29 Dec 2009 12:16:39 -0800
Subject: [Biopython] Comparison between bioperl and biopython?
In-Reply-To: <81277ce10912291155x6dde10ewe2055b9692d077c1@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
	<366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
	<81277ce10912291155x6dde10ewe2055b9692d077c1@mail.gmail.com>
Message-ID: <f08ddf990912291216h32988b8cv20830c1b6701caf6@mail.gmail.com>

The biggest reason to go with python is the ease of use.  Biologists are not
programmers and the learning curve for python is much smaller than that of
perl.  I like perl but choose python because of this issue.  Perl 6 does
address some of these issues however but this has not been fully implemented
as of yet.

-Tim

P.S.

I love, love, love cpan though which is only for perl right now :(

On Tue, Dec 29, 2009 at 11:55 AM, Jonathan Hilmer <jkhilmer at gmail.com>wrote:

> Personally, I think that the differences between Python and Perl
> (although substantial) are not large enough to make the language
> itself the deciding factor.
>
> Instead, consider the larger community of software.  I haven't yet
> found a situation in which Python cannot be applied: it can be used
> with R (statistics); lower-level code C or fortran; visualization
> software such as PyMol, Chimera, Blender, VTK; plotting with
> matplotlib; and scipy/numpy or sage, which provide innumerable
> benefits for computation, data-processing, etc.
>
> Although I don't claim to have a great deal of experience with Perl, I
> haven't seen the same integration with that language: I'm assuming it
> can be used with R and VTK (not sure about C or fortran?).  For this
> reason, unless your work is highly targeted and you have no use
> programming language integration with other software, I would
> recommend Python.
>
> For perl experts, I would truly appreciate any corrections you could
> offer to these observations of mine, since I wouldn't mind using perl
> if it offers benefits either in general or for specific applications.
>
>
> Jonathan
>
> On Tue, Dec 29, 2009 at 12:15 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> > On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov>
> wrote:
> >> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> >>> May I ask somebody who are versitile in both bioperl and biopython
> >>> comment on the pros and cons of bioperl and biopython? I'm sending
> >>> this email to both bioperl and biopython mailing lists. But I hope
> >>> that it will not result in any contention.
> >>>
> >>> I assume that the functionality between bioperl or biopython is the
> >>> same, i.e., tasks can be done in bioperl can be done biopython and
> >>> vice versa, as both libraries have been out there over 10 years.
> >>> Please correct me if my understanding is not true.
> >>
> >> The two projects have similar goals, but saying that the functionality
> >> is the same would be an extreme oversimplification.  You will need to
> >> define what you want to do and then check to see what the two projects
> >> have to offer.  This will, in general, require perusing the websites
> >> for both projects as well as the relevant documentation.
> >
> > According to your experience, are there some tasks that are easier
> > with one than with another?
> >
> >>> Given that a task that can be done with either bioperl or biopython,
> >>> I, in particularly, want to know how long it will take to write the
> >>> code for the task in bioperl and biopython, with the same readability
> >>> requirement (see below) and the assumption that users have the same
> >>> fluency in perl and python.
> >>
> >> Again, you will want to define the task(s) to be accomplished and then
> >> weigh the pros and cons of each project combined with local expertise.
> >>  If you don't know what you want to do, then you can certainly read
> >> some examples on the websites and see which project strikes you as a
> >> "winner" for you.
> >>
> >>> python is claimed to be good for maintainability. But perl is
> >>> criticized for there-are-many-ways-for-a-given-task. Since there are
> >>> multiple ways in perl, let us assume that we always use perl in a
> >>> readable way.
> >>
> >> These two statements are generalizations that provide little insight
> >> into the strengths or weaknesses of the languages.  In other words,
> >> one can write good or bad code in both languages.
> >>
> >> Hope that helps.
> >>
> >> Sean
> >>
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From jason at bioperl.org  Tue Dec 29 21:57:49 2009
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 29 Dec 2009 13:57:49 -0800
Subject: [Biopython] [Bioperl-l] Comparison between bioperl and
	biopython?
In-Reply-To: <366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
References: <366c6f340912290808q6edea4d8ncb59a270f9d11f1a@mail.gmail.com>
	<264855a00912290903m213d7cc4l607e8fa0bad55571@mail.gmail.com>
	<366c6f340912291115o58ba0b82kce74e18fecd833c8@mail.gmail.com>
Message-ID: <02851B8A-E74E-453E-9725-6FA8F3995F82@bioperl.org>


On Dec 29, 2009, at 11:15 AM, Peng Yu wrote:

> On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov>  
> wrote:
>> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com>  
>> wrote:
>>> May I ask somebody who are versitile in both bioperl and biopython
>>> comment on the pros and cons of bioperl and biopython? I'm sending
>>> this email to both bioperl and biopython mailing lists. But I hope
>>> that it will not result in any contention.
>>>
>>> I assume that the functionality between bioperl or biopython is the
>>> same, i.e., tasks can be done in bioperl can be done biopython and
>>> vice versa, as both libraries have been out there over 10 years.
>>> Please correct me if my understanding is not true.
>>
>> The two projects have similar goals, but saying that the  
>> functionality
>> is the same would be an extreme oversimplification.  You will need to
>> define what you want to do and then check to see what the two  
>> projects
>> have to offer.  This will, in general, require perusing the websites
>> for both projects as well as the relevant documentation.
>
> According to your experience, are there some tasks that are easier
> with one than with another?

As you have still failed to give much insight into the 'tasks' it is  
hard to give you a better answer.

If there is a module or set of routines already written then yes one  
might be easier than the other. Otherwise it just depends on your  
strengths in the programming language.
We discussed the strengths of the different toolkits briefly on the  
podcast last month.  http://twit.tv/floss96

I echo Sean. Use whichever language you are a better programmer in.   
BioPerl is more mature in some facets than is BioPython, but BioPython  
has some components that are more heavily developed and supported than  
BioPerl (structures being one of those and interfacing that to pyMol  
would be a strength).   I personally think the Gbrowse, Bio-Graphics,  
and Bio::DB::GFF/Bio::DB::SeqFeature::Store interface to Sequence  
databases and Features is a critical aspect of mining  genomic data  
and features and use these heavily in my work, making BioPerl easy and  
powerful for my tasks. That and sequence and alignment parsing and  
reformatting.  But there are comparable tools written in python with  
and without BioPython that you can also use so mainly it is about  
building up an expertise in a toolkit and going forward.  The BioPerl  
faithful will probably say it is more useful toolkit to us, but we are  
of course a biased sample.

Both projects can benefit from more users and developers contributing  
code and documentation so I would just jump in and give it a try if  
you are unsure which will be easier for you.

>
>>> Given that a task that can be done with either bioperl or biopython,
>>> I, in particularly, want to know how long it will take to write the
>>> code for the task in bioperl and biopython, with the same  
>>> readability
>>> requirement (see below) and the assumption that users have the same
>>> fluency in perl and python.
>>
>> Again, you will want to define the task(s) to be accomplished and  
>> then
>> weigh the pros and cons of each project combined with local  
>> expertise.
>>  If you don't know what you want to do, then you can certainly read
>> some examples on the websites and see which project strikes you as a
>> "winner" for you.
>>
>>> python is claimed to be good for maintainability. But perl is
>>> criticized for there-are-many-ways-for-a-given-task. Since there are
>>> multiple ways in perl, let us assume that we always use perl in a
>>> readable way.
>>
>> These two statements are generalizations that provide little insight
>> into the strengths or weaknesses of the languages.  In other words,
>> one can write good or bad code in both languages.
>>
>> Hope that helps.
>>
>> Sean
>>
>
> _______________________________________________
> 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
http://fungalgenomes.org/



From mitlox at op.pl  Wed Dec 30 02:42:07 2009
From: mitlox at op.pl (xyz)
Date: Wed, 30 Dec 2009 12:42:07 +1000
Subject: [Biopython] fastq-solexa index
In-Reply-To: <320fb6e00911260248w1f6a29b1ucc0bfecec897c67b@mail.gmail.com>
References: <4B0DD08B.6070607@op.pl>
	<320fb6e00911260248w1f6a29b1ucc0bfecec897c67b@mail.gmail.com>
Message-ID: <4B3ABDFF.8030809@op.pl>

Peter wrote:
> In Bio.SeqIO we give each file format a name, in this case "fastq-solexa"
> means the old Solexa FASTQ files (also used by Illumina up to and
> including pipeline 1.2) which use Solexa scores with an ASCII offset
> of 64 (not PHRED scores). The table on the SeqIO wiki page tries to
> summarise this. See also: http://en.wikipedia.org/wiki/FASTQ_format
>
> The "index" column on that table on the SeqIO wiki page indicates if
> each file format can be used with the Bio.SeqIO.index(...) function
> included in Biopython 1.52 onwards. See:
> http://news.open-bio.org/news/2009/09/biopython-seqio-index/
>
> There are also examples in the main Tutorial,
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>
> And in the Bio.SeqIO module's built in help, online here:
> http://biopython.org/DIST/docs/api/Bio.SeqIO-module.html
>
> >From within Python:
>
>   
>>>> from Bio import SeqIO
>>>> help(SeqIO)
>>>>         
> ...
>   
>>>> help(SeqIO.index)
>>>>         
> ...
>
> Peter
>
>   
Thank you.


From mitlox at op.pl  Wed Dec 30 02:51:45 2009
From: mitlox at op.pl (xyz)
Date: Wed, 30 Dec 2009 12:51:45 +1000
Subject: [Biopython] Strand
Message-ID: <4B3AC041.2070008@op.pl>

Hello,
I downloaded data from Phytozome Biomart:

>AC159145_38|MtChr2|AC159145_38|Mtruncatula|17915949|17918990|-1
ATTTCCTCCAGACTTGTTAAAGAAGTTGAGTACAGATTGTATTGTCATGCAAAATCATCA
ATATGGCATATCCCCAGTAAAACTCCTGGGAAATCAAAAGCTATCGAGTTTTTTCGAGAT
CTTGACAACTTCCAACGATCAAGATGATAAGGTTTATGTCTCTACAGTACGTTCACGTAA
CTATCCCGTGACTGGCTTCCAATGGCATCCTGAGAAAAATGCCTTCGAATGGGGCTCACC
AAGCATTCCACACACAGAGGATGCCATTCGAACAACTCAGTATGCTGCAAACTATTTGGT
CAGTGAAGCGAGGAAGTCCTTAAACAGACCAGTTGCTCAGGAATTGTTAGACAATCTCAT
ATACAATTACAGACCCACTTATTGTGGGTATGCAGGTTGTCCACCGCCTAATCCGAACCT
CTACTACCAGCCGGTCATTGGAATTCTCAGCCACCCCGGCGATGGCACTTCAGGCCGCCA
CAGTAATGCTACGGGCGCTTCCTTCATTCACGCCTCTTATGTGAAATTCGTGGAGGCTGC
TGGCGCTAGAGTAGTTCCTCTCATTTACAACGAACCGGAGGAGAAGATTCTCAAGGTATC
AGAAAAGGCCAAAGCTTGA


The above data is from -1 strand, but how could I convert it +1 strand?

Thank you in advance.

Best regards,



From p.j.a.cock at googlemail.com  Wed Dec 30 12:13:42 2009
From: p.j.a.cock at googlemail.com (Peter)
Date: Wed, 30 Dec 2009 12:13:42 +0000
Subject: [Biopython] programming errors
In-Reply-To: <4788465e0912252205l1ac3f26ds98739898ff83dbd9@mail.gmail.com>
References: <4788465e0912252205l1ac3f26ds98739898ff83dbd9@mail.gmail.com>
Message-ID: <389810B4-4CAB-4375-8964-5ABDA9749FFB@googlemail.com>

Hi Rocky,

To send a query to the mailing list please use the Biopython at ...  
address, not the Biopython-owner at ... address. You need to sign up to  
the mailing list first.

Thanks,

Peter

On 26 Dec 2009, at 06:05, Rocky Parida <nirulinga at gmail.com> wrote:

> Hi
> My name is Rocky. I am student at the Grand Valley State University.  
> I am
> doing MS in Bioinformatics. I am currently using python 2.6.I was  
> trying to
> follow a documentation(
> http://www.inb.mu-luebeck.de/biosoft/biopython/tut/Tutorial002.html#toc10 
> )in<http://www.inb.mu-luebeck.de/biosoft/biopython/tut/Tutorial002.html#toc10%29in 
> >
> order to connect to a biological databases. I am facing some troubles
> regarding importing data from NCBI. I am attaching my snipped word  
> doc with
> this email.
> Can you please suggest me on how to perform statistical data  
> analysis using
> python. I am very much interested to learn but i am facing some  
> troubles
> following the documentation. Is there a step by step documentation  
> that has
> all the information regarding what to write, what to download and  
> how to do
> statistics using python codes. If you please refer those sites and  
> books in
> you reply. I have very little back ground in programming. So, please  
> keep
> that in you consideration as well.
> Thanking you
> Rocky


From chapmanb at 50mail.com  Wed Dec 30 12:59:42 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Wed, 30 Dec 2009 07:59:42 -0500
Subject: [Biopython] Strand
In-Reply-To: <4B3AC041.2070008@op.pl>
References: <4B3AC041.2070008@op.pl>
Message-ID: <20091230125942.GB39741@sobchak.mgh.harvard.edu>

Hello;

> I downloaded data from Phytozome Biomart:
> 
> >AC159145_38|MtChr2|AC159145_38|Mtruncatula|17915949|17918990|-1
> ATTTCCTCCAGACTTGTTAAAGAAGTTGAGTACAGATTGTATTGTCATGCAAAATCATCA
> ATATGGCATATCCCCAGTAAAACTCCTGGGAAATCAAAAGCTATCGAGTTTTTTCGAGAT
> CTTGACAACTTCCAACGATCAAGATGATAAGGTTTATGTCTCTACAGTACGTTCACGTAA
> CTATCCCGTGACTGGCTTCCAATGGCATCCTGAGAAAAATGCCTTCGAATGGGGCTCACC
> AAGCATTCCACACACAGAGGATGCCATTCGAACAACTCAGTATGCTGCAAACTATTTGGT
> CAGTGAAGCGAGGAAGTCCTTAAACAGACCAGTTGCTCAGGAATTGTTAGACAATCTCAT
> ATACAATTACAGACCCACTTATTGTGGGTATGCAGGTTGTCCACCGCCTAATCCGAACCT
> CTACTACCAGCCGGTCATTGGAATTCTCAGCCACCCCGGCGATGGCACTTCAGGCCGCCA
> CAGTAATGCTACGGGCGCTTCCTTCATTCACGCCTCTTATGTGAAATTCGTGGAGGCTGC
> TGGCGCTAGAGTAGTTCCTCTCATTTACAACGAACCGGAGGAGAAGATTCTCAAGGTATC
> AGAAAAGGCCAAAGCTTGA
> 
> The above data is from -1 strand, but how could I convert it +1 strand?

If you got this from BioMart and retrieved something like cDNA
sequence or transcript, this is probably already reverse
complemented for you. In this case it looks like a coding sequence
starting at base 47 and proceeding to the stop codon at the end.

To answer your question, please see the Tutorial documentation,
specifically Chapter 5 Sequence Input/Output:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc44

and section 3.7 Nucleotide sequences and (reverse) complements:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc23

This should lead you to:

in_file = "your_data.fa"
with open(in_file) as in_handle:
    rec = SeqIO.read(in_handle, "fasta")

rc = rec.seq.reverse_complement()

Hope this helps,
Brad


From pedro.al at fenhi.uh.cu  Wed Dec 30 20:05:55 2009
From: pedro.al at fenhi.uh.cu (Yasser Almeida =?iso-8859-1?b?SGVybuFuZGV6?=)
Date: Wed, 30 Dec 2009 15:05:55 -0500
Subject: [Biopython] Save custom structure...
Message-ID: <20091230150555.ojbth0gp34g088os@correo.fenhi.uh.cu>

Hi all...
I've extracted a residue and an atom as two separated objects...
How can i save them as a single structure .pdb file?

Thanks

-- 
Lic. Yasser Almeida Hern?ndez
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 271-7933, ext. 221

----------------------------------------------------------------
Correo FENHI