From rmb32 at cornell.edu Sun Aug 1 15:17:14 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Sun, 01 Aug 2010 12:17:14 -0700
Subject: [Biopython] GMOD Evo Hackathon Open Call for Participation
Message-ID: <4C55C83A.3060700@cornell.edu>
We are seeking participants for the GMOD Tools for Evolutionary Biology
Hackathon, held November 8-12, 2010 at the US National Evolutionary
Synthesis Center (NESCent) in Durham, NC.
This hackathon targets three critical gaps in the capabilities of the
GMOD toolbox that currently limit its utility for evolutionary research:
1. Visualization of comparative genomics data
2. Visualization of phylogenetic data and trees
3. Support for population diversity and phenotype data
If you are interested in these areas and have relevant expertise, you
are strongly encouraged to apply. Relevant areas of expertise include
more than just software development: if you are a GMOD power user,
visualization guru, domain expert (comparative, phylogenetics,
population, ...), or documentation wizard, then your skills are needed!
How To Apply:
Fill out the online application form at http://bit.ly/gmodevohack.
Applications are due August 25.
About GMOD:
GMOD is an intercompatible suite of open-source software components for
storing, managing, analyzing, and visualizing genome-scale data. GMOD
includes many widely-used software components: GBrowse and JBrowse, both
genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a
generic and modular database schema; CMap, a comparative map viewer; as
well as many other components including Apollo, MAKER, BioMart,
InterMine, and Galaxy. We hope to extend the functionality of existing
GMOD components, and integrate new components as well.
About Hackathons:
A hackathon is an intense event at which a group of programmers with
different backgrounds and skills collaborate hands-on and face-to-face
to develop working code that is of utility to the community as a whole.
The mix of people will include domain experts and computer-savvy end-users.
More details about the event, its motivation, organization, procedures,
and attendees, as well as URLs to the hackathon and related websites are
included below.
Sincerely,
The GMOD EvoHack Organizing Committee (and project affiliations as
relevant):
Nicole Washington, Chair (LBNL, modENCODE, Phenote)
Robert Buels (SGN, Chado NatDiv)
Scott Cain (OICR, GMOD)
Dave Clements (NESCent, GMOD)
Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv)
Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)
-----------------------------
About the GMOD Evo Hackathon
Overview
We are organizing a hackathon to fill critical gaps in the capabilities
of the Generic Model Organism Database (GMOD) toolbox that currently
limit its utility for evolutionary research. Specifically, we will focus
on tools for
1) viewing comparative genomics data;
2) visualizing phylogenomic data; and
3) supporting population diversity data and phenotype annotation.
The event will be hosted at NESCent and bring together a group of about
20+ software developers, end-user representatives, and documentation
experts who would otherwise not meet. The participants will include key
developers of GMOD components that currently lack features critical for
emerging evolutionary biology research, developers of informatics tools
in evolutionary research that lack GMOD integration, and
informatics-savvy biologists who can represent end-user requirements.
The event will provide a unique opportunity to infuse the GMOD developer
community with a heightened awareness of unmet needs in evolutionary
biology that GMOD components have the potential to fill, and for tool
developers in evolutionary biology to better understand how best to
extend or integrate with already existing GMOD components.
Before the Event
Discussion of ideas and sometimes even design actually starts well
before the hackathon, on mailing lists, wiki pages, and conference calls
set up among accepted attendees. This advance work lays the foundation
for participants to be productive from the very first day. This also
means that participants should be willing to contribute some time in
advance of the hackathon itself to participate in this preparatory
discussion.
During the Event
Typically, hackathon participants use the morning of the first day of
the event to organize themselves into working groups of between 3 and 6
people, each with a focused implementation objective. Ideas and
objectives are discussed, and attendees coalesce around the projects in
which they have the most experience or interest.
Deliverables / Event Results
The meeting's attendance, working groups, and outcomes will be fully
logged and documented on the GMOD wiki (http://gmod.org). Each working
group during the event will typically have its own wiki page, linked
from the main EvoHack page, where it documents its minutes and design
notes, and provides links to the code and documentation it produces.
Also, since GMOD and NESCent are both committed to open source
principles, all code and documentation produced by participants during
the hackathon must be published under an OSI-approved open source
license. As contributions to existing GMOD tools, all hackathon products
will most likely satisfy this requirement automatically.
NESCent
This event is sponsored by the US National Evolutionary Synthesis Center
(NESCent, http://www.nescent.org) through its Informatics Whitepapers
program (http://www.nescent.org/informatics/whitepapers.php). NESCent
promotes the synthesis of information, concepts and knowledge to address
significant, emerging, or novel questions in evolutionary science and
its applications. NESCent achieves this by supporting research and
education across disciplinary, institutional, geographic, and
demographic boundaries (see http://www.nescent.org/science/proposals.php).
Links
Main GMOD EvoHack page, and full proposal:
http://gmod.org/wiki/GMOD_Evo_Hackathon
NESCent: http://www.nescent.org/
GMOD: http://gmod.org
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application: http://bit.ly/gmodevohack
--
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback
From phosse1 at students.towson.edu Tue Aug 3 19:53:33 2010
From: phosse1 at students.towson.edu (Parsa Hosseini)
Date: Tue, 3 Aug 2010 19:53:33 -0400
Subject: [Biopython] Biopython SUBA interface
Message-ID:
Hi everyone,
I have some python cgi scripts which interface with the Arabidopsis thaliana
SUBA database.
I'd like to contribute such scripts (and hopefully much more). I was curious
how I can go about submitting such code and/or if anyone would find such a
script/interface of use?
Thanks alot,
--------------------------------------------
Parsa Hosseini
Parsa.Hosseini at ars.usda.gov
http://tiger.towson.edu/~phosse1/
301-875-6525
From biopython at maubp.freeserve.co.uk Wed Aug 4 04:12:07 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 4 Aug 2010 09:12:07 +0100
Subject: [Biopython] Biopython SUBA interface
In-Reply-To:
References:
Message-ID:
On Wed, Aug 4, 2010 at 12:53 AM, Parsa Hosseini
wrote:
> Hi everyone,
> I have some python cgi scripts which interface with the Arabidopsis
> thaliana SUBA database.
> I'd like to contribute such scripts (and hopefully much more). I was
> curious how I can go about submitting such code and/or if anyone
> would find such a script/interface of use?
> Thanks alot,
Hi Parsa,
Are these stand alone scripts that you would use at the command
line, or a Python module you can use in a Python script? Either
way we could include them...
I had a quick look at http://suba.plantenergy.uwa.edu.au/ and
it isn't clear if they have an official API. Are you doing this by
building the HTTP request and then parsing the HTML results?
If so, that is worrying for two reasons. First, it is fragile and
will need updates whenever the site makes changes to their
layout (something that has happened to other HTML parsers
in Biopython that have since been deprecated and removed).
Secondly, in the absence of an official API are there any
usage guidelines? The SUBA team may not be happy with
people running scripts that could use up far more resources
than several people using the website interface.
As to would anyone find such a script/interface of use, well,
personally probably not in my current work. But I'm sure there
are people using Biopython working on plant genomes and
Arabidopsis thaliana.
Regards,
Peter
From biopython at maubp.freeserve.co.uk Wed Aug 11 11:14:27 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 11 Aug 2010 16:14:27 +0100
Subject: [Biopython] Using a dictionary rather than list for hierachy in
Bio.SCOP.Cla
Message-ID:
Dear Biopythoneers - especially those using SCOP,
Jeffrey Finkelstein has proposed a change to the Record class in Bio.SCOP.Cla
to use a dictionary rather than a list for the hierarchy member to better match
the SCOP specification, see his email quoted below and Bug 3109 for details:
http://bugzilla.open-bio.org/show_bug.cgi?id=3109
This would be a backwards incompatible change, so feedback from anyone
using Biopython's SCOP module would be important in deciding how to
proceed. Comments please?
Thank you,
Peter
On the dev list Jeffrey Finkelstein wrote:
> I have submitted a bug report and a patch for a current feature of the
> Bio.SCOP.Cla module that makes using it somewhat difficult. Specifically,
> the Bio.Scop.Cla.Record class has a "hierarchy" member which is currently a
> list, but should be a dictionary, according to the SCOP parseable
> classification file format "specification" (it is an informal specification)
> here:
> http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html#scop-parseable-files.
>
> For a usage example, see the comments I have made at:
> http://bugzilla.open-bio.org/show_bug.cgi?id=3109
>
> I have CC'ed the original author of the module. Gavin (or anyone else), do
> you have any objections to this change?
>
> Jeffrey
See http://lists.open-bio.org/pipermail/biopython-dev/2010-August/008134.html
From biopython at maubp.freeserve.co.uk Thu Aug 19 11:43:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 19 Aug 2010 16:43:56 +0100
Subject: [Biopython] Biopython 1.55 beta released
Message-ID:
Dear Biopythoneers,
We?ve just released a beta of Biopython 1.55 for user testing, as
announced on the news server (which has RSS and atom feeds) and on
twitter:
http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/
http://twitter.com/biopython
Since Biopython 1.54 was released three months ago, we?ve made a good
start on work for Python 3 support (via the 2to3 script), but as a
side effect of this we?ve had to update quite a lot of the older parts
of the library. Although the unit tests are all fine, there is a small
but real chance that we?ve accidentally broken things ? which is why
we?re doing this beta release.
In terms of new features, the most noticeable highlight is that the
command line tool application wrapper classes are now executable,
which should make it much easier to call external tools. This is
described in the updated documentation.
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
Note we are phasing out support for Python 2.4. We will continue to
support it for at least one further release (i.e. Biopython 1.56).
This could be delayed given feedback from our users (e.g. if this
proves to be a problem in combination with other libraries or a
popular Linux distribution).
(At least) 10 people have contributed to this release (so far),
including 5 new people - thank you all:
* Andres Colubri (first contribution)
* Carlos Rios Vera (first contribution)
* Claude Paroz (first contribution)
* Eric Talevich
* Frank Kauff
* Joao Rodrigues (first contribution)
* Konstantin Okonechnikov (first contribution)
* Michiel de Hoon
* Peter Cock
* Tiago Antao
Source distributions and Windows installers are available from the
downloads page on the Biopython website:
http://www.biopython.org/wiki/Download
Feedback is welcome through the mailing lists (or bugzilla),
especially if you find something that doesn't work.
Thank you,
Peter
From rmb32 at cornell.edu Thu Aug 19 13:09:45 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 19 Aug 2010 10:09:45 -0700
Subject: [Biopython] reminder: Aug 25 deadline for GMOD Hackathon application
Message-ID: <4C6D6559.3080809@cornell.edu>
Hi all,
This is your one-week reminder: the deadline for open applications to
the GMOD Evo hackathon is Wednesday, August 25th.
Rob
========================================
We are seeking participants for the GMOD Tools for Evolutionary Biology
Hackathon, held November 8-12, 2010 at the US National Evolutionary
Synthesis Center (NESCent) in Durham, NC.
This hackathon targets three critical gaps in the capabilities of the
GMOD toolbox that currently limit its utility for evolutionary research:
1. Visualization of comparative genomics data
2. Visualization of phylogenetic data and trees
3. Support for population diversity and phenotype data
If you are interested in these areas and have relevant expertise, you
are strongly encouraged to apply. Relevant areas of expertise include
more than just software development: if you are a GMOD power user,
visualization guru, domain expert (comparative, phylogenetics,
population, ...), or documentation wizard, then your skills are needed!
How To Apply:
Fill out the online application form at http://bit.ly/gmodevohack.
Applications are due August 25.
About GMOD:
GMOD is an intercompatible suite of open-source software components for
storing, managing, analyzing, and visualizing genome-scale data. GMOD
includes many widely-used software components: GBrowse and JBrowse, both
genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a
generic and modular database schema; CMap, a comparative map viewer; as
well as many other components including Apollo, MAKER, BioMart,
InterMine, and Galaxy. We hope to extend the functionality of existing
GMOD components, and integrate new components as well.
About Hackathons:
A hackathon is an intense event at which a group of programmers with
different backgrounds and skills collaborate hands-on and face-to-face
to develop working code that is of utility to the community as a whole.
The mix of people will include domain experts and computer-savvy end-users.
More details about the event, its motivation, organization, procedures,
and attendees, as well as URLs to the hackathon and related websites are
included below.
Sincerely,
The GMOD EvoHack Organizing Committee (and project affiliations as
relevant):
Nicole Washington, Chair (LBNL, modENCODE, Phenote)
Robert Buels (SGN, Chado NatDiv)
Scott Cain (OICR, GMOD)
Dave Clements (NESCent, GMOD)
Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv)
Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)
-----------------------------
About the GMOD Evo Hackathon
Overview
We are organizing a hackathon to fill critical gaps in the capabilities
of the Generic Model Organism Database (GMOD) toolbox that currently
limit its utility for evolutionary research. Specifically, we will focus
on tools for
1) viewing comparative genomics data;
2) visualizing phylogenomic data; and
3) supporting population diversity data and phenotype annotation.
The event will be hosted at NESCent and bring together a group of about
20+ software developers, end-user representatives, and documentation
experts who would otherwise not meet. The participants will include key
developers of GMOD components that currently lack features critical for
emerging evolutionary biology research, developers of informatics tools
in evolutionary research that lack GMOD integration, and
informatics-savvy biologists who can represent end-user requirements.
The event will provide a unique opportunity to infuse the GMOD developer
community with a heightened awareness of unmet needs in evolutionary
biology that GMOD components have the potential to fill, and for tool
developers in evolutionary biology to better understand how best to
extend or integrate with already existing GMOD components.
Before the Event
Discussion of ideas and sometimes even design actually starts well
before the hackathon, on mailing lists, wiki pages, and conference calls
set up among accepted attendees. This advance work lays the foundation
for participants to be productive from the very first day. This also
means that participants should be willing to contribute some time in
advance of the hackathon itself to participate in this preparatory
discussion.
During the Event
Typically, hackathon participants use the morning of the first day of
the event to organize themselves into working groups of between 3 and 6
people, each with a focused implementation objective. Ideas and
objectives are discussed, and attendees coalesce around the projects in
which they have the most experience or interest.
Deliverables / Event Results
The meeting's attendance, working groups, and outcomes will be fully
logged and documented on the GMOD wiki (http://gmod.org). Each working
group during the event will typically have its own wiki page, linked
from the main EvoHack page, where it documents its minutes and design
notes, and provides links to the code and documentation it produces.
Also, since GMOD and NESCent are both committed to open source
principles, all code and documentation produced by participants during
the hackathon must be published under an OSI-approved open source
license. As contributions to existing GMOD tools, all hackathon products
will most likely satisfy this requirement automatically.
NESCent
This event is sponsored by the US National Evolutionary Synthesis Center
(NESCent, http://www.nescent.org) through its Informatics Whitepapers
program (http://www.nescent.org/informatics/whitepapers.php). NESCent
promotes the synthesis of information, concepts and knowledge to address
significant, emerging, or novel questions in evolutionary science and
its applications. NESCent achieves this by supporting research and
education across disciplinary, institutional, geographic, and
demographic boundaries (see http://www.nescent.org/science/proposals.php).
Links
Main GMOD EvoHack page, and full proposal:
http://gmod.org/wiki/GMOD_Evo_Hackathon
NESCent: http://www.nescent.org/
GMOD: http://gmod.org
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application: http://bit.ly/gmodevohack
--
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback
From biopython at maubp.freeserve.co.uk Mon Aug 23 12:05:43 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 23 Aug 2010 17:05:43 +0100
Subject: [Biopython] Biopython 1.55 beta released
In-Reply-To:
References:
Message-ID:
On Thu, Aug 19, 2010 at 4:43 PM, Peter wrote:
> Dear Biopythoneers,
>
> We?ve just released a beta of Biopython 1.55 for user testing, as
> announced on the news server (which has RSS and atom feeds) and on
> twitter:
> http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/
> http://twitter.com/biopython
>
> ...
>
> Feedback is welcome through the mailing lists (or bugzilla),
> especially if you find something that doesn't work.
Hi all,
Is no news good news? So far there have been no problems reported. I've
had a least one person report (off list) that the windows installers worked
fine for them on Windows XP (32bit).
Any other feedback on the beta?
Thanks
Peter
From cgohlke at uci.edu Mon Aug 23 16:43:20 2010
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Mon, 23 Aug 2010 13:43:20 -0700
Subject: [Biopython] Biopython 1.55 beta released (Peter)
In-Reply-To:
References:
Message-ID: <4C72DD68.20309@uci.edu>
> Dear Biopythoneers,
>
> We?ve just released a beta of Biopython 1.55 for user testing, as
> announced on the news server (which has RSS and atom feeds) and on
> twitter:
> http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/
> http://twitter.com/biopython
>
> Since Biopython 1.54 was released three months ago, we?ve made a good
> start on work for Python 3 support (via the 2to3 script), but as a
> side effect of this we?ve had to update quite a lot of the older parts
> of the library. Although the unit tests are all fine, there is a small
> but real chance that we?ve accidentally broken things ? which is why
> we?re doing this beta release.
>
> In terms of new features, the most noticeable highlight is that the
> command line tool application wrapper classes are now executable,
> which should make it much easier to call external tools. This is
> described in the updated documentation.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>
> Note we are phasing out support for Python 2.4. We will continue to
> support it for at least one further release (i.e. Biopython 1.56).
> This could be delayed given feedback from our users (e.g. if this
> proves to be a problem in combination with other libraries or a
> popular Linux distribution).
>
> (At least) 10 people have contributed to this release (so far),
> including 5 new people - thank you all:
>
> * Andres Colubri (first contribution)
> * Carlos Rios Vera (first contribution)
> * Claude Paroz (first contribution)
> * Eric Talevich
> * Frank Kauff
> * Joao Rodrigues (first contribution)
> * Konstantin Okonechnikov (first contribution)
> * Michiel de Hoon
> * Peter Cock
> * Tiago Antao
>
> Source distributions and Windows installers are available from the
> downloads page on the Biopython website:
> http://www.biopython.org/wiki/Download
>
> Feedback is welcome through the mailing lists (or bugzilla),
> especially if you find something that doesn't work.
>
> Thank you,
>
> Peter
>
Looks good. There are no test failures for the 32/64 bit msvc9 builds
for Python 2.6/2.7 and numpy 1.4.1/1.5b2.
--
Christoph
From biopython at maubp.freeserve.co.uk Tue Aug 24 05:26:17 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 24 Aug 2010 10:26:17 +0100
Subject: [Biopython] Biopython 1.55 beta released (Peter)
In-Reply-To: <4C72DD68.20309@uci.edu>
References:
<4C72DD68.20309@uci.edu>
Message-ID:
On Mon, Aug 23, 2010 at 9:43 PM, Christoph Gohlke wrote:
>
> Looks good. There are no test failures for the 32/64 bit msvc9 builds for
> Python 2.6/2.7 and numpy 1.4.1/1.5b2.
>
Thank you - as far as I know you are the only person building Biopython
on Windows 64 bit, so that is reassuring.
Peter
From schaefer at rostlab.org Tue Aug 24 09:37:19 2010
From: schaefer at rostlab.org (Christian Schaefer)
Date: Tue, 24 Aug 2010 15:37:19 +0200
Subject: [Biopython] Contact Area Difference as an alternative to RMSD
Message-ID: <4C73CB0F.7060100@rostlab.org>
Hi,
I'd be interested in the above alternative measure for structural
difference as desribed in [1]. I know that there exists an
implementation to make it useable via Python: It's a wrapper around
icm-browser [2] implemented in the Biskit library [3]. However, it's a
real pain to get the whole pipeline working and I haven't succeeded so far.
So, does anybody know of an alternative implementation of CAD that is
easy to use via python?
Thanks,
Chris
[1] Abagyan RA, Totrov MM. Contact area difference (CAD): a robust
measure to evaluate accuracy of protein models. J Mol Biol. 1997 May
9;268(3):678-85.
[2] http://www.molsoft.com/index.html
[3] http://biskit.pasteur.fr/
--
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
Boltzmannstr. 3
D-85748 Garching b. Muenchen
Germany
http://www.rostlab.org/~schaefer
From vishal4linux2 at gmail.com Wed Aug 25 07:12:38 2010
From: vishal4linux2 at gmail.com (vishal bhardwa)
Date: Wed, 25 Aug 2010 16:42:38 +0530
Subject: [Biopython] installing Biopython in Centos
Message-ID:
hello sir/mam
how can i install biopython on Centos System Pls tell me any
solution
Vishal Bhardwaj
Mb:-91-7696619429
From mitlox at op.pl Wed Aug 25 07:22:24 2010
From: mitlox at op.pl (xyz)
Date: Wed, 25 Aug 2010 21:22:24 +1000
Subject: [Biopython] Writting fasta file
Message-ID: <4C74FCF0.4070401@op.pl>
Hello,
the following code saves a multiple fasta file in a list and after
reverse complement it writes the content back in a fasta file.
in_handle = open(opts.inputFasta, "r")
records = list(SeqIO.parse(in_handle, "fasta"))
for record in records:
record.seq = record.seq.reverse_complement()
out_handle = open(opts.outputFasta, "w")
SeqIO.write(records, out_handle, "fasta")
How is it possible to do it without a list?
Thank you in advance.
From mitlox at op.pl Wed Aug 25 08:02:00 2010
From: mitlox at op.pl (xyz)
Date: Wed, 25 Aug 2010 22:02:00 +1000
Subject: [Biopython] installing Biopython in Centos
In-Reply-To:
References:
Message-ID: <4C750638.8090007@op.pl>
Hi,
I use Cent OS, but Python 2.6.5 is in my home directory installed and
following both methods working fine for me:
http://biopython.org/wiki/Download#Installation_Instructions
http://biopython.org/wiki/Download#Easy_Install
Cheers,
On 25/08/10 21:12, vishal bhardwa wrote:
> hello sir/mam
>
> how can i install biopython on Centos System Pls tell me any
> solution
>
>
>
>
>
> Vishal Bhardwaj
> Mb:-91-7696619429
> _______________________________________________
> 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 Aug 25 08:59:58 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 25 Aug 2010 13:59:58 +0100
Subject: [Biopython] installing Biopython in Centos
In-Reply-To:
References:
Message-ID:
On Wed, Aug 25, 2010 at 12:12 PM, vishal bhardwa
wrote:
> hello sir/mam
>
> ? ? ? ? how can i install biopython on Centos System Pls tell me any
> solution
>
> Vishal Bhardwaj
> Mb:-91-7696619429
Hello Vishal,
CentOS currently comes with Python 2.4, so you should be able
to use that and install Biopython from source as normal.
However, Python 2.4 is now very out of date so many packages
don't support it anymore. It lacks a few useful modules like
SQLite3 support and ElementTree for XML parser. It is also
noticeable slower than more recent releases, but that may not
be an issue for you.
NumPy still supports Python 2.4, and Biopython still supports
Python 2.4, but we plan to drop support for Python 2.4 after
Biopython 1.56 is released (which will be some time later this
year).
We have servers running CentOS release 5.4 (Final) and
CentOS 5.5 (final) where the administrator has installed
Python 2.6 at /usr/local/bin/python2.6 or Python 2.7 at
/usr/local/bin/python2.7 and Biopython works fine there.
It would be worth considering installing Python 2.6 or 2.7.
Ask your systems administrator if they can do this for you,
or do it yourself under your user directory as "xyz" suggested.
Peter
From biopython at maubp.freeserve.co.uk Wed Aug 25 09:08:41 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 25 Aug 2010 14:08:41 +0100
Subject: [Biopython] Writting fasta file
In-Reply-To: <4C74FCF0.4070401@op.pl>
References: <4C74FCF0.4070401@op.pl>
Message-ID:
On Wed, Aug 25, 2010 at 12:22 PM, xyz wrote:
> Hello,
> the following code saves a multiple fasta file in a list and after reverse
> complement it writes the content back in a fasta file.
>
> ?in_handle = open(opts.inputFasta, "r")
> ?records = list(SeqIO.parse(in_handle, "fasta"))
>
> ?for record in records:
> ? ? ?record.seq = record.seq.reverse_complement()
>
> ?out_handle = open(opts.outputFasta, "w")
> ?SeqIO.write(records, out_handle, "fasta")
>
> How is it possible to do it without a list?
>
> Thank you in advance.
Hi "xyz",
Did you try looking in the tutorial? i.e.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
You could modify your code to use a generator expression like this:
def make_rc(record):
"""Modifies a SeqRecord in place, and returns it."""
record.seq = record.seq.reverse_complement()
return record
records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
SeqIO.write(records, out_opts.outputFasta, "fasta")
I also changed it to pass filenames directly to SeqIO - its shorter ;)
See also this thread about adding a reverse complement
method to the SeqRecord which would make this easier:
http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html
Peter
From mjldehoon at yahoo.com Wed Aug 25 09:52:58 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Wed, 25 Aug 2010 06:52:58 -0700 (PDT)
Subject: [Biopython] Deprecated code to be removed from Biopython
Message-ID: <556514.21952.qm@web62405.mail.re1.yahoo.com>
Dear all,
Below are the bits of code in Biopython that are currently deprecated (with a DeprecationWarning). These have been deprecated since Biopython 1.51, and we are considering to remove them completely for the final release of Biopython 1.55. Any objections? Is anybody still using any of this code?
Thanks,
--Michiel.
Bio.Align.FormatConvert
Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter
Bio.Entrez.efetch: rettype="genbank" option
Bio.Fasta
Bio.SCOP.Dom.Parser
Bio.SwissProt.SProt
Bio.Transcribe
Bio.Translate
BioSQL.BioSeqDatabase.open_database: driver="psycopg" option
From ajperry at pansapiens.com Thu Aug 26 00:03:46 2010
From: ajperry at pansapiens.com (Andrew Perry)
Date: Thu, 26 Aug 2010 14:03:46 +1000
Subject: [Biopython] Deprecated code to be removed from Biopython
In-Reply-To: <556514.21952.qm@web62405.mail.re1.yahoo.com>
References: <556514.21952.qm@web62405.mail.re1.yahoo.com>
Message-ID:
On 25 August 2010 23:52, Michiel de Hoon wrote:
> Dear all,
>
> Below are the bits of code in Biopython that are currently deprecated (with
> a DeprecationWarning). These have been deprecated since Biopython 1.51, and
> we are considering to remove them completely for the final release of
> Biopython 1.55. Any objections? Is anybody still using any of this code?
>
> Thanks,
> --Michiel.
>
> Bio.Align.FormatConvert
> Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter
> Bio.Entrez.efetch: rettype="genbank" option
> Bio.Fasta
> Bio.SCOP.Dom.Parser
> Bio.SwissProt.SProt
> Bio.Transcribe
> Bio.Translate
> BioSQL.BioSeqDatabase.open_database: driver="psycopg" option
>
>
No objections here. I did a quick grep over some of my code from the last
two or three years - while I'm still using things
like Bio.Align.FormatConvert (probably because I was cut and pasting from
even older code), and Bio.SwissProt.SProt in some even older scripts, a
quick look at the API documentation for these deprecated parts provides
clear and simple pointers on how to migrate, so I'm happy.
Good work on the docs in this respect !
Andrew Perry
From biopython at maubp.freeserve.co.uk Thu Aug 26 06:57:27 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 11:57:27 +0100
Subject: [Biopython] Problem with biopython.org domain
Message-ID:
Hi all,
We appear to have a temporary problem with our biopython.org domain,
which I trust the OBF admin team will address shortly.
As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page
and http://biopython.open-bio.org/DIST/ for the downloads.
Source code is hosted separately on github,
http://github.com/biopython/biopython/
Apologies,
Peter
From jfi.mamede at gmail.com Thu Aug 26 07:02:30 2010
From: jfi.mamede at gmail.com (=?ISO-8859-1?Q?Jo=E3o_Mamede?=)
Date: Thu, 26 Aug 2010 13:02:30 +0200
Subject: [Biopython] Something happened to the domain?
Message-ID: <4C7649C6.1080503@gmail.com>
I was trying to see the new changes in biopython in the website,
however when I type biopython.org it asks me if I want to rent the domain.
What's the direct ip if the machine is up?
Thanks
From biopython at maubp.freeserve.co.uk Thu Aug 26 07:15:35 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 12:15:35 +0100
Subject: [Biopython] Something happened to the domain?
In-Reply-To: <4C7649C6.1080503@gmail.com>
References: <4C7649C6.1080503@gmail.com>
Message-ID:
On Thu, Aug 26, 2010 at 12:02 PM, Jo?o Mamede wrote:
> ?I was trying to see the new changes in biopython in the website, however
> when I type biopython.org it asks me if I want to rent the domain.
> What's the direct ip if the machine is up?
>
> Thanks
Hi Jo?o,
I sent out an email shortly before your query - hopefully you've
received it now:
http://lists.open-bio.org/pipermail/biopython/2010-August/006712.html
Peter
From dag at sonsorol.org Thu Aug 26 07:26:57 2010
From: dag at sonsorol.org (Chris Dagdigian)
Date: Thu, 26 Aug 2010 07:26:57 -0400
Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain
In-Reply-To:
References:
Message-ID: <4C764F81.1060100@sonsorol.org>
I manage or am the admin/technical/billing account holder for 24
domains, among them most of the open-bio.org ones.
Biopython.org is one that I do not own. Actually since NetSol is
offering to let me change DNS maybe I'm the technical contact - have to
wait and see on this. Normally for domains I control netsol starts email
nagging me constantly - never got emails about this one.
However, Networksolutions allows *anyone* with a payment method to renew
any domain for any reason.
I've renewed biopython.org for a 2-year term, paying out of pocket like
I do for all OBF domains so our $$ stays in our bank account.
> Order Confirmation
>
> Order Number: 375229424
> Today's Charges: $65.98
> Future Charges: $0.00
> Credit Card: xxxxxxxxxxx1002
The site should be back up soonish. I can't change the DNS entry that
points the website to the expired splash page until netsol processes the
renewal.
Upcoming domain expiration dates:
biomoby.org will expire Oct 1
bior.org will expire Nov 5
biosoap.org will expire Oct 9
-Chris
Peter wrote:
> Hi all,
>
> We appear to have a temporary problem with our biopython.org domain,
> which I trust the OBF admin team will address shortly.
>
> As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page
> and http://biopython.open-bio.org/DIST/ for the downloads.
>
> Source code is hosted separately on github,
> http://github.com/biopython/biopython/
>
> Apologies,
>
> Peter
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
From mitlox at op.pl Thu Aug 26 07:27:31 2010
From: mitlox at op.pl (xyz)
Date: Thu, 26 Aug 2010 21:27:31 +1000
Subject: [Biopython] Writting fasta file
In-Reply-To:
References: <4C74FCF0.4070401@op.pl>
Message-ID: <4C764FA3.6080805@op.pl>
On 25/08/10 23:08, Peter wrote:
>
> Hi "xyz",
>
> Did you try looking in the tutorial? i.e.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
>
> You could modify your code to use a generator expression like this:
>
> def make_rc(record):
> """Modifies a SeqRecord in place, and returns it."""
> record.seq = record.seq.reverse_complement()
> return record
> records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
> SeqIO.write(records, out_opts.outputFasta, "fasta")
>
> I also changed it to pass filenames directly to SeqIO - its shorter ;)
>
> See also this thread about adding a reverse complement
> method to the SeqRecord which would make this easier:
> http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html
>
> Peter
>
Thank you for your code it looks much better than mine.
In order to save memory is it possible to write each record ie. one by
one with SeqIO.write instead of all records at once?
From biopython at maubp.freeserve.co.uk Thu Aug 26 07:59:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 12:59:56 +0100
Subject: [Biopython] Writting fasta file
In-Reply-To: <4C764FA3.6080805@op.pl>
References: <4C74FCF0.4070401@op.pl>
<4C764FA3.6080805@op.pl>
Message-ID:
On Thu, Aug 26, 2010 at 12:27 PM, xyz wrote:
> On 25/08/10 23:08, Peter wrote:
>>
>> Hi "xyz",
>>
>> Did you try looking in the tutorial? i.e.
>>
>> http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
>>
>> You could modify your code to use a generator expression like this:
>>
>> def make_rc(record):
>> ? ? """Modifies a SeqRecord in place, and returns it."""
>> ? ? record.seq = record.seq.reverse_complement()
>> ? ? return record
>> records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
>> SeqIO.write(records, out_opts.outputFasta, "fasta")
>>
>> I also changed it to pass filenames directly to SeqIO - its shorter ;)
>
> Thank you for your code it looks much better than mine.
>
> In order to save memory is it possible to write each record ie. one by one
> with SeqIO.write instead of all records at once?
The code is already doing it one by one.
It uses a generator expression (rather than a list or list comprehension
which would put all the records into memory at once) to make the
reverse complemented records:
For writing FASTA files (and most other formats), SeqIO.write() only
needs to look at one record at a time, and won't load them all into
memory.
Peter
From chapmanb at 50mail.com Thu Aug 26 07:55:17 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Thu, 26 Aug 2010 07:55:17 -0400
Subject: [Biopython] Writting fasta file
In-Reply-To: <4C764FA3.6080805@op.pl>
References: <4C74FCF0.4070401@op.pl>
<4C764FA3.6080805@op.pl>
Message-ID: <20100826115517.GW23299@sobchak.mgh.harvard.edu>
Hello;
> >Did you try looking in the tutorial? i.e.
> >http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
> >
> >You could modify your code to use a generator expression like this:
> >
> >def make_rc(record):
> > """Modifies a SeqRecord in place, and returns it."""
> > record.seq = record.seq.reverse_complement()
> > return record
> >records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
> >SeqIO.write(records, out_opts.outputFasta, "fasta")
[...]
> In order to save memory is it possible to write each record ie. one
> by one with SeqIO.write instead of all records at once?
That's what Peter's code does. The write function pulls one record at
a time from the records generator. In addition to the Biopython
documentation, Andrew has a nice tutorial which goes into the
details of generators:
http://www.dalkescientific.com/writings/NBN/generators.html
Brad
From biopython at maubp.freeserve.co.uk Thu Aug 26 08:03:48 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 13:03:48 +0100
Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain
In-Reply-To: <4C764F81.1060100@sonsorol.org>
References:
<4C764F81.1060100@sonsorol.org>
Message-ID:
On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote:
>
> I manage or am the admin/technical/billing account holder for 24 domains,
> among them most of the open-bio.org ones.
>
> Biopython.org is one that I do not own. Actually since NetSol is offering to
> let me change DNS maybe I'm the technical contact - have to wait and see on
> this. Normally for domains I control netsol starts email nagging me
> constantly - never got emails about this one.
>
>
> However, Networksolutions allows *anyone* with a payment method to renew any
> domain for any reason.
>
> I've renewed biopython.org for a 2-year term, paying out of pocket like I do
> for all OBF domains so our $$ stays in our bank account.
>
>
>> Order Confirmation
>>
>> Order Number: 375229424
>> Today's Charges: $65.98
>> Future Charges: $0.00
>> Credit Card: xxxxxxxxxxx1002
>
> The site should be back up soonish. I can't change the DNS entry that points
> the website to the expired splash page until netsol processes the renewal.
>
> Upcoming domain expiration dates:
>
> biomoby.org will expire Oct 1
> bior.org will expire Nov 5
> biosoap.org will expire Oct 9
>
>
> -Chris
Thanks Chris :)
Will you be able to update the domain's contact details to be consistent
with the other Bio* domains?
Peter
From vishal4linux2 at gmail.com Thu Aug 26 08:16:20 2010
From: vishal4linux2 at gmail.com (vishal bhardwa)
Date: Thu, 26 Aug 2010 05:16:20 -0700
Subject: [Biopython] vishal bhardwa wants to chat
Message-ID:
-----------------------------------------------------------------------
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From biopython at maubp.freeserve.co.uk Thu Aug 26 08:28:18 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 13:28:18 +0100
Subject: [Biopython] vishal bhardwa wants to chat
In-Reply-To:
References:
Message-ID:
On Thu, Aug 26, 2010 at 1:16 PM, vishal bhardwa wrote:
> -----------------------------------------------------------------------
>
> vishal bhardwa wants to stay in better touch using some of Google's coolest new
> products.
>
> If you already have Gmail or Google Talk, visit ...
Hi all,
Vishal and other - please try not to sending these kinds of product or service
adverts to mailing lists.
Thank you,
Peter
From nje5 at georgetown.edu Thu Aug 26 21:43:08 2010
From: nje5 at georgetown.edu (Nathan J. Edwards)
Date: Thu, 26 Aug 2010 21:43:08 -0400
Subject: [Biopython] Problem with Bio.Entrez...
Message-ID: <4C77182C.40007@georgetown.edu>
Seems to be a problem with Entrez XML parsing:
from Bio import Entrez
Entrez.email = 'xxxyy at georgetown.edu'
handle = Entrez.einfo(db='pubmed')
result = Entrez.read(handle)
results in:
Traceback (most recent call last):
File "C:/Documents and Settings/Nathan/My
Documents/BCHB524/testing.py", line 5, in
result = Entrez.read(handle)
File
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py",
line 261, in read
record = handler.read(handle)
File
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line
150, in read
self.parser.ParseFile(handle)
File
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line
295, in endElementHandler
current[name] = value
TypeError: 'str' object does not support item assignment
error is in Parser.endElementHandler:
current = self.stack[-1]
try:
current.append(value)
except AttributeError:
295: current[name] = value
because current is the empty string "".
The problem is probably that the empty string shouldn't be on the stack,
given the logic here and elsewhere, but a simple test for the empty
string does get things working again.
current = self.stack[-1]
if current == "":
return
try:
current.append(value)
except AttributeError:
295: current[name] = value
Cheers!
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From mjldehoon at yahoo.com Thu Aug 26 22:40:52 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 26 Aug 2010 19:40:52 -0700 (PDT)
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C77182C.40007@georgetown.edu>
Message-ID: <108175.26561.qm@web62405.mail.re1.yahoo.com>
The problem is with the XML returned by NCBI.
Currently, the XML returned by einfo contains elements that are not described in the corresponding DTD (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The parser therefore doesn't know how to handle them.
Could you write an email to NCBI that einfo generates XML that is inconsistent with the corresponding DTD?
Best,
--Michiel.
--- On Thu, 8/26/10, Nathan J. Edwards wrote:
> From: Nathan J. Edwards
> Subject: [Biopython] Problem with Bio.Entrez...
> To: biopython at lists.open-bio.org
> Date: Thursday, August 26, 2010, 9:43 PM
>
> Seems to be a problem with Entrez XML parsing:
>
> from Bio import Entrez
> Entrez.email = 'xxxyy at georgetown.edu'
>
> handle = Entrez.einfo(db='pubmed')
> result = Entrez.read(handle)
>
> results in:
>
> Traceback (most recent call last):
> ? File "C:/Documents and Settings/Nathan/My
> Documents/BCHB524/testing.py", line 5, in
> ? ? result = Entrez.read(handle)
> ? File
> "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py",
> line 261, in read
> ? ? record = handler.read(handle)
> ? File
> "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py",
> line 150, in read
> ? ? self.parser.ParseFile(handle)
> ? File
> "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py",
> line 295, in endElementHandler
> ? ? current[name] = value
> TypeError: 'str' object does not support item assignment
>
> error is in Parser.endElementHandler:
>
> ? ? ? ? ? ? current =
> self.stack[-1]
> ? ? ? ? ? ? try:
> ? ? ? ? ? ? ? ?
> current.append(value)
> ? ? ? ? ? ? except
> AttributeError:
> 295:? ? ? ? ? ? current[name]
> = value
>
> because current is the empty string "".
>
> The problem is probably that the empty string shouldn't be
> on the stack, given the logic here and elsewhere, but a
> simple test for the empty string does get things working
> again.
>
> ? ? ? ? ? ? current =
> self.stack[-1]
> ??? ? ? if current == "":
> ??? ??? return
> ? ? ? ? ? ? try:
> ? ? ? ? ? ? ? ?
> current.append(value)
> ? ? ? ? ? ? except
> AttributeError:
> 295:? ? ? ? ? ? current[name]
> = value
>
>
> Cheers!
>
> - n
>
> -- Dr. Nathan Edwards? ? ? ? ?
> ? ? ? ? ? ? nje5 at georgetown.edu
> Department of Biochemistry and Molecular & Cellular
> Biology
> ? ? ? ? ???Georgetown
> University Medical Center
> Room 1215, Harris Building? ? ? ?
> ? Room 347, Basic Science
> 3300 Whitehaven St, NW? ? ? ? ?
> ? ? 3900 Reservoir Road, NW
> Washington DC 20007? ? ? ? ?
> ? ? ? ? ???Washington DC
> 20007
> Phone: 202-687-7042? ? ? ? ?
> ? ? ? ? ???Phone:
> 202-687-1618
> Fax: 202-687-0057? ? ? ? ? ?
> ? ? ? ? ? ???Fax:
> 202-687-7186
> _______________________________________________
> Biopython mailing list? -? Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
From nje5 at georgetown.edu Fri Aug 27 00:13:29 2010
From: nje5 at georgetown.edu (Nathan J. Edwards)
Date: Fri, 27 Aug 2010 00:13:29 -0400
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <108175.26561.qm@web62405.mail.re1.yahoo.com>
References: <108175.26561.qm@web62405.mail.re1.yahoo.com>
Message-ID: <4C773B69.3050308@georgetown.edu>
On 8/26/2010 10:40 PM, Michiel de Hoon wrote:
> The problem is with the XML returned by NCBI. Currently, the XML
> returned by einfo contains elements that are not described
> in the corresponding DTD
> (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The
> parser therefore doesn't know how to handle them. Could you write an
> email to NCBI that einfo generates XML that is inconsistent with the
> corresponding DTD?
Sent.
It would be nice (IWBN) if the parser threw an exception that indicated
that the returned XML didn't validate...at least then the (very
cryptic!) error message wouldn't look like a logic error in the parser.
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From nje5 at georgetown.edu Fri Aug 27 00:39:06 2010
From: nje5 at georgetown.edu (Nathan J. Edwards)
Date: Fri, 27 Aug 2010 00:39:06 -0400
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C773B69.3050308@georgetown.edu>
References: <108175.26561.qm@web62405.mail.re1.yahoo.com>
<4C773B69.3050308@georgetown.edu>
Message-ID: <4C77416A.6030906@georgetown.edu>
On 8/27/2010 12:13 AM, Nathan J. Edwards wrote:
>
> It would be nice (IWBN) if the parser threw an exception that indicated
> that the returned XML didn't validate...at least then the (very
> cryptic!) error message wouldn't look like a logic error in the parser.
Actually, after wading though the Parser.py code some more, the bad
element is clearly detected, and an attempt is made to ignore it (the
empty string), which then subsequently leads to the TypeError exception
in endElementHandler.
Maybe the test and return of my first email is sufficient to deal with
the empty strings inserted as part of the "ignore it" strategy.
And, given the frequency with which NCBI seems to break these things, I
_do_ prefer the "ignore it" strategy, if it works. :-)
Cheers!
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From biopython at maubp.freeserve.co.uk Fri Aug 27 04:32:57 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Aug 2010 09:32:57 +0100
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C77416A.6030906@georgetown.edu>
References: <108175.26561.qm@web62405.mail.re1.yahoo.com>
<4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu>
Message-ID:
On Fri, Aug 27, 2010 at 5:39 AM, Nathan J. Edwards wrote:
> On 8/27/2010 12:13 AM, Nathan J. Edwards wrote:
>>
>> It would be nice (IWBN) if the parser threw an exception that indicated
>> that the returned XML didn't validate...at least then the (very
>> cryptic!) error message wouldn't look like a logic error in the parser.
>
> Actually, after wading though the Parser.py code some more, the bad element
> is clearly detected, and an attempt is made to ignore it (the empty string),
> which then subsequently leads to the TypeError exception in
> endElementHandler.
I'd suggest issuing a warning for the bad element, rather than silently
ignoring it.
> Maybe the test and return of my first email is sufficient to deal with the
> empty strings inserted as part of the "ignore it" strategy.
>
> And, given the frequency with which NCBI seems to break these things,
> I _do_ prefer the "ignore it" strategy, if it works. :-)
Michiel - does Nathan's fix make sense? We should probably save an example
of this broken XML for a unit test...
Nathan - have you notified the NCBI about this? I assume you would get
an error putting the XML through a validator - if you haven't already done
so that would be worthwhile. Or would you rather one of us contact them?
Thanks,
Peter
From biopython at maubp.freeserve.co.uk Fri Aug 27 04:57:04 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Aug 2010 09:57:04 +0100
Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain
In-Reply-To: <4C764F81.1060100@sonsorol.org>
References:
<4C764F81.1060100@sonsorol.org>
Message-ID:
On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote:
>
> I manage or am the admin/technical/billing account holder for 24
> domains, among them most of the open-bio.org ones. ... I've
> renewed biopython.org for a 2-year term, ... The site should be
> back up soonish.
Thanks for the speedy response Chris - www.biopython.org is back up
now. If anyone is still having trouble, please allow another day or so for
DNS servers to update.
As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page
and http://biopython.open-bio.org/DIST/ for the downloads.
Source code is hosted separately on github,
http://github.com/biopython/biopython/
Peter
From vishal4linux2 at gmail.com Fri Aug 27 05:41:33 2010
From: vishal4linux2 at gmail.com (vishal bhardwa)
Date: Fri, 27 Aug 2010 15:11:33 +0530
Subject: [Biopython] module pylab problem on ceton
Message-ID:
hello friends,
how i can install pylab please give any solution i m useing CentOs operating
system.
thanks in advance
vishal
From biopython at maubp.freeserve.co.uk Fri Aug 27 05:58:51 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Aug 2010 10:58:51 +0100
Subject: [Biopython] module pylab problem on ceton
In-Reply-To:
References:
Message-ID:
On Fri, Aug 27, 2010 at 10:41 AM, vishal bhardwa
wrote:
> hello friends,
> how i can install pylab please give any solution i m useing CentOs operating
> system.
This isn't really a Biopython question. Try:
http://matplotlib.sourceforge.net/users/installing.html
Peter
From nje5 at georgetown.edu Fri Aug 27 12:10:49 2010
From: nje5 at georgetown.edu (Nathan Edwards)
Date: Fri, 27 Aug 2010 12:10:49 -0400
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To:
References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu>
Message-ID: <4C77E389.7080006@georgetown.edu>
> I'd suggest issuing a warning for the bad element, rather than silently
> ignoring it.
Except that I find the warning infrastructure pretty hard to use when I
need to turn something off.
Other alternatives providing a switch to choose between throwing an
exception (probably the default) or silently coping.
>> And, given the frequency with which NCBI seems to break these things,
>> I _do_ prefer the "ignore it" strategy, if it works. :-)
>
> Nathan - have you notified the NCBI about this? I assume you would get
> an error putting the XML through a validator - if you haven't already done
> so that would be worthwhile. Or would you rather one of us contact them?
Yes, NCBI has been notified and I just received a response that the
developers have been notified.
> I will bring this to our developers' attention. However, I will not
> be able to provide your with any ETA of the correction/fix or other
> comparable actions at this time.
Visual inspection is sufficient to verify the element is not mentioned
in the DTD, though I could fire up a validating parser I guess. Just did
and it confirms the error.
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From mjldehoon at yahoo.com Sat Aug 28 03:47:25 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 28 Aug 2010 00:47:25 -0700 (PDT)
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C77E389.7080006@georgetown.edu>
Message-ID: <226633.67137.qm@web62407.mail.re1.yahoo.com>
I think that for Biopython release 1.55, we should silently ignore this error using the fix proposed by Nathan. After the release is out, I suggest we add an optional argument "validate" to the read() and parse() function, defaulting to True. If validate is True, then read()/parse() raise an error if it finds elements in the XML that are not represented in the DTD. If validate is False, then such elements are silently ignored. This will require some other minor changes to the parser, so I'd like to do this after 1.55 is out.
--Michiel.
--- On Fri, 8/27/10, Nathan Edwards wrote:
> From: Nathan Edwards
> Subject: Re: [Biopython] Problem with Bio.Entrez...
> To: "Peter"
> Cc: "Michiel de Hoon" , biopython at lists.open-bio.org
> Date: Friday, August 27, 2010, 12:10 PM
>
> > I'd suggest issuing a warning for the bad element,
> rather than silently
> > ignoring it.
>
> Except that I find the warning infrastructure pretty hard
> to use when I need to turn something off.
>
> Other alternatives providing a switch to choose between
> throwing an exception (probably the default) or silently
> coping.
>
> >> And, given the frequency with which NCBI seems to
> break these things,
> >> I _do_ prefer the "ignore it" strategy, if it
> works. :-)
> >
> > Nathan - have you notified the NCBI about this? I
> assume you would get
> > an error putting the XML through a validator - if you
> haven't already done
> > so that would be worthwhile. Or would you rather one
> of us contact them?
>
> Yes, NCBI has been notified and I just received a response
> that the developers have been notified.
>
> > I will bring this to our developers' attention.
> However, I will not
> > be able to provide your with any ETA of the
> correction/fix or other
> > comparable actions at this time.
>
> Visual inspection is sufficient to verify the element is
> not mentioned in the DTD, though I could fire up a
> validating parser I guess. Just did and it confirms the
> error.
>
> - n
>
> -- Dr. Nathan Edwards? ? ? ? ?
> ? ? ? ? ? ? nje5 at georgetown.edu
> Department of Biochemistry and Molecular & Cellular
> Biology
> ? ? ? ? ???Georgetown
> University Medical Center
> Room 1215, Harris Building? ? ? ?
> ? Room 347, Basic Science
> 3300 Whitehaven St, NW? ? ? ? ?
> ? ? 3900 Reservoir Road, NW
> Washington DC 20007? ? ? ? ?
> ? ? ? ? ???Washington DC
> 20007
> Phone: 202-687-7042? ? ? ? ?
> ? ? ? ? ???Phone:
> 202-687-1618
> Fax: 202-687-0057? ? ? ? ? ?
> ? ? ? ? ? ???Fax:
> 202-687-7186
>
From biopython at maubp.freeserve.co.uk Sat Aug 28 07:32:03 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 28 Aug 2010 12:32:03 +0100
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <226633.67137.qm@web62407.mail.re1.yahoo.com>
References: <4C77E389.7080006@georgetown.edu>
<226633.67137.qm@web62407.mail.re1.yahoo.com>
Message-ID:
On Sat, Aug 28, 2010 at 8:47 AM, Michiel de Hoon wrote:
> I think that for Biopython release 1.55, we should silently ignore this
> error using the fix proposed by Nathan. After the release is out, I
> suggest we add an optional argument "validate" to the read() and
> parse() function, defaulting to True. If validate is True, then read()/
> parse() raise an error if it finds elements in the XML that are not
> represented in the DTD. If validate is False, then such elements
> are silently ignored. This will require some other minor changes
> to the parser, so I'd like to do this after 1.55 is out.
>
> --Michiel.
Sounds good :)
Peter
From p.j.a.cock at googlemail.com Tue Aug 31 19:00:37 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 1 Sep 2010 00:00:37 +0100
Subject: [Biopython] Biopython 1.55 released
Message-ID:
Dear Biopythoneers,
After the beta earlier this month (thank you to everyone who
helped test this), we?ve just released Biopython 1.55 . For
full details see:
http://news.open-bio.org/news/2010/08/biopython-1-55-released/
Note we are phasing out support for Python 2.4. We will continue
to support it for at least one further release (i.e. Biopython 1.56).
This could be delayed given feedback from our users (e.g. if this
proves to be a problem in combination with other libraries or a
popular Linux distribution).
(At least) 12 people have contributed to this release, including
6 new people ? thank you all:
* Andres Colubri (first contribution)
* Carlos Rios Vera (first contribution)
* Claude Paroz (first contribution)
* Cymon Cox
* Eric Talevich
* Frank Kauff
* Joao Rodrigues (first contribution)
* Konstantin Okonechnikov (first contribution)
* Michiel de Hoon
* Nathan Edwards (first contribution)
* Peter Cock
* Tiago Antao
Source distributions and Windows installers are available
from the downloads page on the Biopython website:
http://www.biopython.org/wiki/Download
As usual, feedback is most welcome on the mailing lists
(or bugzilla).
Regards,
Peter
P.S. You can follow Biopython on Twitter,
http://twitter.com/biopython
From Achim.Treumann at NEPAF.com Sun Aug 1 01:53:17 2010
From: Achim.Treumann at NEPAF.com (Achim Treumann)
Date: Sun, 1 Aug 2010 02:53:17 +0100
Subject: [Biopython] problem with SeqIO.index() and get_raw
References: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>
Message-ID: <01798D2396253A449511F31F1CDE83550C3E6D@srv1.NEPAF.local>
Hi Peter, Jordan andd others,
many thanks for the fast replies.
You are obviously right - installing 1.54 got me rolling.
I now noticed that the tutorial I was working with was indeed 1.54 (should have checked that when I downloaded it separately from the distribution). When I was going through the tutorial I did not realise that the version I was working with was not 1.54... Don't think that it would be essential to put this into the FAQ - neither google nor searching this discussion list brought up other people who were struggling with this, I must have been the only one too thick to check version numbers :-)
Thanks a lot again for your rapid help,
Achim
-----Original Message-----
From: p.j.a.cock at googlemail.com on behalf of Peter
Sent: Sat 31/07/2010 18:16
To: Achim Treumann
Cc: biopython at lists.open-bio.org
Subject: Re: [Biopython] problem with SeqIO.index() and get_raw
On Sat, Jul 31, 2010 at 7:05 AM, Achim Treumann
wrote:
> Dear all,
>
> I am new to biopython and trying to familiarise myself with its utilities.
> When I was trying to parse a swissprot.dat file to then copy the full
> data back using the get_raw attribute, I got stuck (Biopython 1.53,
> Python 2.6 on WinXP).
>
>...
>
> As I am typing, I realise that get_raw might only have been
> implemented in Biopython 1.54... I will post this anyway, and if
> upgrading sorts it, I will send a reply.
Hi Achim,
Well guessed. Yes, get_raw was added in Biopython 1.54, see
http://news.open-bio.org/news/2010/05/biopython-release-154/
Are you reading the current tutorial on line (rather than the
version shipped with Biopython 1.53)? It does mention this,
although maybe it could be in the FAQ as well... would that
help?
Peter
From rmb32 at cornell.edu Sun Aug 1 19:17:14 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Sun, 01 Aug 2010 12:17:14 -0700
Subject: [Biopython] GMOD Evo Hackathon Open Call for Participation
Message-ID: <4C55C83A.3060700@cornell.edu>
We are seeking participants for the GMOD Tools for Evolutionary Biology
Hackathon, held November 8-12, 2010 at the US National Evolutionary
Synthesis Center (NESCent) in Durham, NC.
This hackathon targets three critical gaps in the capabilities of the
GMOD toolbox that currently limit its utility for evolutionary research:
1. Visualization of comparative genomics data
2. Visualization of phylogenetic data and trees
3. Support for population diversity and phenotype data
If you are interested in these areas and have relevant expertise, you
are strongly encouraged to apply. Relevant areas of expertise include
more than just software development: if you are a GMOD power user,
visualization guru, domain expert (comparative, phylogenetics,
population, ...), or documentation wizard, then your skills are needed!
How To Apply:
Fill out the online application form at http://bit.ly/gmodevohack.
Applications are due August 25.
About GMOD:
GMOD is an intercompatible suite of open-source software components for
storing, managing, analyzing, and visualizing genome-scale data. GMOD
includes many widely-used software components: GBrowse and JBrowse, both
genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a
generic and modular database schema; CMap, a comparative map viewer; as
well as many other components including Apollo, MAKER, BioMart,
InterMine, and Galaxy. We hope to extend the functionality of existing
GMOD components, and integrate new components as well.
About Hackathons:
A hackathon is an intense event at which a group of programmers with
different backgrounds and skills collaborate hands-on and face-to-face
to develop working code that is of utility to the community as a whole.
The mix of people will include domain experts and computer-savvy end-users.
More details about the event, its motivation, organization, procedures,
and attendees, as well as URLs to the hackathon and related websites are
included below.
Sincerely,
The GMOD EvoHack Organizing Committee (and project affiliations as
relevant):
Nicole Washington, Chair (LBNL, modENCODE, Phenote)
Robert Buels (SGN, Chado NatDiv)
Scott Cain (OICR, GMOD)
Dave Clements (NESCent, GMOD)
Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv)
Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)
-----------------------------
About the GMOD Evo Hackathon
Overview
We are organizing a hackathon to fill critical gaps in the capabilities
of the Generic Model Organism Database (GMOD) toolbox that currently
limit its utility for evolutionary research. Specifically, we will focus
on tools for
1) viewing comparative genomics data;
2) visualizing phylogenomic data; and
3) supporting population diversity data and phenotype annotation.
The event will be hosted at NESCent and bring together a group of about
20+ software developers, end-user representatives, and documentation
experts who would otherwise not meet. The participants will include key
developers of GMOD components that currently lack features critical for
emerging evolutionary biology research, developers of informatics tools
in evolutionary research that lack GMOD integration, and
informatics-savvy biologists who can represent end-user requirements.
The event will provide a unique opportunity to infuse the GMOD developer
community with a heightened awareness of unmet needs in evolutionary
biology that GMOD components have the potential to fill, and for tool
developers in evolutionary biology to better understand how best to
extend or integrate with already existing GMOD components.
Before the Event
Discussion of ideas and sometimes even design actually starts well
before the hackathon, on mailing lists, wiki pages, and conference calls
set up among accepted attendees. This advance work lays the foundation
for participants to be productive from the very first day. This also
means that participants should be willing to contribute some time in
advance of the hackathon itself to participate in this preparatory
discussion.
During the Event
Typically, hackathon participants use the morning of the first day of
the event to organize themselves into working groups of between 3 and 6
people, each with a focused implementation objective. Ideas and
objectives are discussed, and attendees coalesce around the projects in
which they have the most experience or interest.
Deliverables / Event Results
The meeting's attendance, working groups, and outcomes will be fully
logged and documented on the GMOD wiki (http://gmod.org). Each working
group during the event will typically have its own wiki page, linked
from the main EvoHack page, where it documents its minutes and design
notes, and provides links to the code and documentation it produces.
Also, since GMOD and NESCent are both committed to open source
principles, all code and documentation produced by participants during
the hackathon must be published under an OSI-approved open source
license. As contributions to existing GMOD tools, all hackathon products
will most likely satisfy this requirement automatically.
NESCent
This event is sponsored by the US National Evolutionary Synthesis Center
(NESCent, http://www.nescent.org) through its Informatics Whitepapers
program (http://www.nescent.org/informatics/whitepapers.php). NESCent
promotes the synthesis of information, concepts and knowledge to address
significant, emerging, or novel questions in evolutionary science and
its applications. NESCent achieves this by supporting research and
education across disciplinary, institutional, geographic, and
demographic boundaries (see http://www.nescent.org/science/proposals.php).
Links
Main GMOD EvoHack page, and full proposal:
http://gmod.org/wiki/GMOD_Evo_Hackathon
NESCent: http://www.nescent.org/
GMOD: http://gmod.org
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application: http://bit.ly/gmodevohack
--
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback
From phosse1 at students.towson.edu Tue Aug 3 23:53:33 2010
From: phosse1 at students.towson.edu (Parsa Hosseini)
Date: Tue, 3 Aug 2010 19:53:33 -0400
Subject: [Biopython] Biopython SUBA interface
Message-ID:
Hi everyone,
I have some python cgi scripts which interface with the Arabidopsis thaliana
SUBA database.
I'd like to contribute such scripts (and hopefully much more). I was curious
how I can go about submitting such code and/or if anyone would find such a
script/interface of use?
Thanks alot,
--------------------------------------------
Parsa Hosseini
Parsa.Hosseini at ars.usda.gov
http://tiger.towson.edu/~phosse1/
301-875-6525
From biopython at maubp.freeserve.co.uk Wed Aug 4 08:12:07 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 4 Aug 2010 09:12:07 +0100
Subject: [Biopython] Biopython SUBA interface
In-Reply-To:
References:
Message-ID:
On Wed, Aug 4, 2010 at 12:53 AM, Parsa Hosseini
wrote:
> Hi everyone,
> I have some python cgi scripts which interface with the Arabidopsis
> thaliana SUBA database.
> I'd like to contribute such scripts (and hopefully much more). I was
> curious how I can go about submitting such code and/or if anyone
> would find such a script/interface of use?
> Thanks alot,
Hi Parsa,
Are these stand alone scripts that you would use at the command
line, or a Python module you can use in a Python script? Either
way we could include them...
I had a quick look at http://suba.plantenergy.uwa.edu.au/ and
it isn't clear if they have an official API. Are you doing this by
building the HTTP request and then parsing the HTML results?
If so, that is worrying for two reasons. First, it is fragile and
will need updates whenever the site makes changes to their
layout (something that has happened to other HTML parsers
in Biopython that have since been deprecated and removed).
Secondly, in the absence of an official API are there any
usage guidelines? The SUBA team may not be happy with
people running scripts that could use up far more resources
than several people using the website interface.
As to would anyone find such a script/interface of use, well,
personally probably not in my current work. But I'm sure there
are people using Biopython working on plant genomes and
Arabidopsis thaliana.
Regards,
Peter
From biopython at maubp.freeserve.co.uk Wed Aug 11 15:14:27 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 11 Aug 2010 16:14:27 +0100
Subject: [Biopython] Using a dictionary rather than list for hierachy in
Bio.SCOP.Cla
Message-ID:
Dear Biopythoneers - especially those using SCOP,
Jeffrey Finkelstein has proposed a change to the Record class in Bio.SCOP.Cla
to use a dictionary rather than a list for the hierarchy member to better match
the SCOP specification, see his email quoted below and Bug 3109 for details:
http://bugzilla.open-bio.org/show_bug.cgi?id=3109
This would be a backwards incompatible change, so feedback from anyone
using Biopython's SCOP module would be important in deciding how to
proceed. Comments please?
Thank you,
Peter
On the dev list Jeffrey Finkelstein wrote:
> I have submitted a bug report and a patch for a current feature of the
> Bio.SCOP.Cla module that makes using it somewhat difficult. Specifically,
> the Bio.Scop.Cla.Record class has a "hierarchy" member which is currently a
> list, but should be a dictionary, according to the SCOP parseable
> classification file format "specification" (it is an informal specification)
> here:
> http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html#scop-parseable-files.
>
> For a usage example, see the comments I have made at:
> http://bugzilla.open-bio.org/show_bug.cgi?id=3109
>
> I have CC'ed the original author of the module. Gavin (or anyone else), do
> you have any objections to this change?
>
> Jeffrey
See http://lists.open-bio.org/pipermail/biopython-dev/2010-August/008134.html
From biopython at maubp.freeserve.co.uk Thu Aug 19 15:43:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 19 Aug 2010 16:43:56 +0100
Subject: [Biopython] Biopython 1.55 beta released
Message-ID:
Dear Biopythoneers,
We?ve just released a beta of Biopython 1.55 for user testing, as
announced on the news server (which has RSS and atom feeds) and on
twitter:
http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/
http://twitter.com/biopython
Since Biopython 1.54 was released three months ago, we?ve made a good
start on work for Python 3 support (via the 2to3 script), but as a
side effect of this we?ve had to update quite a lot of the older parts
of the library. Although the unit tests are all fine, there is a small
but real chance that we?ve accidentally broken things ? which is why
we?re doing this beta release.
In terms of new features, the most noticeable highlight is that the
command line tool application wrapper classes are now executable,
which should make it much easier to call external tools. This is
described in the updated documentation.
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
Note we are phasing out support for Python 2.4. We will continue to
support it for at least one further release (i.e. Biopython 1.56).
This could be delayed given feedback from our users (e.g. if this
proves to be a problem in combination with other libraries or a
popular Linux distribution).
(At least) 10 people have contributed to this release (so far),
including 5 new people - thank you all:
* Andres Colubri (first contribution)
* Carlos Rios Vera (first contribution)
* Claude Paroz (first contribution)
* Eric Talevich
* Frank Kauff
* Joao Rodrigues (first contribution)
* Konstantin Okonechnikov (first contribution)
* Michiel de Hoon
* Peter Cock
* Tiago Antao
Source distributions and Windows installers are available from the
downloads page on the Biopython website:
http://www.biopython.org/wiki/Download
Feedback is welcome through the mailing lists (or bugzilla),
especially if you find something that doesn't work.
Thank you,
Peter
From rmb32 at cornell.edu Thu Aug 19 17:09:45 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 19 Aug 2010 10:09:45 -0700
Subject: [Biopython] reminder: Aug 25 deadline for GMOD Hackathon application
Message-ID: <4C6D6559.3080809@cornell.edu>
Hi all,
This is your one-week reminder: the deadline for open applications to
the GMOD Evo hackathon is Wednesday, August 25th.
Rob
========================================
We are seeking participants for the GMOD Tools for Evolutionary Biology
Hackathon, held November 8-12, 2010 at the US National Evolutionary
Synthesis Center (NESCent) in Durham, NC.
This hackathon targets three critical gaps in the capabilities of the
GMOD toolbox that currently limit its utility for evolutionary research:
1. Visualization of comparative genomics data
2. Visualization of phylogenetic data and trees
3. Support for population diversity and phenotype data
If you are interested in these areas and have relevant expertise, you
are strongly encouraged to apply. Relevant areas of expertise include
more than just software development: if you are a GMOD power user,
visualization guru, domain expert (comparative, phylogenetics,
population, ...), or documentation wizard, then your skills are needed!
How To Apply:
Fill out the online application form at http://bit.ly/gmodevohack.
Applications are due August 25.
About GMOD:
GMOD is an intercompatible suite of open-source software components for
storing, managing, analyzing, and visualizing genome-scale data. GMOD
includes many widely-used software components: GBrowse and JBrowse, both
genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a
generic and modular database schema; CMap, a comparative map viewer; as
well as many other components including Apollo, MAKER, BioMart,
InterMine, and Galaxy. We hope to extend the functionality of existing
GMOD components, and integrate new components as well.
About Hackathons:
A hackathon is an intense event at which a group of programmers with
different backgrounds and skills collaborate hands-on and face-to-face
to develop working code that is of utility to the community as a whole.
The mix of people will include domain experts and computer-savvy end-users.
More details about the event, its motivation, organization, procedures,
and attendees, as well as URLs to the hackathon and related websites are
included below.
Sincerely,
The GMOD EvoHack Organizing Committee (and project affiliations as
relevant):
Nicole Washington, Chair (LBNL, modENCODE, Phenote)
Robert Buels (SGN, Chado NatDiv)
Scott Cain (OICR, GMOD)
Dave Clements (NESCent, GMOD)
Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv)
Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)
-----------------------------
About the GMOD Evo Hackathon
Overview
We are organizing a hackathon to fill critical gaps in the capabilities
of the Generic Model Organism Database (GMOD) toolbox that currently
limit its utility for evolutionary research. Specifically, we will focus
on tools for
1) viewing comparative genomics data;
2) visualizing phylogenomic data; and
3) supporting population diversity data and phenotype annotation.
The event will be hosted at NESCent and bring together a group of about
20+ software developers, end-user representatives, and documentation
experts who would otherwise not meet. The participants will include key
developers of GMOD components that currently lack features critical for
emerging evolutionary biology research, developers of informatics tools
in evolutionary research that lack GMOD integration, and
informatics-savvy biologists who can represent end-user requirements.
The event will provide a unique opportunity to infuse the GMOD developer
community with a heightened awareness of unmet needs in evolutionary
biology that GMOD components have the potential to fill, and for tool
developers in evolutionary biology to better understand how best to
extend or integrate with already existing GMOD components.
Before the Event
Discussion of ideas and sometimes even design actually starts well
before the hackathon, on mailing lists, wiki pages, and conference calls
set up among accepted attendees. This advance work lays the foundation
for participants to be productive from the very first day. This also
means that participants should be willing to contribute some time in
advance of the hackathon itself to participate in this preparatory
discussion.
During the Event
Typically, hackathon participants use the morning of the first day of
the event to organize themselves into working groups of between 3 and 6
people, each with a focused implementation objective. Ideas and
objectives are discussed, and attendees coalesce around the projects in
which they have the most experience or interest.
Deliverables / Event Results
The meeting's attendance, working groups, and outcomes will be fully
logged and documented on the GMOD wiki (http://gmod.org). Each working
group during the event will typically have its own wiki page, linked
from the main EvoHack page, where it documents its minutes and design
notes, and provides links to the code and documentation it produces.
Also, since GMOD and NESCent are both committed to open source
principles, all code and documentation produced by participants during
the hackathon must be published under an OSI-approved open source
license. As contributions to existing GMOD tools, all hackathon products
will most likely satisfy this requirement automatically.
NESCent
This event is sponsored by the US National Evolutionary Synthesis Center
(NESCent, http://www.nescent.org) through its Informatics Whitepapers
program (http://www.nescent.org/informatics/whitepapers.php). NESCent
promotes the synthesis of information, concepts and knowledge to address
significant, emerging, or novel questions in evolutionary science and
its applications. NESCent achieves this by supporting research and
education across disciplinary, institutional, geographic, and
demographic boundaries (see http://www.nescent.org/science/proposals.php).
Links
Main GMOD EvoHack page, and full proposal:
http://gmod.org/wiki/GMOD_Evo_Hackathon
NESCent: http://www.nescent.org/
GMOD: http://gmod.org
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application: http://bit.ly/gmodevohack
--
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback
From biopython at maubp.freeserve.co.uk Mon Aug 23 16:05:43 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 23 Aug 2010 17:05:43 +0100
Subject: [Biopython] Biopython 1.55 beta released
In-Reply-To:
References:
Message-ID:
On Thu, Aug 19, 2010 at 4:43 PM, Peter wrote:
> Dear Biopythoneers,
>
> We?ve just released a beta of Biopython 1.55 for user testing, as
> announced on the news server (which has RSS and atom feeds) and on
> twitter:
> http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/
> http://twitter.com/biopython
>
> ...
>
> Feedback is welcome through the mailing lists (or bugzilla),
> especially if you find something that doesn't work.
Hi all,
Is no news good news? So far there have been no problems reported. I've
had a least one person report (off list) that the windows installers worked
fine for them on Windows XP (32bit).
Any other feedback on the beta?
Thanks
Peter
From cgohlke at uci.edu Mon Aug 23 20:43:20 2010
From: cgohlke at uci.edu (Christoph Gohlke)
Date: Mon, 23 Aug 2010 13:43:20 -0700
Subject: [Biopython] Biopython 1.55 beta released (Peter)
In-Reply-To:
References:
Message-ID: <4C72DD68.20309@uci.edu>
> Dear Biopythoneers,
>
> We?ve just released a beta of Biopython 1.55 for user testing, as
> announced on the news server (which has RSS and atom feeds) and on
> twitter:
> http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/
> http://twitter.com/biopython
>
> Since Biopython 1.54 was released three months ago, we?ve made a good
> start on work for Python 3 support (via the 2to3 script), but as a
> side effect of this we?ve had to update quite a lot of the older parts
> of the library. Although the unit tests are all fine, there is a small
> but real chance that we?ve accidentally broken things ? which is why
> we?re doing this beta release.
>
> In terms of new features, the most noticeable highlight is that the
> command line tool application wrapper classes are now executable,
> which should make it much easier to call external tools. This is
> described in the updated documentation.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>
> Note we are phasing out support for Python 2.4. We will continue to
> support it for at least one further release (i.e. Biopython 1.56).
> This could be delayed given feedback from our users (e.g. if this
> proves to be a problem in combination with other libraries or a
> popular Linux distribution).
>
> (At least) 10 people have contributed to this release (so far),
> including 5 new people - thank you all:
>
> * Andres Colubri (first contribution)
> * Carlos Rios Vera (first contribution)
> * Claude Paroz (first contribution)
> * Eric Talevich
> * Frank Kauff
> * Joao Rodrigues (first contribution)
> * Konstantin Okonechnikov (first contribution)
> * Michiel de Hoon
> * Peter Cock
> * Tiago Antao
>
> Source distributions and Windows installers are available from the
> downloads page on the Biopython website:
> http://www.biopython.org/wiki/Download
>
> Feedback is welcome through the mailing lists (or bugzilla),
> especially if you find something that doesn't work.
>
> Thank you,
>
> Peter
>
Looks good. There are no test failures for the 32/64 bit msvc9 builds
for Python 2.6/2.7 and numpy 1.4.1/1.5b2.
--
Christoph
From biopython at maubp.freeserve.co.uk Tue Aug 24 09:26:17 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 24 Aug 2010 10:26:17 +0100
Subject: [Biopython] Biopython 1.55 beta released (Peter)
In-Reply-To: <4C72DD68.20309@uci.edu>
References:
<4C72DD68.20309@uci.edu>
Message-ID:
On Mon, Aug 23, 2010 at 9:43 PM, Christoph Gohlke wrote:
>
> Looks good. There are no test failures for the 32/64 bit msvc9 builds for
> Python 2.6/2.7 and numpy 1.4.1/1.5b2.
>
Thank you - as far as I know you are the only person building Biopython
on Windows 64 bit, so that is reassuring.
Peter
From schaefer at rostlab.org Tue Aug 24 13:37:19 2010
From: schaefer at rostlab.org (Christian Schaefer)
Date: Tue, 24 Aug 2010 15:37:19 +0200
Subject: [Biopython] Contact Area Difference as an alternative to RMSD
Message-ID: <4C73CB0F.7060100@rostlab.org>
Hi,
I'd be interested in the above alternative measure for structural
difference as desribed in [1]. I know that there exists an
implementation to make it useable via Python: It's a wrapper around
icm-browser [2] implemented in the Biskit library [3]. However, it's a
real pain to get the whole pipeline working and I haven't succeeded so far.
So, does anybody know of an alternative implementation of CAD that is
easy to use via python?
Thanks,
Chris
[1] Abagyan RA, Totrov MM. Contact area difference (CAD): a robust
measure to evaluate accuracy of protein models. J Mol Biol. 1997 May
9;268(3):678-85.
[2] http://www.molsoft.com/index.html
[3] http://biskit.pasteur.fr/
--
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
Boltzmannstr. 3
D-85748 Garching b. Muenchen
Germany
http://www.rostlab.org/~schaefer
From vishal4linux2 at gmail.com Wed Aug 25 11:12:38 2010
From: vishal4linux2 at gmail.com (vishal bhardwa)
Date: Wed, 25 Aug 2010 16:42:38 +0530
Subject: [Biopython] installing Biopython in Centos
Message-ID:
hello sir/mam
how can i install biopython on Centos System Pls tell me any
solution
Vishal Bhardwaj
Mb:-91-7696619429
From mitlox at op.pl Wed Aug 25 11:22:24 2010
From: mitlox at op.pl (xyz)
Date: Wed, 25 Aug 2010 21:22:24 +1000
Subject: [Biopython] Writting fasta file
Message-ID: <4C74FCF0.4070401@op.pl>
Hello,
the following code saves a multiple fasta file in a list and after
reverse complement it writes the content back in a fasta file.
in_handle = open(opts.inputFasta, "r")
records = list(SeqIO.parse(in_handle, "fasta"))
for record in records:
record.seq = record.seq.reverse_complement()
out_handle = open(opts.outputFasta, "w")
SeqIO.write(records, out_handle, "fasta")
How is it possible to do it without a list?
Thank you in advance.
From mitlox at op.pl Wed Aug 25 12:02:00 2010
From: mitlox at op.pl (xyz)
Date: Wed, 25 Aug 2010 22:02:00 +1000
Subject: [Biopython] installing Biopython in Centos
In-Reply-To:
References:
Message-ID: <4C750638.8090007@op.pl>
Hi,
I use Cent OS, but Python 2.6.5 is in my home directory installed and
following both methods working fine for me:
http://biopython.org/wiki/Download#Installation_Instructions
http://biopython.org/wiki/Download#Easy_Install
Cheers,
On 25/08/10 21:12, vishal bhardwa wrote:
> hello sir/mam
>
> how can i install biopython on Centos System Pls tell me any
> solution
>
>
>
>
>
> Vishal Bhardwaj
> Mb:-91-7696619429
> _______________________________________________
> 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 Aug 25 12:59:58 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 25 Aug 2010 13:59:58 +0100
Subject: [Biopython] installing Biopython in Centos
In-Reply-To:
References:
Message-ID:
On Wed, Aug 25, 2010 at 12:12 PM, vishal bhardwa
wrote:
> hello sir/mam
>
> ? ? ? ? how can i install biopython on Centos System Pls tell me any
> solution
>
> Vishal Bhardwaj
> Mb:-91-7696619429
Hello Vishal,
CentOS currently comes with Python 2.4, so you should be able
to use that and install Biopython from source as normal.
However, Python 2.4 is now very out of date so many packages
don't support it anymore. It lacks a few useful modules like
SQLite3 support and ElementTree for XML parser. It is also
noticeable slower than more recent releases, but that may not
be an issue for you.
NumPy still supports Python 2.4, and Biopython still supports
Python 2.4, but we plan to drop support for Python 2.4 after
Biopython 1.56 is released (which will be some time later this
year).
We have servers running CentOS release 5.4 (Final) and
CentOS 5.5 (final) where the administrator has installed
Python 2.6 at /usr/local/bin/python2.6 or Python 2.7 at
/usr/local/bin/python2.7 and Biopython works fine there.
It would be worth considering installing Python 2.6 or 2.7.
Ask your systems administrator if they can do this for you,
or do it yourself under your user directory as "xyz" suggested.
Peter
From biopython at maubp.freeserve.co.uk Wed Aug 25 13:08:41 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 25 Aug 2010 14:08:41 +0100
Subject: [Biopython] Writting fasta file
In-Reply-To: <4C74FCF0.4070401@op.pl>
References: <4C74FCF0.4070401@op.pl>
Message-ID:
On Wed, Aug 25, 2010 at 12:22 PM, xyz wrote:
> Hello,
> the following code saves a multiple fasta file in a list and after reverse
> complement it writes the content back in a fasta file.
>
> ?in_handle = open(opts.inputFasta, "r")
> ?records = list(SeqIO.parse(in_handle, "fasta"))
>
> ?for record in records:
> ? ? ?record.seq = record.seq.reverse_complement()
>
> ?out_handle = open(opts.outputFasta, "w")
> ?SeqIO.write(records, out_handle, "fasta")
>
> How is it possible to do it without a list?
>
> Thank you in advance.
Hi "xyz",
Did you try looking in the tutorial? i.e.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
You could modify your code to use a generator expression like this:
def make_rc(record):
"""Modifies a SeqRecord in place, and returns it."""
record.seq = record.seq.reverse_complement()
return record
records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
SeqIO.write(records, out_opts.outputFasta, "fasta")
I also changed it to pass filenames directly to SeqIO - its shorter ;)
See also this thread about adding a reverse complement
method to the SeqRecord which would make this easier:
http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html
Peter
From mjldehoon at yahoo.com Wed Aug 25 13:52:58 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Wed, 25 Aug 2010 06:52:58 -0700 (PDT)
Subject: [Biopython] Deprecated code to be removed from Biopython
Message-ID: <556514.21952.qm@web62405.mail.re1.yahoo.com>
Dear all,
Below are the bits of code in Biopython that are currently deprecated (with a DeprecationWarning). These have been deprecated since Biopython 1.51, and we are considering to remove them completely for the final release of Biopython 1.55. Any objections? Is anybody still using any of this code?
Thanks,
--Michiel.
Bio.Align.FormatConvert
Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter
Bio.Entrez.efetch: rettype="genbank" option
Bio.Fasta
Bio.SCOP.Dom.Parser
Bio.SwissProt.SProt
Bio.Transcribe
Bio.Translate
BioSQL.BioSeqDatabase.open_database: driver="psycopg" option
From ajperry at pansapiens.com Thu Aug 26 04:03:46 2010
From: ajperry at pansapiens.com (Andrew Perry)
Date: Thu, 26 Aug 2010 14:03:46 +1000
Subject: [Biopython] Deprecated code to be removed from Biopython
In-Reply-To: <556514.21952.qm@web62405.mail.re1.yahoo.com>
References: <556514.21952.qm@web62405.mail.re1.yahoo.com>
Message-ID:
On 25 August 2010 23:52, Michiel de Hoon wrote:
> Dear all,
>
> Below are the bits of code in Biopython that are currently deprecated (with
> a DeprecationWarning). These have been deprecated since Biopython 1.51, and
> we are considering to remove them completely for the final release of
> Biopython 1.55. Any objections? Is anybody still using any of this code?
>
> Thanks,
> --Michiel.
>
> Bio.Align.FormatConvert
> Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter
> Bio.Entrez.efetch: rettype="genbank" option
> Bio.Fasta
> Bio.SCOP.Dom.Parser
> Bio.SwissProt.SProt
> Bio.Transcribe
> Bio.Translate
> BioSQL.BioSeqDatabase.open_database: driver="psycopg" option
>
>
No objections here. I did a quick grep over some of my code from the last
two or three years - while I'm still using things
like Bio.Align.FormatConvert (probably because I was cut and pasting from
even older code), and Bio.SwissProt.SProt in some even older scripts, a
quick look at the API documentation for these deprecated parts provides
clear and simple pointers on how to migrate, so I'm happy.
Good work on the docs in this respect !
Andrew Perry
From biopython at maubp.freeserve.co.uk Thu Aug 26 10:57:27 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 11:57:27 +0100
Subject: [Biopython] Problem with biopython.org domain
Message-ID:
Hi all,
We appear to have a temporary problem with our biopython.org domain,
which I trust the OBF admin team will address shortly.
As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page
and http://biopython.open-bio.org/DIST/ for the downloads.
Source code is hosted separately on github,
http://github.com/biopython/biopython/
Apologies,
Peter
From jfi.mamede at gmail.com Thu Aug 26 11:02:30 2010
From: jfi.mamede at gmail.com (=?ISO-8859-1?Q?Jo=E3o_Mamede?=)
Date: Thu, 26 Aug 2010 13:02:30 +0200
Subject: [Biopython] Something happened to the domain?
Message-ID: <4C7649C6.1080503@gmail.com>
I was trying to see the new changes in biopython in the website,
however when I type biopython.org it asks me if I want to rent the domain.
What's the direct ip if the machine is up?
Thanks
From biopython at maubp.freeserve.co.uk Thu Aug 26 11:15:35 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 12:15:35 +0100
Subject: [Biopython] Something happened to the domain?
In-Reply-To: <4C7649C6.1080503@gmail.com>
References: <4C7649C6.1080503@gmail.com>
Message-ID:
On Thu, Aug 26, 2010 at 12:02 PM, Jo?o Mamede wrote:
> ?I was trying to see the new changes in biopython in the website, however
> when I type biopython.org it asks me if I want to rent the domain.
> What's the direct ip if the machine is up?
>
> Thanks
Hi Jo?o,
I sent out an email shortly before your query - hopefully you've
received it now:
http://lists.open-bio.org/pipermail/biopython/2010-August/006712.html
Peter
From dag at sonsorol.org Thu Aug 26 11:26:57 2010
From: dag at sonsorol.org (Chris Dagdigian)
Date: Thu, 26 Aug 2010 07:26:57 -0400
Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain
In-Reply-To:
References:
Message-ID: <4C764F81.1060100@sonsorol.org>
I manage or am the admin/technical/billing account holder for 24
domains, among them most of the open-bio.org ones.
Biopython.org is one that I do not own. Actually since NetSol is
offering to let me change DNS maybe I'm the technical contact - have to
wait and see on this. Normally for domains I control netsol starts email
nagging me constantly - never got emails about this one.
However, Networksolutions allows *anyone* with a payment method to renew
any domain for any reason.
I've renewed biopython.org for a 2-year term, paying out of pocket like
I do for all OBF domains so our $$ stays in our bank account.
> Order Confirmation
>
> Order Number: 375229424
> Today's Charges: $65.98
> Future Charges: $0.00
> Credit Card: xxxxxxxxxxx1002
The site should be back up soonish. I can't change the DNS entry that
points the website to the expired splash page until netsol processes the
renewal.
Upcoming domain expiration dates:
biomoby.org will expire Oct 1
bior.org will expire Nov 5
biosoap.org will expire Oct 9
-Chris
Peter wrote:
> Hi all,
>
> We appear to have a temporary problem with our biopython.org domain,
> which I trust the OBF admin team will address shortly.
>
> As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page
> and http://biopython.open-bio.org/DIST/ for the downloads.
>
> Source code is hosted separately on github,
> http://github.com/biopython/biopython/
>
> Apologies,
>
> Peter
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
From mitlox at op.pl Thu Aug 26 11:27:31 2010
From: mitlox at op.pl (xyz)
Date: Thu, 26 Aug 2010 21:27:31 +1000
Subject: [Biopython] Writting fasta file
In-Reply-To:
References: <4C74FCF0.4070401@op.pl>
Message-ID: <4C764FA3.6080805@op.pl>
On 25/08/10 23:08, Peter wrote:
>
> Hi "xyz",
>
> Did you try looking in the tutorial? i.e.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
>
> You could modify your code to use a generator expression like this:
>
> def make_rc(record):
> """Modifies a SeqRecord in place, and returns it."""
> record.seq = record.seq.reverse_complement()
> return record
> records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
> SeqIO.write(records, out_opts.outputFasta, "fasta")
>
> I also changed it to pass filenames directly to SeqIO - its shorter ;)
>
> See also this thread about adding a reverse complement
> method to the SeqRecord which would make this easier:
> http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html
>
> Peter
>
Thank you for your code it looks much better than mine.
In order to save memory is it possible to write each record ie. one by
one with SeqIO.write instead of all records at once?
From biopython at maubp.freeserve.co.uk Thu Aug 26 11:59:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 12:59:56 +0100
Subject: [Biopython] Writting fasta file
In-Reply-To: <4C764FA3.6080805@op.pl>
References: <4C74FCF0.4070401@op.pl>
<4C764FA3.6080805@op.pl>
Message-ID:
On Thu, Aug 26, 2010 at 12:27 PM, xyz wrote:
> On 25/08/10 23:08, Peter wrote:
>>
>> Hi "xyz",
>>
>> Did you try looking in the tutorial? i.e.
>>
>> http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
>>
>> You could modify your code to use a generator expression like this:
>>
>> def make_rc(record):
>> ? ? """Modifies a SeqRecord in place, and returns it."""
>> ? ? record.seq = record.seq.reverse_complement()
>> ? ? return record
>> records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
>> SeqIO.write(records, out_opts.outputFasta, "fasta")
>>
>> I also changed it to pass filenames directly to SeqIO - its shorter ;)
>
> Thank you for your code it looks much better than mine.
>
> In order to save memory is it possible to write each record ie. one by one
> with SeqIO.write instead of all records at once?
The code is already doing it one by one.
It uses a generator expression (rather than a list or list comprehension
which would put all the records into memory at once) to make the
reverse complemented records:
For writing FASTA files (and most other formats), SeqIO.write() only
needs to look at one record at a time, and won't load them all into
memory.
Peter
From chapmanb at 50mail.com Thu Aug 26 11:55:17 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Thu, 26 Aug 2010 07:55:17 -0400
Subject: [Biopython] Writting fasta file
In-Reply-To: <4C764FA3.6080805@op.pl>
References: <4C74FCF0.4070401@op.pl>
<4C764FA3.6080805@op.pl>
Message-ID: <20100826115517.GW23299@sobchak.mgh.harvard.edu>
Hello;
> >Did you try looking in the tutorial? i.e.
> >http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement
> >
> >You could modify your code to use a generator expression like this:
> >
> >def make_rc(record):
> > """Modifies a SeqRecord in place, and returns it."""
> > record.seq = record.seq.reverse_complement()
> > return record
> >records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta"))
> >SeqIO.write(records, out_opts.outputFasta, "fasta")
[...]
> In order to save memory is it possible to write each record ie. one
> by one with SeqIO.write instead of all records at once?
That's what Peter's code does. The write function pulls one record at
a time from the records generator. In addition to the Biopython
documentation, Andrew has a nice tutorial which goes into the
details of generators:
http://www.dalkescientific.com/writings/NBN/generators.html
Brad
From biopython at maubp.freeserve.co.uk Thu Aug 26 12:03:48 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 13:03:48 +0100
Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain
In-Reply-To: <4C764F81.1060100@sonsorol.org>
References:
<4C764F81.1060100@sonsorol.org>
Message-ID:
On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote:
>
> I manage or am the admin/technical/billing account holder for 24 domains,
> among them most of the open-bio.org ones.
>
> Biopython.org is one that I do not own. Actually since NetSol is offering to
> let me change DNS maybe I'm the technical contact - have to wait and see on
> this. Normally for domains I control netsol starts email nagging me
> constantly - never got emails about this one.
>
>
> However, Networksolutions allows *anyone* with a payment method to renew any
> domain for any reason.
>
> I've renewed biopython.org for a 2-year term, paying out of pocket like I do
> for all OBF domains so our $$ stays in our bank account.
>
>
>> Order Confirmation
>>
>> Order Number: 375229424
>> Today's Charges: $65.98
>> Future Charges: $0.00
>> Credit Card: xxxxxxxxxxx1002
>
> The site should be back up soonish. I can't change the DNS entry that points
> the website to the expired splash page until netsol processes the renewal.
>
> Upcoming domain expiration dates:
>
> biomoby.org will expire Oct 1
> bior.org will expire Nov 5
> biosoap.org will expire Oct 9
>
>
> -Chris
Thanks Chris :)
Will you be able to update the domain's contact details to be consistent
with the other Bio* domains?
Peter
From vishal4linux2 at gmail.com Thu Aug 26 12:16:20 2010
From: vishal4linux2 at gmail.com (vishal bhardwa)
Date: Thu, 26 Aug 2010 05:16:20 -0700
Subject: [Biopython] vishal bhardwa wants to chat
Message-ID:
-----------------------------------------------------------------------
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From biopython at maubp.freeserve.co.uk Thu Aug 26 12:28:18 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Aug 2010 13:28:18 +0100
Subject: [Biopython] vishal bhardwa wants to chat
In-Reply-To:
References:
Message-ID:
On Thu, Aug 26, 2010 at 1:16 PM, vishal bhardwa wrote:
> -----------------------------------------------------------------------
>
> vishal bhardwa wants to stay in better touch using some of Google's coolest new
> products.
>
> If you already have Gmail or Google Talk, visit ...
Hi all,
Vishal and other - please try not to sending these kinds of product or service
adverts to mailing lists.
Thank you,
Peter
From nje5 at georgetown.edu Fri Aug 27 01:43:08 2010
From: nje5 at georgetown.edu (Nathan J. Edwards)
Date: Thu, 26 Aug 2010 21:43:08 -0400
Subject: [Biopython] Problem with Bio.Entrez...
Message-ID: <4C77182C.40007@georgetown.edu>
Seems to be a problem with Entrez XML parsing:
from Bio import Entrez
Entrez.email = 'xxxyy at georgetown.edu'
handle = Entrez.einfo(db='pubmed')
result = Entrez.read(handle)
results in:
Traceback (most recent call last):
File "C:/Documents and Settings/Nathan/My
Documents/BCHB524/testing.py", line 5, in
result = Entrez.read(handle)
File
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py",
line 261, in read
record = handler.read(handle)
File
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line
150, in read
self.parser.ParseFile(handle)
File
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line
295, in endElementHandler
current[name] = value
TypeError: 'str' object does not support item assignment
error is in Parser.endElementHandler:
current = self.stack[-1]
try:
current.append(value)
except AttributeError:
295: current[name] = value
because current is the empty string "".
The problem is probably that the empty string shouldn't be on the stack,
given the logic here and elsewhere, but a simple test for the empty
string does get things working again.
current = self.stack[-1]
if current == "":
return
try:
current.append(value)
except AttributeError:
295: current[name] = value
Cheers!
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From mjldehoon at yahoo.com Fri Aug 27 02:40:52 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 26 Aug 2010 19:40:52 -0700 (PDT)
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C77182C.40007@georgetown.edu>
Message-ID: <108175.26561.qm@web62405.mail.re1.yahoo.com>
The problem is with the XML returned by NCBI.
Currently, the XML returned by einfo contains elements that are not described in the corresponding DTD (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The parser therefore doesn't know how to handle them.
Could you write an email to NCBI that einfo generates XML that is inconsistent with the corresponding DTD?
Best,
--Michiel.
--- On Thu, 8/26/10, Nathan J. Edwards wrote:
> From: Nathan J. Edwards
> Subject: [Biopython] Problem with Bio.Entrez...
> To: biopython at lists.open-bio.org
> Date: Thursday, August 26, 2010, 9:43 PM
>
> Seems to be a problem with Entrez XML parsing:
>
> from Bio import Entrez
> Entrez.email = 'xxxyy at georgetown.edu'
>
> handle = Entrez.einfo(db='pubmed')
> result = Entrez.read(handle)
>
> results in:
>
> Traceback (most recent call last):
> ? File "C:/Documents and Settings/Nathan/My
> Documents/BCHB524/testing.py", line 5, in
> ? ? result = Entrez.read(handle)
> ? File
> "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py",
> line 261, in read
> ? ? record = handler.read(handle)
> ? File
> "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py",
> line 150, in read
> ? ? self.parser.ParseFile(handle)
> ? File
> "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py",
> line 295, in endElementHandler
> ? ? current[name] = value
> TypeError: 'str' object does not support item assignment
>
> error is in Parser.endElementHandler:
>
> ? ? ? ? ? ? current =
> self.stack[-1]
> ? ? ? ? ? ? try:
> ? ? ? ? ? ? ? ?
> current.append(value)
> ? ? ? ? ? ? except
> AttributeError:
> 295:? ? ? ? ? ? current[name]
> = value
>
> because current is the empty string "".
>
> The problem is probably that the empty string shouldn't be
> on the stack, given the logic here and elsewhere, but a
> simple test for the empty string does get things working
> again.
>
> ? ? ? ? ? ? current =
> self.stack[-1]
> ??? ? ? if current == "":
> ??? ??? return
> ? ? ? ? ? ? try:
> ? ? ? ? ? ? ? ?
> current.append(value)
> ? ? ? ? ? ? except
> AttributeError:
> 295:? ? ? ? ? ? current[name]
> = value
>
>
> Cheers!
>
> - n
>
> -- Dr. Nathan Edwards? ? ? ? ?
> ? ? ? ? ? ? nje5 at georgetown.edu
> Department of Biochemistry and Molecular & Cellular
> Biology
> ? ? ? ? ???Georgetown
> University Medical Center
> Room 1215, Harris Building? ? ? ?
> ? Room 347, Basic Science
> 3300 Whitehaven St, NW? ? ? ? ?
> ? ? 3900 Reservoir Road, NW
> Washington DC 20007? ? ? ? ?
> ? ? ? ? ???Washington DC
> 20007
> Phone: 202-687-7042? ? ? ? ?
> ? ? ? ? ???Phone:
> 202-687-1618
> Fax: 202-687-0057? ? ? ? ? ?
> ? ? ? ? ? ???Fax:
> 202-687-7186
> _______________________________________________
> Biopython mailing list? -? Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
From nje5 at georgetown.edu Fri Aug 27 04:13:29 2010
From: nje5 at georgetown.edu (Nathan J. Edwards)
Date: Fri, 27 Aug 2010 00:13:29 -0400
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <108175.26561.qm@web62405.mail.re1.yahoo.com>
References: <108175.26561.qm@web62405.mail.re1.yahoo.com>
Message-ID: <4C773B69.3050308@georgetown.edu>
On 8/26/2010 10:40 PM, Michiel de Hoon wrote:
> The problem is with the XML returned by NCBI. Currently, the XML
> returned by einfo contains elements that are not described
> in the corresponding DTD
> (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The
> parser therefore doesn't know how to handle them. Could you write an
> email to NCBI that einfo generates XML that is inconsistent with the
> corresponding DTD?
Sent.
It would be nice (IWBN) if the parser threw an exception that indicated
that the returned XML didn't validate...at least then the (very
cryptic!) error message wouldn't look like a logic error in the parser.
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From nje5 at georgetown.edu Fri Aug 27 04:39:06 2010
From: nje5 at georgetown.edu (Nathan J. Edwards)
Date: Fri, 27 Aug 2010 00:39:06 -0400
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C773B69.3050308@georgetown.edu>
References: <108175.26561.qm@web62405.mail.re1.yahoo.com>
<4C773B69.3050308@georgetown.edu>
Message-ID: <4C77416A.6030906@georgetown.edu>
On 8/27/2010 12:13 AM, Nathan J. Edwards wrote:
>
> It would be nice (IWBN) if the parser threw an exception that indicated
> that the returned XML didn't validate...at least then the (very
> cryptic!) error message wouldn't look like a logic error in the parser.
Actually, after wading though the Parser.py code some more, the bad
element is clearly detected, and an attempt is made to ignore it (the
empty string), which then subsequently leads to the TypeError exception
in endElementHandler.
Maybe the test and return of my first email is sufficient to deal with
the empty strings inserted as part of the "ignore it" strategy.
And, given the frequency with which NCBI seems to break these things, I
_do_ prefer the "ignore it" strategy, if it works. :-)
Cheers!
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From biopython at maubp.freeserve.co.uk Fri Aug 27 08:32:57 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Aug 2010 09:32:57 +0100
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C77416A.6030906@georgetown.edu>
References: <108175.26561.qm@web62405.mail.re1.yahoo.com>
<4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu>
Message-ID:
On Fri, Aug 27, 2010 at 5:39 AM, Nathan J. Edwards wrote:
> On 8/27/2010 12:13 AM, Nathan J. Edwards wrote:
>>
>> It would be nice (IWBN) if the parser threw an exception that indicated
>> that the returned XML didn't validate...at least then the (very
>> cryptic!) error message wouldn't look like a logic error in the parser.
>
> Actually, after wading though the Parser.py code some more, the bad element
> is clearly detected, and an attempt is made to ignore it (the empty string),
> which then subsequently leads to the TypeError exception in
> endElementHandler.
I'd suggest issuing a warning for the bad element, rather than silently
ignoring it.
> Maybe the test and return of my first email is sufficient to deal with the
> empty strings inserted as part of the "ignore it" strategy.
>
> And, given the frequency with which NCBI seems to break these things,
> I _do_ prefer the "ignore it" strategy, if it works. :-)
Michiel - does Nathan's fix make sense? We should probably save an example
of this broken XML for a unit test...
Nathan - have you notified the NCBI about this? I assume you would get
an error putting the XML through a validator - if you haven't already done
so that would be worthwhile. Or would you rather one of us contact them?
Thanks,
Peter
From biopython at maubp.freeserve.co.uk Fri Aug 27 08:57:04 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Aug 2010 09:57:04 +0100
Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain
In-Reply-To: <4C764F81.1060100@sonsorol.org>
References:
<4C764F81.1060100@sonsorol.org>
Message-ID:
On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote:
>
> I manage or am the admin/technical/billing account holder for 24
> domains, among them most of the open-bio.org ones. ... I've
> renewed biopython.org for a 2-year term, ... The site should be
> back up soonish.
Thanks for the speedy response Chris - www.biopython.org is back up
now. If anyone is still having trouble, please allow another day or so for
DNS servers to update.
As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page
and http://biopython.open-bio.org/DIST/ for the downloads.
Source code is hosted separately on github,
http://github.com/biopython/biopython/
Peter
From vishal4linux2 at gmail.com Fri Aug 27 09:41:33 2010
From: vishal4linux2 at gmail.com (vishal bhardwa)
Date: Fri, 27 Aug 2010 15:11:33 +0530
Subject: [Biopython] module pylab problem on ceton
Message-ID:
hello friends,
how i can install pylab please give any solution i m useing CentOs operating
system.
thanks in advance
vishal
From biopython at maubp.freeserve.co.uk Fri Aug 27 09:58:51 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Aug 2010 10:58:51 +0100
Subject: [Biopython] module pylab problem on ceton
In-Reply-To:
References:
Message-ID:
On Fri, Aug 27, 2010 at 10:41 AM, vishal bhardwa
wrote:
> hello friends,
> how i can install pylab please give any solution i m useing CentOs operating
> system.
This isn't really a Biopython question. Try:
http://matplotlib.sourceforge.net/users/installing.html
Peter
From nje5 at georgetown.edu Fri Aug 27 16:10:49 2010
From: nje5 at georgetown.edu (Nathan Edwards)
Date: Fri, 27 Aug 2010 12:10:49 -0400
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To:
References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu>
Message-ID: <4C77E389.7080006@georgetown.edu>
> I'd suggest issuing a warning for the bad element, rather than silently
> ignoring it.
Except that I find the warning infrastructure pretty hard to use when I
need to turn something off.
Other alternatives providing a switch to choose between throwing an
exception (probably the default) or silently coping.
>> And, given the frequency with which NCBI seems to break these things,
>> I _do_ prefer the "ignore it" strategy, if it works. :-)
>
> Nathan - have you notified the NCBI about this? I assume you would get
> an error putting the XML through a validator - if you haven't already done
> so that would be worthwhile. Or would you rather one of us contact them?
Yes, NCBI has been notified and I just received a response that the
developers have been notified.
> I will bring this to our developers' attention. However, I will not
> be able to provide your with any ETA of the correction/fix or other
> comparable actions at this time.
Visual inspection is sufficient to verify the element is not mentioned
in the DTD, though I could fire up a validating parser I guess. Just did
and it confirms the error.
- n
--
Dr. Nathan Edwards nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center
Room 1215, Harris Building Room 347, Basic Science
3300 Whitehaven St, NW 3900 Reservoir Road, NW
Washington DC 20007 Washington DC 20007
Phone: 202-687-7042 Phone: 202-687-1618
Fax: 202-687-0057 Fax: 202-687-7186
From mjldehoon at yahoo.com Sat Aug 28 07:47:25 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 28 Aug 2010 00:47:25 -0700 (PDT)
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <4C77E389.7080006@georgetown.edu>
Message-ID: <226633.67137.qm@web62407.mail.re1.yahoo.com>
I think that for Biopython release 1.55, we should silently ignore this error using the fix proposed by Nathan. After the release is out, I suggest we add an optional argument "validate" to the read() and parse() function, defaulting to True. If validate is True, then read()/parse() raise an error if it finds elements in the XML that are not represented in the DTD. If validate is False, then such elements are silently ignored. This will require some other minor changes to the parser, so I'd like to do this after 1.55 is out.
--Michiel.
--- On Fri, 8/27/10, Nathan Edwards wrote:
> From: Nathan Edwards
> Subject: Re: [Biopython] Problem with Bio.Entrez...
> To: "Peter"
> Cc: "Michiel de Hoon" , biopython at lists.open-bio.org
> Date: Friday, August 27, 2010, 12:10 PM
>
> > I'd suggest issuing a warning for the bad element,
> rather than silently
> > ignoring it.
>
> Except that I find the warning infrastructure pretty hard
> to use when I need to turn something off.
>
> Other alternatives providing a switch to choose between
> throwing an exception (probably the default) or silently
> coping.
>
> >> And, given the frequency with which NCBI seems to
> break these things,
> >> I _do_ prefer the "ignore it" strategy, if it
> works. :-)
> >
> > Nathan - have you notified the NCBI about this? I
> assume you would get
> > an error putting the XML through a validator - if you
> haven't already done
> > so that would be worthwhile. Or would you rather one
> of us contact them?
>
> Yes, NCBI has been notified and I just received a response
> that the developers have been notified.
>
> > I will bring this to our developers' attention.
> However, I will not
> > be able to provide your with any ETA of the
> correction/fix or other
> > comparable actions at this time.
>
> Visual inspection is sufficient to verify the element is
> not mentioned in the DTD, though I could fire up a
> validating parser I guess. Just did and it confirms the
> error.
>
> - n
>
> -- Dr. Nathan Edwards? ? ? ? ?
> ? ? ? ? ? ? nje5 at georgetown.edu
> Department of Biochemistry and Molecular & Cellular
> Biology
> ? ? ? ? ???Georgetown
> University Medical Center
> Room 1215, Harris Building? ? ? ?
> ? Room 347, Basic Science
> 3300 Whitehaven St, NW? ? ? ? ?
> ? ? 3900 Reservoir Road, NW
> Washington DC 20007? ? ? ? ?
> ? ? ? ? ???Washington DC
> 20007
> Phone: 202-687-7042? ? ? ? ?
> ? ? ? ? ???Phone:
> 202-687-1618
> Fax: 202-687-0057? ? ? ? ? ?
> ? ? ? ? ? ???Fax:
> 202-687-7186
>
From biopython at maubp.freeserve.co.uk Sat Aug 28 11:32:03 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 28 Aug 2010 12:32:03 +0100
Subject: [Biopython] Problem with Bio.Entrez...
In-Reply-To: <226633.67137.qm@web62407.mail.re1.yahoo.com>
References: <4C77E389.7080006@georgetown.edu>
<226633.67137.qm@web62407.mail.re1.yahoo.com>
Message-ID:
On Sat, Aug 28, 2010 at 8:47 AM, Michiel de Hoon wrote:
> I think that for Biopython release 1.55, we should silently ignore this
> error using the fix proposed by Nathan. After the release is out, I
> suggest we add an optional argument "validate" to the read() and
> parse() function, defaulting to True. If validate is True, then read()/
> parse() raise an error if it finds elements in the XML that are not
> represented in the DTD. If validate is False, then such elements
> are silently ignored. This will require some other minor changes
> to the parser, so I'd like to do this after 1.55 is out.
>
> --Michiel.
Sounds good :)
Peter
From p.j.a.cock at googlemail.com Tue Aug 31 23:00:37 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 1 Sep 2010 00:00:37 +0100
Subject: [Biopython] Biopython 1.55 released
Message-ID:
Dear Biopythoneers,
After the beta earlier this month (thank you to everyone who
helped test this), we?ve just released Biopython 1.55 . For
full details see:
http://news.open-bio.org/news/2010/08/biopython-1-55-released/
Note we are phasing out support for Python 2.4. We will continue
to support it for at least one further release (i.e. Biopython 1.56).
This could be delayed given feedback from our users (e.g. if this
proves to be a problem in combination with other libraries or a
popular Linux distribution).
(At least) 12 people have contributed to this release, including
6 new people ? thank you all:
* Andres Colubri (first contribution)
* Carlos Rios Vera (first contribution)
* Claude Paroz (first contribution)
* Cymon Cox
* Eric Talevich
* Frank Kauff
* Joao Rodrigues (first contribution)
* Konstantin Okonechnikov (first contribution)
* Michiel de Hoon
* Nathan Edwards (first contribution)
* Peter Cock
* Tiago Antao
Source distributions and Windows installers are available
from the downloads page on the Biopython website:
http://www.biopython.org/wiki/Download
As usual, feedback is most welcome on the mailing lists
(or bugzilla).
Regards,
Peter
P.S. You can follow Biopython on Twitter,
http://twitter.com/biopython