From p.j.a.cock at googlemail.com  Thu Mar  3 05:37:07 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 10:37:07 +0000
Subject: [Biopython-dev] Biopython 1.57 release plans
Message-ID: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>

Hi all,

It is probably about time to do the Biopython 1.57 release.

Thanks to Tiago's work on the buildbot, see http://testing.open-bio.org
for this, we can be reasonably confident that all the offline unit tests
are passing on the main platforms and different versions of Python.
However, it would be a good idea for people to run the full test suite
on their machines now.

What (minor) issues need to be addressed?

Note I don't want this to be an excuse to land any big units of code (but
now would be a good time to discuss preparations for merging after the
release is done).

Would anyone like to proof read the current tutorial? You don't need to
mess about with LaTeX since there should be a nightly update here:
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.pdf

Regards,

Peter

From anaryin at gmail.com  Thu Mar  3 06:35:14 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Thu, 3 Mar 2011 12:35:14 +0100
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
Message-ID: <AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>

Hey Peter, should we include the Bio.PDB things we've been discussing for a
while now? That has been a bit quiet lately so I dunno how it stands with
you guys.

Cheers,

Jo?o


On Thu, Mar 3, 2011 at 11:37 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi all,
>
> It is probably about time to do the Biopython 1.57 release.
>
> Thanks to Tiago's work on the buildbot, see http://testing.open-bio.org
> for this, we can be reasonably confident that all the offline unit tests
> are passing on the main platforms and different versions of Python.
> However, it would be a good idea for people to run the full test suite
> on their machines now.
>
> What (minor) issues need to be addressed?
>
> Note I don't want this to be an excuse to land any big units of code (but
> now would be a good time to discuss preparations for merging after the
> release is done).
>
> Would anyone like to proof read the current tutorial? You don't need to
> mess about with LaTeX since there should be a nightly update here:
> http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html
> http://biopython.org/DIST/docs/tutorial/Tutorial-dev.pdf
>
> Regards,
>
> Peter
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>


From p.j.a.cock at googlemail.com  Thu Mar  3 06:41:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 11:41:15 +0000
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
	<AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
Message-ID: <AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>

On Thu, Mar 3, 2011 at 11:35 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
> Hey Peter, should we include the Bio.PDB things we've been discussing for a
> while now? That has been a bit quiet lately so I dunno how it stands with
> you guys.

I'm tempted to say no, try and get the release out within a week, and
then work with you and Eric to merge the code. I'm worried the merge
might push the release back, and I would like to get it out this month.
What's your impression Eric?

Also which github branch are you considering merging? I can do a trial
merge (offline) and run some tests here (I have access to all the main
platforms).

Peter


From eric.talevich at gmail.com  Thu Mar  3 15:10:34 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Thu, 3 Mar 2011 15:10:34 -0500
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
	<AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
	<AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>
Message-ID: <AANLkTi=eM-H88O-eUG_HRZJn0qeu44MpeDRXsnFMSt-w@mail.gmail.com>

On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Mar 3, 2011 at 11:35 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
> > Hey Peter, should we include the Bio.PDB things we've been discussing for
> a
> > while now? That has been a bit quiet lately so I dunno how it stands with
> > you guys.
>
> I'm tempted to say no, try and get the release out within a week, and
> then work with you and Eric to merge the code. I'm worried the merge
> might push the release back, and I would like to get it out this month.
> What's your impression Eric?
>

Jo?o, I'm sorry to put this off again -- but I think we should do that merge
after the 1.57 release. The API for the functions renumber_residues and
remove_disordered_atoms is tricky to get right, because they have to support
so many variations on the same concept. I'd like to give dev-version testers
some time with it before locking down the API with a stable release.

I'm looking at the NEWS file and I don't see any mention of the GSoC work
that we already merged -- was that in time for the 1.56 release, or just
after?

Here's what's already in 1.57 (pre-release):

 - index_db(), which I think people will really like
 - Blast+ support: blast_formatter
 - Some improvements to SeqiO and SeqRecord
 - Last release to support Python 2.4, for real this time


Dropping 2.4 support might also let us tighten up the Bio.PDB code a bit.


> Also which github branch are you considering merging? I can do a trial
> merge (offline) and run some tests here (I have access to all the main
> platforms).
>

It's here:
https://github.com/JoaoRodrigues/biopython/commits/pdb_enhancements

Comment on remove_disordered_atoms: I'm trying to think of a more obvious
way to make the "Average" option work. It's the default, so users won't
normally have to type it, but having "A" and "Average" seems prone to
autocomplete issues (mentally or in the IDE). How about making "average"
lowercase?

Best,
Eric


From p.j.a.cock at googlemail.com  Thu Mar  3 15:16:40 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:16:40 +0000
Subject: [Biopython-dev] Testing examples in the Tutorial
Message-ID: <AANLkTimJoYu6doCHNt1R_Yi6TxT0_UAaD3hani1Z_dCD@mail.gmail.com>

Hi all,

In part prompted by recent discussions on the BioPerl and BioRuby
mailing lists about documentation and testing, I was inspired to try
and code up something I'd been thinking about doing for some time:
treat the embedded examples in our tutorial as doctests.

This required adding a little extra markup to the LaTeX file since
I wanted the tests to be "opt in" (some examples will not make
good tests, for example random outputs or command line tool
dependencies). I've gone for a special comment line, %doctest
(which can include an optional name for the test) to mark the
the following verbatim block is a doctest. Likewise, %cont-doctest
indicates the following verbatim block is a continuation of the
previous doctest - important when there is text in the middle
so variable definitions or import statements would otherwise
need to be repeated.

Then I wrote test_Tutorial.py which parses Tutorial.tex to find
these examples, and turn them into doctests. It is a bit hacky
but appears to do the job. Running it like this:

python run_tests.py test_Tutorial.py

you can very minimal output from failures. For more details,
use this:

python test_Tutorial.py

I've already marked up some basic Seq examples (and in the
process fixed a couple of trivial errors and one typo) so you
can see how this works:

https://github.com/biopython/biopython/commit/dd3f5f7cf9a4bd120e4b8634f530f6de0b873622

Yes, maybe I should have asked before committing this,
but I wanted to run it on all our platforms via the buildbot.
That was a good idea as the is a tuple issue on Jython
and Python 2.4 that I've seen before:

https://github.com/biopython/biopython/commit/45cb3e05aa86c96820a3d866d766d0fc62cb830a

So, any comments or feedback? If people have ideas for
improvement that's great - otherwise I think we should begin
to mark up the rest of Tutorial.tex for maximum test coverage...

Peter

From p.j.a.cock at googlemail.com  Thu Mar  3 15:22:46 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:22:46 +0000
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTi=eM-H88O-eUG_HRZJn0qeu44MpeDRXsnFMSt-w@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
	<AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
	<AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>
	<AANLkTi=eM-H88O-eUG_HRZJn0qeu44MpeDRXsnFMSt-w@mail.gmail.com>
Message-ID: <AANLkTin4+fWkDpcpngW67ODxtgmV3=gwDA_5TdECMRDn@mail.gmail.com>

2011/3/3 Eric Talevich <eric.talevich at gmail.com>:
> On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock wrote:
>>
>> On Thu, Mar 3, 2011 at 11:35 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
>> > Hey Peter, should we include the Bio.PDB things we've been discussing
>> > for a
>> > while now? That has been a bit quiet lately so I dunno how it stands
>> > with
>> > you guys.
>>
>> I'm tempted to say no, try and get the release out within a week, and
>> then work with you and Eric to merge the code. I'm worried the merge
>> might push the release back, and I would like to get it out this month.
>> What's your impression Eric?
>
> Jo?o, I'm sorry to put this off again -- but I think we should do that merge
> after the 1.57 release. The API for the functions renumber_residues and
> remove_disordered_atoms is tricky to get right, because they have to support
> so many variations on the same concept. I'd like to give dev-version testers
> some time with it before locking down the API with a stable release.

OK then.

> I'm looking at the NEWS file and I don't see any mention of the GSoC work
> that we already merged -- was that in time for the 1.56 release, or just
> after?
>
> Here's what's already in 1.57 (pre-release):
>
> ?- index_db(), which I think people will really like
> ?- Blast+ support: blast_formatter
> ?- Some improvements to SeqiO and SeqRecord

Yeah, making sure nothing major is missing in the NEWS file is on
the TODO list for each release. I thought it was up to date...

>
> ?- Last release to support Python 2.4, for real this time
>
>
> Dropping 2.4 support might also let us tighten up the Bio.PDB code a bit.
>

Looks about right - on the Python 2.4 side, I'm hoping other projects
like Galaxy will drop Python 2.4 ASAP, and that Biopython 1.57 really
will be the last release to work on Python 2.4 (all be it lacking some
features). In practice many of the things Python 2.4 lacks (e.g. SQLite)
also apply to Jython, but that is a different issue really.

>>
>> Also which github branch are you considering merging? I can do a trial
>> merge (offline) and run some tests here (I have access to all the main
>> platforms).
>
> It's here:
> https://github.com/JoaoRodrigues/biopython/commits/pdb_enhancements
>
> Comment on remove_disordered_atoms: I'm trying to think of a more obvious
> way to make the "Average" option work. It's the default, so users won't
> normally have to type it, but having "A" and "Average" seems prone to
> autocomplete issues (mentally or in the IDE). How about making "average"
> lowercase?
>

Probably best to discuss this on a new thread. Also consider "mean"
since there is more than one average ;)

Peter


From p.j.a.cock at googlemail.com  Thu Mar  3 15:32:11 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:32:11 +0000
Subject: [Biopython-dev] Fwd: [Bosc] Bioinformatics Open Source Conference
 (BOSC 2011)--Call for Abstracts
In-Reply-To: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
References: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
Message-ID: <AANLkTimNQ=o6Unw461vjPPGUB4VKnB+Ww+qFhT-D2iXq@mail.gmail.com>

Dear Biopythoneers,

BOSC will be in Vienna, Austria this year.

Peter

---------- Forwarded message ----------
From: Nomi Harris <nlharris at lbl.gov>
Date: Thu, Mar 3, 2011 at 7:37 PM
Subject: [Bosc] Bioinformatics Open Source Conference (BOSC
2011)--Call for Abstracts
To: bosc-announce at lists.open-bio.org, members at open-bio.org, GMOD
Announcements List <gmod-announce at lists.sourceforge.net>, GMOD
Developers List <gmod-devel at lists.sourceforge.net>
Cc: Nomi Harris <nlharris at lbl.gov>


We invite you to submit an abstract to BOSC 2011! ?Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source
Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to
corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see
http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters. ?Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock,
Erwin Frise, Darin London, Ron Taylor


_______________________________________________
BOSC mailing list
BOSC at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bosc


From tiagoantao at gmail.com  Thu Mar  3 18:27:45 2011
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Thu, 3 Mar 2011 23:27:45 +0000
Subject: [Biopython-dev] buildbot failure in Biopython on Linux 64 -
	Jython 2.5.2
In-Reply-To: <201103032000.p23K0Fhp002513@testing.open-bio.org>
References: <201103032000.p23K0Fhp002513@testing.open-bio.org>
Message-ID: <AANLkTi=vQq+74CDaMQOUqxgJMRf-Qn34rSHsESGApgai@mail.gmail.com>

On Thu, Mar 3, 2011 at 8:00 PM,  <biopython-dev at biopython.org> wrote:
> ?http://testing.open-bio.org:8010/buildbotbuilders/Linux%2064%20-%20Jython%202.5.2/builds/61

Argh... these links are wrong. I will have a look.


From bugzilla-daemon at portal.open-bio.org  Mon Mar  7 10:48:56 2011
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 7 Mar 2011 10:48:56 -0500
Subject: [Biopython-dev] [Bug 2968] Modifications to Emboss eprimer3 parser
	and associated files
In-Reply-To: <bug-2968-42@http.bugzilla.open-bio.org/>
Message-ID: <201103071548.p27Fmum8005492@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2968





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2011-03-07 10:48 EST -------
I've committed some fixes based on Leighton's ideas,
https://github.com/biopython/biopython/commit/b550da19d1749bb160711d240074010ebbd7252f


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

From komalsnehal1991 at gmail.com  Tue Mar  8 02:58:11 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Tue, 8 Mar 2011 13:28:11 +0530
Subject: [Biopython-dev] Biopython Projects
Message-ID: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>

Hi everyone,

I'm Komal, a Junior Undergraduate Student from India studying
Bioengineering. I'm a fan of Python and I love Computational Biology and I
plan to do my further studies in the same.
I went through the projects on the Biopython page. I was very much
interested in the RNA Structure project mentioned. Any contribution which I
make will help me a lot and the organisation too. In fact, I am currently
doing a project on RNA Editing. I'll be very happy to integrate my
knowledge.

Please help me on how I should proceed.

Komal

From komalsnehal1991 at gmail.com  Wed Mar  9 05:49:23 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Wed, 9 Mar 2011 02:49:23 -0800
Subject: [Biopython-dev] ::Biopython Project
Message-ID: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>

Hi everyone,

I'm Komal, a Junior Undergraduate Student from India
studying Bioengineering. I'm a fan of Python and I love Computational
Biology and I plan to do my further studies in the same.
I went through the projects on the Biopython page. I was very
much interested in the RNA Structure project mentioned. Any contribution
which I make will help me a lot and the organisation too. In fact, I am
currently doing a project on RNA Editing. I'll be very happy to integrate
my knowledge.

In fact, I have been trying to contact people on #obf-soc IRC. I think there
is no separate IRC for Biopython.

Please help me on how I should proceed.


Komal

From p.j.a.cock at googlemail.com  Wed Mar  9 05:58:33 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 9 Mar 2011 10:58:33 +0000
Subject: [Biopython-dev] Biopython Projects
In-Reply-To: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>
References: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>
Message-ID: <AANLkTi=e=x54B3yeu4VGZAO7MRtTJnEBuvdUA+Togq5z@mail.gmail.com>

On Tue, Mar 8, 2011 at 7:58 AM, Komal S <komalsnehal1991 at gmail.com> wrote:
> Hi everyone,
>
> I'm Komal, a Junior Undergraduate Student from India studying
> Bioengineering. I'm a fan of Python and I love Computational Biology and I
> plan to do my further studies in the same.
> I went through the projects on the Biopython page. I was very much
> interested in the RNA Structure project mentioned. Any contribution which I
> make will help me a lot and the organisation too. In fact, I am currently
> doing a project on RNA Editing. I'll be very happy to integrate my
> knowledge.
>
> Please help me on how I should proceed.
>
> Komal

Hi Kamal,

Since you expressed an interest in the RNA structure project list here,
http://www.biopython.org/wiki/Active_projects I was hoping Kristian
would comment. I have CC'd him on this email.

Peter

P.S. Are you interested in the Google Summer of Code, or in general?

From krother at rubor.de  Wed Mar  9 06:36:14 2011
From: krother at rubor.de (Kristian Rother)
Date: Wed, 9 Mar 2011 12:36:14 +0100
Subject: [Biopython-dev] [Biopython] ::Biopython Project
In-Reply-To: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
References: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
Message-ID: <d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>


Hi,

I'll take Peters hint to give a short summary what is going on on
RNA at biopython. Actually, there are three lines of development:

- Adding an extended sequence format that can handle modified RNA
nucleotides (works with preliminary tests done).
- Adding some simple parsers for common RNA 2D structure formats (Vienna,
Ct, Bpseq) (something already works).
- Adding the FCCD loop closer algorithm by Thomas Hamelryck (got the code
but needs to be contributed).

Basically all three require at the moment an independent person to take a
look at them and state 'yes, this is useful for me' (if so).

Komal, if you like to get involved could you write a little about what you
are working with (RNA editing). If we find something thats not too far off
for you we could get it moving.

Best regards,
    Kristian



> Hi everyone,
>
> I'm Komal, a Junior Undergraduate Student from India
> studying Bioengineering. I'm a fan of Python and I love Computational
> Biology and I plan to do my further studies in the same.
> I went through the projects on the Biopython page. I was very
> much interested in the RNA Structure project mentioned. Any contribution
> which I make will help me a lot and the organisation too. In fact, I am
> currently doing a project on RNA Editing. I'll be very happy to integrate
> my knowledge.
>
> In fact, I have been trying to contact people on #obf-soc IRC. I think
> there
> is no separate IRC for Biopython.
>
> Please help me on how I should proceed.
>
>
> Komal
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>


From komalsnehal1991 at gmail.com  Wed Mar  9 08:00:04 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Wed, 9 Mar 2011 05:00:04 -0800
Subject: [Biopython-dev] Biopython Projects
In-Reply-To: <AANLkTi=e=x54B3yeu4VGZAO7MRtTJnEBuvdUA+Togq5z@mail.gmail.com>
References: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>
	<AANLkTi=e=x54B3yeu4VGZAO7MRtTJnEBuvdUA+Togq5z@mail.gmail.com>
Message-ID: <AANLkTikcWBA49RLx4R7DqJA8wxda9dCgYPx3txhHrNVE@mail.gmail.com>

Hi Peter,

Thanks a lot for your reply.

Well, both. I really don't know whether OBF has applied for GSOC this year
or not. If yes, GSOC will help me a lot. Nonetheless, I want to involve
myself in Computational Biology related projects so that they help me in the
future. I'm planning a PhD in Computational Biology in the next 2 years. I
want a good background and experience for that.

Komal


On Wed, Mar 9, 2011 at 2:58 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Mar 8, 2011 at 7:58 AM, Komal S <komalsnehal1991 at gmail.com> wrote:
> > Hi everyone,
> >
> > I'm Komal, a Junior Undergraduate Student from India studying
> > Bioengineering. I'm a fan of Python and I love Computational Biology and
> I
> > plan to do my further studies in the same.
> > I went through the projects on the Biopython page. I was very much
> > interested in the RNA Structure project mentioned. Any contribution which
> I
> > make will help me a lot and the organisation too. In fact, I am currently
> > doing a project on RNA Editing. I'll be very happy to integrate my
> > knowledge.
> >
> > Please help me on how I should proceed.
> >
> > Komal
>
> Hi Kamal,
>
> Since you expressed an interest in the RNA structure project list here,
> http://www.biopython.org/wiki/Active_projects I was hoping Kristian
> would comment. I have CC'd him on this email.
>
> Peter
>
> P.S. Are you interested in the Google Summer of Code, or in general?
>

From komalsnehal1991 at gmail.com  Wed Mar  9 08:18:00 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Wed, 9 Mar 2011 05:18:00 -0800
Subject: [Biopython-dev] [Biopython] ::Biopython Project
In-Reply-To: <d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>
References: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
	<d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>
Message-ID: <AANLkTinqXqJQhizkJhWcpqkD_D8pffj_1V7mk7o_851G@mail.gmail.com>

Hi Kristian,

Well, my work is basically the construction of a database of RNA Editing.
I'm part of a team from UCC, Ireland. I joined this project around a month
ago.

I'm interested in this project and I'm ready to get involved.

Komal


On Wed, Mar 9, 2011 at 3:36 AM, Kristian Rother <krother at rubor.de> wrote:

>
> Hi,
>
> I'll take Peters hint to give a short summary what is going on on
> RNA at biopython. Actually, there are three lines of development:
>
> - Adding an extended sequence format that can handle modified RNA
> nucleotides (works with preliminary tests done).
> - Adding some simple parsers for common RNA 2D structure formats (Vienna,
> Ct, Bpseq) (something already works).
> - Adding the FCCD loop closer algorithm by Thomas Hamelryck (got the code
> but needs to be contributed).
>
> Basically all three require at the moment an independent person to take a
> look at them and state 'yes, this is useful for me' (if so).
>
> Komal, if you like to get involved could you write a little about what you
> are working with (RNA editing). If we find something thats not too far off
> for you we could get it moving.
>
> Best regards,
>    Kristian
>
>
>
> > Hi everyone,
> >
> > I'm Komal, a Junior Undergraduate Student from India
> > studying Bioengineering. I'm a fan of Python and I love Computational
> > Biology and I plan to do my further studies in the same.
> > I went through the projects on the Biopython page. I was very
> > much interested in the RNA Structure project mentioned. Any contribution
> > which I make will help me a lot and the organisation too. In fact, I am
> > currently doing a project on RNA Editing. I'll be very happy to integrate
> > my knowledge.
> >
> > In fact, I have been trying to contact people on #obf-soc IRC. I think
> > there
> > is no separate IRC for Biopython.
> >
> > Please help me on how I should proceed.
> >
> >
> > Komal
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
> >
>
>

From anaryin at gmail.com  Wed Mar  9 08:23:54 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Wed, 9 Mar 2011 14:23:54 +0100
Subject: [Biopython-dev] [Biopython] ::Biopython Project
In-Reply-To: <AANLkTinqXqJQhizkJhWcpqkD_D8pffj_1V7mk7o_851G@mail.gmail.com>
References: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
	<d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>
	<AANLkTinqXqJQhizkJhWcpqkD_D8pffj_1V7mk7o_851G@mail.gmail.com>
Message-ID: <AANLkTi=ShGChKK=jDL=Q=+xD+gYmsOUtW_eZLAG5XEJb@mail.gmail.com>

Hello Komal,

I assume you're talking about this:
http://www.ncbi.nlm.nih.gov/pubmed/20547637.

Which features from the current Biopython RNA modules would fit your work
and how do you think you could improve them? Do you already have some ideas?

Cheers,

J

From p.j.a.cock at googlemail.com  Thu Mar 10 12:42:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 10 Mar 2011 17:42:58 +0000
Subject: [Biopython-dev] Bugzilla -> Redmine migration
Message-ID: <AANLkTi=VuX3+ymNEo34f2XY1N-OmSGJ1MPFp7TNbginn@mail.gmail.com>

Hi all,

Anyone who has tried to file a bug recently will have noticed a big
red message "Sorry, entering bugs into the product Biopython has been
disabled."

The reason for this is the OBF team are about to move us (and all the
other Bio* projects using Bugzilla) to a Redmine server instead.
See http://www.redmine.org/

I expect this to be completed in the next few days (with all the old
bugs and accounts carried across). Hopefully this will include
integration with our git repository as well.

We'll make an announcement once it is ready, in the mean time, any new
bugs could be emailed to the mailing list as a short term measure.

Peter

From updates at feedmyinbox.com  Sat Mar 12 04:11:34 2011
From: updates at feedmyinbox.com (Feed My Inbox)
Date: Sat, 12 Mar 2011 04:11:34 -0500
Subject: [Biopython-dev] 3/12 biopython Questions - BioStar
Message-ID: <59619d8d66b2e5c275645a69e1951352@74.63.51.88>

// Plotting DNA sequence traces
// March 11, 2011 at 11:00 AM

http://biostar.stackexchange.com/questions/6356/plotting-dna-sequence-traces
I have read/consulted these two threads here, the ABI file format document, the BioPython project, the R project, the BioConductor project and have searched extensively on the Internet, but I am not able to find an answer or explanation for what I would like to do.  

I would like to know how to interpret trace data from an ABI/AB1 trace file and how to plot this data. Ideally, I'd like to plot it on a web-page (in some format that allows for scrolling of course, but I haven't thought that much about this yet), but first I need to understand the trace data itself and how to plot it with Python and/or R.


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From updates at feedmyinbox.com  Fri Mar 18 09:05:29 2011
From: updates at feedmyinbox.com (Feed My Inbox)
Date: Fri, 18 Mar 2011 09:05:29 -0400
Subject: [Biopython-dev] 3/18 biopython Questions - BioStar
Message-ID: <aa2c8676d8752537ccfbac508cb3b969@74.63.51.88>

// Error translating genbank CDS using BioPython
// March 17, 2011 at 4:28 AM

http://biostar.stackexchange.com/questions/6560/error-translating-genbank-cds-using-biopython
Hi all,

I'm trying to translate the a genbank record using BioPython 1.53, ignoring the already given translation in the CDS feature. The code I've written to translate this is pretty straight forward:

...
for gb_record in SeqIO.parse(file_handle, 'genbank'):#Bio.GenBank.Record
    for gb_feature in gb_record.features:#Bio.SeqFeature
        #Skip any non coding sequence features
        if gb_feature.type != 'CDS':
            continue

        #Protein identifier is a property of the genbank feature
        protein_id = gb_feature.qualifiers['protein_id'][0]

        #Original sequence retrieved through BioPython 1.53+'s internal method 
        extracted_seq = gb_feature.extract(gb_record.seq)#Bio.Seq.Seq

        #Translation table is a property of the genbank feature
        transl_table = gb_feature.qualifiers['transl_table'][0]

        #Translate entire sequence as coding sequence using translation table
        #Additional CodonTables optionally available from Bio.Data.CodonTable
        try:
            protein_seq = extracted_seq.translate(table = transl_table, cds = True)
        except TranslationError, err:
            log.error('%s: Error in translating %s\n%s', gb_record.id, protein_id, extracted_seq)
            raise err

        #Write out fasta. Header format as requested: >genome_ac|protein_id
        _write_fasta_line(write_handle, '{0}|{1}'.format(gb_record.id, protein_id), str(protein_seq))


The translate line throws a TranslationError on the following feature:

 CDS             complement(2276255..2279302)
                 /locus_tag="ECBD_2165"
                 /EC_number="1.7.99.4"
                 /inference="protein motif:TFAM:TIGR01553"
                 /note="KEGG: ssn:SSON_1650 formate dehydrogenase-N,
                 nitrate-inducible, alpha subunit;
                 TIGRFAM: formate dehydrogenase, alpha subunit;
                 PFAM: molybdopterin oxidoreductase; molybdopterin
                 oxidoreductase Fe4S4 region; molydopterin
                 dinucleotide-binding region"
                 /codon_start=1
                 /transl_except=(pos:complement(2278715..2278717),aa:Sec)
                 /transl_table=11
                 /product="formate dehydrogenase, alpha subunit"
                 /protein_id="YP_003036386.1"
                 /db_xref="GI:253773555"
                 /db_xref="InterPro:IPR006311"
                 /db_xref="InterPro:IPR006443"
                 /db_xref="InterPro:IPR006655"
                 /db_xref="InterPro:IPR006656"
                 /db_xref="InterPro:IPR006657"
                 /db_xref="InterPro:IPR006963"
                 /db_xref="GeneID:8157271"
                 /translation="MDVSRRQFFKICAGGMAGTTVAALGFAPKQALAQARNYKLLRAK
                 EIRNTCTYCSVGCGLLMYSLGDGAKNAREAIYHIEGDPDHPVSRGALCPKGAGLLDYV
                 NSENRLRYPEYRAPGSDKWQRISWEEAFSRIAKLMKADRDANFIEKNEQGVTVNRWLS
                 TGMLCASGASNETGMLTQKFARSLGMLAVDNQARVUHGPTVASLAPTFGRGAMTNHWV
                 DIKNANVVMVMGGNAAEAHPVGFRWAMEAKNNNDATLIVVDPRFTRTASVADIYAPIR
                 SGTDITFLSGVLRYLIENNKINAEYVKHYTNASLLVRDDFAFEDGLFSGYDAEKRQYD
                 KSSWNYQFDENGYAKRDETLTHPRCVWNLLKEHVSRYTPDVVENICGTPKADFLKVCE
                 VLASTSAPDRTTTFLYALGWTQHTVGAQNIRTMAMIQLLLGNMGMAGGGVNALRGHSN
                 IQGLTDLGLLSTSLPGYLTLPSEKQVDLQSYLEANTPKATLADQVNYWSNYPKFFVSL
                 MKSFYGDAAQKENNWGYDWLPKWDQTYDVIKYFNMMDEGKVTGYFCQGFNPVASFPDK
                 NKVVSCLSKLKYMVVIDPLVTETSTFWQNHGESNDVDPASIQTEVFRLPSTCFAEEDG
                 SIANSGRWLQWHWKGQDAPGEARNDGEILAGIYHHLRELYQAEGGKGVEPLMKMSWNY
                 KQPHEPQSDEVAKENNGYALEDLYDANGVLIAKKGQLLSSFAHLRDDGTTASSCWIYT
                 GSWTEQGNQMANRDNSDPSGLGNTLGWAWAWPLNRRVLYNRASADINGKPWDPKRMLI
                 QWNGSKWTGNDIPDFGNAAPGTPTGPFIMQPEGMGRLFAINKMAEGPFPEHYEPIETP
                 LGTNPLHPNVVSNPVVRLYEQDALRMGKKEQFPYVGTTYRLTEHFHTWTKHALLNAIA
                 QPEQFVEISETLAAAKGINNGDRVTVSSKRGFIRAVAVVTRRLKPLNVNGQQVETVGI
                 PIHWGFEGVARKGYIANTLTPNVGDANSQTPEYKAFLVNIEKA"

root: ERROR: NC_012947.1: Error in translating YP_003036386.1
ATGGACGTCAGTCGCAGACAATTTTTTAAAATCTGCGCGGGCGGTATGGCTGGAACAACGGTAGCGGCATTGGGCTTTGCCCCGAAGCAAGCACTGGCTCAGGCGCGAAACTACAAATTATTACGCGCTAAAGAGATCCGTAACACCTGCACATACTGTTCCGTAGGTTGCGGGCTATTGATGTATAGCCTGGGTGATGGCGCGAAAAACGCCAGAGAAGCGATTTATCACATTGAAGGTGACCCGGATCATCCGGTAAGCCGTGGTGCGCTGTGCCCAAAAGGGGCCGGTTTGCTGGATTACGTCAACAGCGAAAACCGTCTGCGCTACCCGGAATATCGTGCGCCAGGTTCTGACAAATGGCAGCGCATTAGCTGGGAAGAAGCATTCTCCCGTATTGCAAAGCTGATGAAAGCTGACCGTGACGCTAACTTTATTGAAAAGAACGAGCAGGGCGTAACGGTAAACCGTTGGCTTTCTACCGGTATGCTGTGTGCCTCCGGTGCCAGCAACGAAACCGGGATGCTGACACAGAAATTTGCCCGCTCCCTCGGGATGCTGGCGGTAGACAACCAGGCGCGCGTCTGACACGGACCAACGGTAGCAAGTCTTGCTCCAACATTTGGTCGCGGTGCGATGACCAACCACTGGGTGGATATCAAAAACGCTAACGTCGTAATGGTAATGGGCGGTAACGCTGCTGAAGCGCATCCCGTCGGTTTCCGCTGGGCGATGGAAGCGAAAAACAACAACGATGCAACCTTGATCGTTGTCGATCCTCGTTTTACGCGTACCGCTTCTGTGGCGGATATTTACGCACCTATTCGTTCCGGTACGGACATTACGTTCCTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAACATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGCCTGTTCAGCGGTTATGACGCTGAAAAACGCCAGT
ACGACAAATCGTCCTGGAACTATCAGTTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGACTCATCCGCGCTGTGTGTGGAACCTGCTGAAAGAGCACGTTTCCCGCTACACGCCGGACGTCGTTGAAAACATCTGCGGTACGCCAAAAGCCGACTTCCTGAAAGTGTGTGAAGTGCTGGCCTCCACCAGCGCACCGGATCGCACAACCACCTTCCTGTACGCGCTGGGCTGGACGCAGCACACCGTGGGTGCGCAGAACATCCGTACTATGGCGATGATCCAGTTACTGCTCGGTAACATGGGTATGGCCGGTGGCGGCGTGAACGCATTGCGTGGTCACTCCAACATTCAGGGCCTGACTGACTTAGGTCTGCTCTCTACCAGCCTGCCAGGTTATCTGACGCTGCCGTCAGAAAAACAGGTTGATTTGCAGTCGTATCTGGAAGCGAACACGCCGAAAGCGACGCTGGCTGATCAGGTGAACTACTGGAGCAACTATCCGAAGTTCTTCGTTAGCCTGATGAAATCTTTCTATGGCGATGCCGCGCAGAAAGAGAACAACTGGGGCTATGACTGGCTGCCGAAGTGGGACCAGACCTACGACGTCATCAAGTATTTCAACATGATGGACGAAGGCAAAGTCACCGGTTATTTCTGCCAGGGCTTTAACCCGGTTGCGTCCTTCCCGGACAAAAACAAAGTGGTGAGCTGCCTGAGCAAGCTGAAGTACATGGTGGTTATCGATCCGCTGGTGACTGAAACCTCTACCTTCTGGCAGAACCACGGCGAGTCGAACGATGTCGATCCGGCGTCTATTCAGACTGAAGTATTCCGTCTGCCTTCGACCTGCTTTGCTGAAGAAGATGGTTCTATTGCTAACTCCGGTCGCTGGCTGCAGTGGCACTGGAAAGGTCAGGATGCGCCGGGCGAAGCGCGTAACGACGGTGAAATTCTGGCGGGTATCTACCATCACCTGCGCGAGCTGTACCA
GGCCGAAGGTGGTAAAGGCGTAGAACCGCTGATGAAGATGAGCTGGAACTACAAGCAGCCGCACGAACCGCAATCTGACGAAGTAGCTAAAGAGAACAACGGCTATGCGCTGGAAGATCTCTATGATGCTAATGGCGTGCTGATTGCGAAGAAAGGTCAGTTGCTGAGTAGCTTTGCGCATCTGCGTGATGACGGTACAACCGCATCTTCTTGCTGGATCTACACCGGTAGCTGGACAGAGCAGGGCAACCAGATGGCTAACCGCGATAACTCCGACCCGTCCGGTCTGGGGAATACGCTGGGATGGGCCTGGGCGTGGCCGCTCAACCGTCGCGTGCTGTACAACCGTGCTTCGGCGGATATCAACGGTAAACCGTGGGATCCGAAACGGATGCTGATCCAGTGGAACGGCAGCAAGTGGACGGGTAACGATATTCCTGACTTCGGCAATGCCGCACCGGGTACGCCAACCGGGCCGTTTATCATGCAGCCGGAAGGGATGGGACGCCTGTTTGCTATCAACAAAATGGCGGAAGGTCCGTTCCCGGAACACTACGAGCCGATTGAAACGCCGCTGGGCACTAACCCGCTGCATCCGAACGTGGTGTCTAACCCGGTTGTTCGTCTGTATGAACAAGACGCACTGCGGATGGGTAAAAAAGAGCAGTTCCCGTATGTGGGTACGACCTATCGTCTGACCGAGCACTTCCACACCTGGACCAAGCACGCATTGCTCAACGCAATTGCTCAGCCGGAACAGTTTGTGGAAATCAGCGAAACGCTGGCGGCGGCGAAAGGCATTAATAATGGCGATCGTGTCACTGTCTCAAGCAAGCGTGGCTTTATCCGCGCGGTGGCTGTGGTAACGCGTCGTCTGAAACCACTGAATGTAAATGGTCAGCAGGTTGAAACGGTGGGTATTCCAATCCACTGGGGCTTTGAGGGTGTCGCGCGTAAAGGTTATATCGCTAACACTCTGACGCCGAATGTCGGTGAT
GCAAACTCGCAAACGCCGGAATATAAAGCGTTCTTAGTCAACATCGAGAAGGCGTAA


Error:

Traceback (most recent call last):
  File "/usr/lib/python2.6/unittest.py", line 279, in run
    testMethod()
  File "/home/user/jenkins/workspace/Divergence/divergence/src/divergence/test/test_translate.py", line 33, in test_translate_ecoli_and_salmo
    fasta_file = translate_genbank_to_protein(genbank_file, ptt_file)
  File "/home/user/jenkins/workspace/Divergence/divergence/src/divergence/translate.py", line 73, in translate_genbank_to_protein
    raise err
TranslationError: Extra in frame stop codon found.


Now I'm guessing this has something to do with the /transl_except I'm seeing in the GenBank record, but I'm not (yet) sure. (The GenBank supplied translation contains a Selenocysteine.) But even if this is the cause: How would I properly handle this in my BioPython translation? I can't find any method to exclude certain sections from translation..

Can anyone help me fix the translation?

Best regards,
Tim

(Ps. Should anyone wonder why I'm not using the translation in the GenBank file directly: It's a requirement that I translate from the DNA sequence to protein myself...)


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From mnaik28 at gmail.com  Wed Mar 23 01:50:59 2011
From: mnaik28 at gmail.com (Medha Naik)
Date: Wed, 23 Mar 2011 00:50:59 -0500
Subject: [Biopython-dev] Project ideas for CS grad
Message-ID: <4D898A43.5010407@gmail.com>

Hi All,

I am a Computer Science Master's student from Texas with an inclination 
towards Bioinformatics. I love coding in Python and would like to 
contribute to some code development in Biopython. I do have basic 
understanding of the biology and genetics concepts in bioinformatics but 
I am primarily looking to work on the computational aspects like coding 
some algorithms, data structures or database interactions.

I read Dan Gusfield's book, 'Algorithms on Strings, Trees and 
Sequences', as part of my coursework and got interested in implementing 
an algorithm or two from the same using the sequence and tree classes 
already defined in Biopython.

Is there any open project that I could contribute to by doing the above? 
I do not want to independently begin something without some guidance 
from a person from the team.

I am open to all ideas/suggestions  and I hope that I can contribute 
something to this amazing module that integrates python, computer 
science concepts and biology!

Regards,
Medha Naik



From updates at feedmyinbox.com  Wed Mar 23 04:06:27 2011
From: updates at feedmyinbox.com (Feed My Inbox)
Date: Wed, 23 Mar 2011 04:06:27 -0400
Subject: [Biopython-dev] 3/23 active questions tagged biopython - Stack
	Overflow
Message-ID: <cb8d4903fb229180f66226d9544ec6e3@74.63.51.88>

// marking up mutation positions in a sequence with html in python
// March 22, 2011 at 7:03 AM

http://stackoverflow.com/questions/5390170/marking-up-mutation-positions-in-a-sequence-with-html-in-python
Hello,

I was wondering if there are any methods in python or biopython that allows one to markup a sequence in html.

I would like to mark positions on a sequence (ie colour bases differently) according to if that position is a known snp/indel etc 

Having a list of mutation positions in an array (read from a database) eg

mutation_position = [10,20,30,40]

I can change case for the affected base using something like:
seq = seq[0:b] + mutation_positions[b].lower() + seq[(b+1):len(seq)]

But is it possible to add some html code eg add the tag pos for each of the mutation positions. (when the html markup is added to the sequence, the length of the sequence is altered and so the mutation positions don't match to the newly marked up sequence during each iteration of the loop!)

I hope this makes sense!

Thanks.


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From p.j.a.cock at googlemail.com  Sun Mar 27 09:32:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sun, 27 Mar 2011 14:32:28 +0100
Subject: [Biopython-dev] New test_Phylo.py test on Python 3
Message-ID: <AANLkTin4vj27c6YRxY6Lf7CbdhgrOvg97a=20WnGxxuL@mail.gmail.com>

Hi Eric,

You'll need to handle None explicitly for the comparison to pass under
Python 3 (see below), or you get:

Traceback (most recent call last):
  ...
  File "/home/buildslave/BuildBot/lin3264/build/build/py3.2/Tests/test_Phylo.py",
line 280, in <lambda>
    tree.collapse_all(lambda c: c.branch_length < 0.1)
TypeError: unorderable types: NoneType() < float()

http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100/steps/shell/logs/stdio
http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.1/builds/179/steps/shell/logs/stdio

Regards,

Peter

---------- Forwarded message ----------
From:  <biopython-dev at biopython.org>
Date: Sun, Mar 27, 2011 at 4:12 AM
Subject: buildbot failure in Biopython on Linux 64 - Python 3.2
To: p.j.a.cock at googlemail.com, tiagoantao at gmail.com


The Buildbot has detected a new failure on builder Linux 64 - Python
3.2 while building Biopython.
Full details are available at:
?http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100

Buildbot URL: http://testing.open-bio.org/biopython/

Buildslave for this Build: peter_linux64

Build Reason: The Nightly scheduler named 'nightly' triggered this build
Build Source Stamp: HEAD
Blamelist:

BUILD FAILED: failed shell

sincerely,
?-The Buildbot


From p.j.a.cock at googlemail.com  Mon Mar 28 08:43:40 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 28 Mar 2011 13:43:40 +0100
Subject: [Biopython-dev] Fwd: [Biopython - Bug #3187] pip install biopython
In-Reply-To: <redmine.journal-14249.20110328123532@redmine.open-bio.org>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
Message-ID: <AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>

Hi Brad (et al),

It looks like automatic emails from Redmine to the biopython-dev list
are not working properly... anyway, could you take a look at Bug 3187?

https://redmine.open-bio.org/issues/3187

I suspect this is related to PIP issue 8, i.e. PIP doesn't like our
setup.py file.

https://github.com/pypa/pip/issues/8

Thanks,

Peter


---------- Forwarded message ----------
From:  <redmine at redmine.open-bio.org>
Date: Mon, Mar 28, 2011 at 1:35 PM
Subject: [Biopython - Bug #3187] pip install biopython
To: casbon at gmail.com
Cc: p.j.a.cock at googlemail.com


Issue #3187 has been updated by James Casbon.

File pip.log added

It's pretty much the same as the output I posted, but I have attached.

________________________________

Bug #3187: pip install biopython

Author: James Casbon
Status: New
Priority: Normal
Assignee:
Category: Main Distribution
Target version:
URL:

james at flapjack:/tmp$ virtualenv bp-pip
New python executable in bp-pip/bin/python
Installing setuptools............done.
james at flapjack:/tmp$ source /tmp/bp-pip/bin/activate
(bp-pip)james at flapjack:/tmp$ pip install biopython
Downloading/unpacking biopython
  Downloading biopython-1.56.tar.gz (6.9Mb): 6.9Mb downloaded
  Running setup.py egg_info for package biopython

    warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
    warning: no previously-included files found matching 'Tests/Graphics/*.eps'
    warning: no previously-included files found matching 'Tests/Graphics/*.svg'
    warning: no previously-included files found matching 'Tests/Graphics/*.png'
    warning: no previously-included files matching '*' found under
directory 'Tests/UnitTests'
    warning: no previously-included files matching '.cvsignore' found
under directory '*'
    warning: no previously-included files matching '.gitignore' found
under directory '*'
    warning: no previously-included files matching '*.pyc' found under
directory '*'
Installing collected packages: biopython
  Running setup.py install for biopython
    usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
       or: -c --help [cmd1 cmd2 ...]
       or: -c --help-commands
       or: -c cmd --help

    error: option --single-version-externally-managed not recognized
    Complete output from command /private/tmp/bp-pip/bin/python -c
"import setuptools;
__file__='/private/tmp/bp-pip/build/biopython/setup.py';
execfile('/private/tmp/bp-pip/build/biopython/setup.py')" install
--single-version-externally-managed --record
/var/folders/Gn/GneSaDeKGaGpZXx+hcopdU+++TI/-Tmp-/pip-slq1Hy-record/install-record.txt
--install-headers /private/tmp/bp-pip/bin/../include/site/python2.7:
    usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]

   or: -c --help [cmd1 cmd2 ...]

   or: -c --help-commands

   or: -c cmd --help

error: option --single-version-externally-managed not recognized

----------------------------------------
Command /private/tmp/bp-pip/bin/python -c "import setuptools;
__file__='/private/tmp/bp-pip/build/biopython/setup.py';
execfile('/private/tmp/bp-pip/build/biopython/setup.py')" install
--single-version-externally-managed --record
/var/folders/Gn/GneSaDeKGaGpZXx+hcopdU+++TI/-Tmp-/pip-slq1Hy-record/install-record.txt
--install-headers /private/tmp/bp-pip/bin/../include/site/python2.7
failed with error code 1
Storing complete log in /Users/james/.pip/pip.log

________________________________

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From chapmanb at 50mail.com  Mon Mar 28 09:36:39 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 28 Mar 2011 09:36:39 -0400
Subject: [Biopython-dev] Fwd: [Biopython - Bug #3187] pip install
	biopython
In-Reply-To: <AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
Message-ID: <20110328133639.GD26383@sobchak>

Peter;

[pip install problem]
> https://redmine.open-bio.org/issues/3187

Thanks for the heads up. I pushed a fix for this back in December,
which was unfortunately post-1.56:

https://github.com/biopython/biopython/commit/4e4c3aa1df3d6848afed4783c4e54186a751accd#setup.py

What is our timeline for 1.57? If it's a long way out we can
work on back-porting to 1.56 and re-upload. 

Brad


From p.j.a.cock at googlemail.com  Mon Mar 28 09:55:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 28 Mar 2011 14:55:58 +0100
Subject: [Biopython-dev] Fwd: [Biopython - Bug #3187] pip install
	biopython
In-Reply-To: <20110328133639.GD26383@sobchak>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
	<20110328133639.GD26383@sobchak>
Message-ID: <AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>

On Mon, Mar 28, 2011 at 2:36 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Peter;
>
> [pip install problem]
>> https://redmine.open-bio.org/issues/3187
>
> Thanks for the heads up. I pushed a fix for this back in December,
> which was unfortunately post-1.56:
>
> https://github.com/biopython/biopython/commit/4e4c3aa1df3d6848afed4783c4e54186a751accd#setup.py
>
> What is our timeline for 1.57? If it's a long way out we can
> work on back-porting to 1.56 and re-upload.

I was hoping for some more comments on the tutorial, and ideally fix
http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html
but other than that we're good to go. Do you want to do the honours?

Peter

From eric.talevich at gmail.com  Mon Mar 28 10:17:46 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Mon, 28 Mar 2011 10:17:46 -0400
Subject: [Biopython-dev] New test_Phylo.py test on Python 3
In-Reply-To: <AANLkTin4vj27c6YRxY6Lf7CbdhgrOvg97a=20WnGxxuL@mail.gmail.com>
References: <AANLkTin4vj27c6YRxY6Lf7CbdhgrOvg97a=20WnGxxuL@mail.gmail.com>
Message-ID: <AANLkTi=N51e+JUCHE_0nY0+SstpErW8MSVS+-q+R9iVm@mail.gmail.com>

Thanks, Peter. The build bot is pretty handy!

My fix was here, for the public record:
https://github.com/biopython/biopython/commit/8edd552b72a31179cd53eb1493ac5462f7fb8f7c

Lambda expressions like the one in test_Phylo.py are supposed to Just Work,
since manually handling all the edge cases for comparisons is tedious (or
impossible, since try/except statements aren't allowed in Python's lambda
expressions). So I fixed the way Bio.Phylo wraps lambda expressions,
instead.

-E

On Sun, Mar 27, 2011 at 9:32 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi Eric,
>
> You'll need to handle None explicitly for the comparison to pass under
> Python 3 (see below), or you get:
>
> Traceback (most recent call last):
>  ...
>  File
> "/home/buildslave/BuildBot/lin3264/build/build/py3.2/Tests/test_Phylo.py",
> line 280, in <lambda>
>    tree.collapse_all(lambda c: c.branch_length < 0.1)
> TypeError: unorderable types: NoneType() < float()
>
>
> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100/steps/shell/logs/stdio
>
> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.1/builds/179/steps/shell/logs/stdio
>
> Regards,
>
> Peter
>
> ---------- Forwarded message ----------
> From:  <biopython-dev at biopython.org>
> Date: Sun, Mar 27, 2011 at 4:12 AM
> Subject: buildbot failure in Biopython on Linux 64 - Python 3.2
> To: p.j.a.cock at googlemail.com, tiagoantao at gmail.com
>
>
> The Buildbot has detected a new failure on builder Linux 64 - Python
> 3.2 while building Biopython.
> Full details are available at:
>
> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100
>
> Buildbot URL: http://testing.open-bio.org/biopython/
>
> Buildslave for this Build: peter_linux64
>
> Build Reason: The Nightly scheduler named 'nightly' triggered this build
> Build Source Stamp: HEAD
> Blamelist:
>
> BUILD FAILED: failed shell
>
> sincerely,
>  -The Buildbot
>

From redmine at redmine.open-bio.org  Mon Mar 28 11:04:43 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 28 Mar 2011 15:04:43 +0000
Subject: [Biopython-dev] [Biopython - Bug #3188] Test bug, please ignore
References: <redmine.issue-3188.20110328134006@redmine.open-bio.org>
Message-ID: <redmine.journal-14252.20110328150443@redmine.open-bio.org>


Issue #3188 has been updated by Chris Fields.

Assignee set to Biopython Developer's

retesting with dev account
----------------------------------------
Bug #3188: Test bug, please ignore
https://redmine.open-bio.org/issues/3188

Author: Peter Cock
Status: New
Priority: Normal
Assignee: Biopython Developer's
Category: 
Target version: 
URL: 


The aim of this bug is to test the Redmine "Email on New Issue" option from the Newissuealerts module.

This issue should get emailed to the biopython-dev email list automatically...

Peter


-- 
You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here and login: http://redmine.open-bio.org


From chapmanb at 50mail.com  Tue Mar 29 08:05:32 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 29 Mar 2011 08:05:32 -0400
Subject: [Biopython-dev] 1.57 release plans
In-Reply-To: <AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
	<20110328133639.GD26383@sobchak>
	<AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>
Message-ID: <20110329120532.GL26383@sobchak>

Peter;

> > What is our timeline for 1.57? 

> I was hoping for some more comments on the tutorial, and ideally fix
> http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html
> but other than that we're good to go. Do you want to do the honours?

For your fastq file examples, we could use the EBI short read
archive, which is staying around for a while longer:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000001/

I can do on the release, but probably later this week or over the
weekend. How do you normally get together the list of contributors?
That, and the list of new features, are the major two things I'm not
on top off.

Thanks,
Brad

From p.j.a.cock at googlemail.com  Tue Mar 29 08:26:21 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 29 Mar 2011 13:26:21 +0100
Subject: [Biopython-dev] 1.57 release plans
In-Reply-To: <20110329120532.GL26383@sobchak>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
	<20110328133639.GD26383@sobchak>
	<AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>
	<20110329120532.GL26383@sobchak>
Message-ID: <AANLkTikSRaz_RDDwJvw2YKNwRicnYoOD0sURVUGOvTu0@mail.gmail.com>

On Tue, Mar 29, 2011 at 1:05 PM, Brad Chapman wrote:
> Peter;
>
>> > What is our timeline for 1.57?
>
>> I was hoping for some more comments on the tutorial, and ideally fix
>> http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html
>> but other than that we're good to go. Do you want to do the honours?
>
> For your fastq file examples, we could use the EBI short read
> archive, which is staying around for a while longer:
>
> ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000001/

Good plan - why didn't I think of that the other night when I was
looking at this? I may even be able to find the equivalent files to
the ones we used to use from the NCBI SRA. I'll try and sort
that today or tomorrow...

> I can do on the release, but probably later this week or over the
> weekend.

Cool. That suits me. You can trigger builds on the buildbot
manually (if you know the password...) and/or wait for the
nightly scheduled build. That is quite handy for a final test
just before tagging the repository and building the archives.
Also useful if you don't have a suitable Windows machine
handy - I can always do the Windows installers a day later
(well, not on weekends).

> How do you normally get together the list of contributors?
> That, and the list of new features, are the major two things
> I'm not on top off.

I try to make sure that the NEWS file is kept up to date as
we go along, so the "release announcement" is a prettified
version of that really. You can take a bit more space to talk
about new stuff, and really big bits of new code could even
warrant their blog post on news.open-bio.org to help raise
awareness. As usual circulating a draft release statement on
the dev list is a good way to avoid missing anything really
obvious :)

Thanks,

Peter

From p.j.a.cock at googlemail.com  Thu Mar  3 10:37:07 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 10:37:07 +0000
Subject: [Biopython-dev] Biopython 1.57 release plans
Message-ID: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>

Hi all,

It is probably about time to do the Biopython 1.57 release.

Thanks to Tiago's work on the buildbot, see http://testing.open-bio.org
for this, we can be reasonably confident that all the offline unit tests
are passing on the main platforms and different versions of Python.
However, it would be a good idea for people to run the full test suite
on their machines now.

What (minor) issues need to be addressed?

Note I don't want this to be an excuse to land any big units of code (but
now would be a good time to discuss preparations for merging after the
release is done).

Would anyone like to proof read the current tutorial? You don't need to
mess about with LaTeX since there should be a nightly update here:
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.pdf

Regards,

Peter


From anaryin at gmail.com  Thu Mar  3 11:35:14 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Thu, 3 Mar 2011 12:35:14 +0100
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
Message-ID: <AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>

Hey Peter, should we include the Bio.PDB things we've been discussing for a
while now? That has been a bit quiet lately so I dunno how it stands with
you guys.

Cheers,

Jo?o


On Thu, Mar 3, 2011 at 11:37 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi all,
>
> It is probably about time to do the Biopython 1.57 release.
>
> Thanks to Tiago's work on the buildbot, see http://testing.open-bio.org
> for this, we can be reasonably confident that all the offline unit tests
> are passing on the main platforms and different versions of Python.
> However, it would be a good idea for people to run the full test suite
> on their machines now.
>
> What (minor) issues need to be addressed?
>
> Note I don't want this to be an excuse to land any big units of code (but
> now would be a good time to discuss preparations for merging after the
> release is done).
>
> Would anyone like to proof read the current tutorial? You don't need to
> mess about with LaTeX since there should be a nightly update here:
> http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html
> http://biopython.org/DIST/docs/tutorial/Tutorial-dev.pdf
>
> Regards,
>
> Peter
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>



From p.j.a.cock at googlemail.com  Thu Mar  3 11:41:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 11:41:15 +0000
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
	<AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
Message-ID: <AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>

On Thu, Mar 3, 2011 at 11:35 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
> Hey Peter, should we include the Bio.PDB things we've been discussing for a
> while now? That has been a bit quiet lately so I dunno how it stands with
> you guys.

I'm tempted to say no, try and get the release out within a week, and
then work with you and Eric to merge the code. I'm worried the merge
might push the release back, and I would like to get it out this month.
What's your impression Eric?

Also which github branch are you considering merging? I can do a trial
merge (offline) and run some tests here (I have access to all the main
platforms).

Peter



From eric.talevich at gmail.com  Thu Mar  3 20:10:34 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Thu, 3 Mar 2011 15:10:34 -0500
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
	<AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
	<AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>
Message-ID: <AANLkTi=eM-H88O-eUG_HRZJn0qeu44MpeDRXsnFMSt-w@mail.gmail.com>

On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Mar 3, 2011 at 11:35 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
> > Hey Peter, should we include the Bio.PDB things we've been discussing for
> a
> > while now? That has been a bit quiet lately so I dunno how it stands with
> > you guys.
>
> I'm tempted to say no, try and get the release out within a week, and
> then work with you and Eric to merge the code. I'm worried the merge
> might push the release back, and I would like to get it out this month.
> What's your impression Eric?
>

Jo?o, I'm sorry to put this off again -- but I think we should do that merge
after the 1.57 release. The API for the functions renumber_residues and
remove_disordered_atoms is tricky to get right, because they have to support
so many variations on the same concept. I'd like to give dev-version testers
some time with it before locking down the API with a stable release.

I'm looking at the NEWS file and I don't see any mention of the GSoC work
that we already merged -- was that in time for the 1.56 release, or just
after?

Here's what's already in 1.57 (pre-release):

 - index_db(), which I think people will really like
 - Blast+ support: blast_formatter
 - Some improvements to SeqiO and SeqRecord
 - Last release to support Python 2.4, for real this time


Dropping 2.4 support might also let us tighten up the Bio.PDB code a bit.


> Also which github branch are you considering merging? I can do a trial
> merge (offline) and run some tests here (I have access to all the main
> platforms).
>

It's here:
https://github.com/JoaoRodrigues/biopython/commits/pdb_enhancements

Comment on remove_disordered_atoms: I'm trying to think of a more obvious
way to make the "Average" option work. It's the default, so users won't
normally have to type it, but having "A" and "Average" seems prone to
autocomplete issues (mentally or in the IDE). How about making "average"
lowercase?

Best,
Eric



From p.j.a.cock at googlemail.com  Thu Mar  3 20:16:40 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:16:40 +0000
Subject: [Biopython-dev] Testing examples in the Tutorial
Message-ID: <AANLkTimJoYu6doCHNt1R_Yi6TxT0_UAaD3hani1Z_dCD@mail.gmail.com>

Hi all,

In part prompted by recent discussions on the BioPerl and BioRuby
mailing lists about documentation and testing, I was inspired to try
and code up something I'd been thinking about doing for some time:
treat the embedded examples in our tutorial as doctests.

This required adding a little extra markup to the LaTeX file since
I wanted the tests to be "opt in" (some examples will not make
good tests, for example random outputs or command line tool
dependencies). I've gone for a special comment line, %doctest
(which can include an optional name for the test) to mark the
the following verbatim block is a doctest. Likewise, %cont-doctest
indicates the following verbatim block is a continuation of the
previous doctest - important when there is text in the middle
so variable definitions or import statements would otherwise
need to be repeated.

Then I wrote test_Tutorial.py which parses Tutorial.tex to find
these examples, and turn them into doctests. It is a bit hacky
but appears to do the job. Running it like this:

python run_tests.py test_Tutorial.py

you can very minimal output from failures. For more details,
use this:

python test_Tutorial.py

I've already marked up some basic Seq examples (and in the
process fixed a couple of trivial errors and one typo) so you
can see how this works:

https://github.com/biopython/biopython/commit/dd3f5f7cf9a4bd120e4b8634f530f6de0b873622

Yes, maybe I should have asked before committing this,
but I wanted to run it on all our platforms via the buildbot.
That was a good idea as the is a tuple issue on Jython
and Python 2.4 that I've seen before:

https://github.com/biopython/biopython/commit/45cb3e05aa86c96820a3d866d766d0fc62cb830a

So, any comments or feedback? If people have ideas for
improvement that's great - otherwise I think we should begin
to mark up the rest of Tutorial.tex for maximum test coverage...

Peter


From p.j.a.cock at googlemail.com  Thu Mar  3 20:22:46 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:22:46 +0000
Subject: [Biopython-dev] Biopython 1.57 release plans
In-Reply-To: <AANLkTi=eM-H88O-eUG_HRZJn0qeu44MpeDRXsnFMSt-w@mail.gmail.com>
References: <AANLkTimDSRH8HOrm8_bRxA=mEPVewVb1ZRTimo8dp8V9@mail.gmail.com>
	<AANLkTimbb_rhhAbhdFVpDOqmPiGmKeLDJBVPYA1khAHk@mail.gmail.com>
	<AANLkTinFXWDPst1we8KKRrFJzwxAfHJCiiX5QEEcHswt@mail.gmail.com>
	<AANLkTi=eM-H88O-eUG_HRZJn0qeu44MpeDRXsnFMSt-w@mail.gmail.com>
Message-ID: <AANLkTin4+fWkDpcpngW67ODxtgmV3=gwDA_5TdECMRDn@mail.gmail.com>

2011/3/3 Eric Talevich <eric.talevich at gmail.com>:
> On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock wrote:
>>
>> On Thu, Mar 3, 2011 at 11:35 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
>> > Hey Peter, should we include the Bio.PDB things we've been discussing
>> > for a
>> > while now? That has been a bit quiet lately so I dunno how it stands
>> > with
>> > you guys.
>>
>> I'm tempted to say no, try and get the release out within a week, and
>> then work with you and Eric to merge the code. I'm worried the merge
>> might push the release back, and I would like to get it out this month.
>> What's your impression Eric?
>
> Jo?o, I'm sorry to put this off again -- but I think we should do that merge
> after the 1.57 release. The API for the functions renumber_residues and
> remove_disordered_atoms is tricky to get right, because they have to support
> so many variations on the same concept. I'd like to give dev-version testers
> some time with it before locking down the API with a stable release.

OK then.

> I'm looking at the NEWS file and I don't see any mention of the GSoC work
> that we already merged -- was that in time for the 1.56 release, or just
> after?
>
> Here's what's already in 1.57 (pre-release):
>
> ?- index_db(), which I think people will really like
> ?- Blast+ support: blast_formatter
> ?- Some improvements to SeqiO and SeqRecord

Yeah, making sure nothing major is missing in the NEWS file is on
the TODO list for each release. I thought it was up to date...

>
> ?- Last release to support Python 2.4, for real this time
>
>
> Dropping 2.4 support might also let us tighten up the Bio.PDB code a bit.
>

Looks about right - on the Python 2.4 side, I'm hoping other projects
like Galaxy will drop Python 2.4 ASAP, and that Biopython 1.57 really
will be the last release to work on Python 2.4 (all be it lacking some
features). In practice many of the things Python 2.4 lacks (e.g. SQLite)
also apply to Jython, but that is a different issue really.

>>
>> Also which github branch are you considering merging? I can do a trial
>> merge (offline) and run some tests here (I have access to all the main
>> platforms).
>
> It's here:
> https://github.com/JoaoRodrigues/biopython/commits/pdb_enhancements
>
> Comment on remove_disordered_atoms: I'm trying to think of a more obvious
> way to make the "Average" option work. It's the default, so users won't
> normally have to type it, but having "A" and "Average" seems prone to
> autocomplete issues (mentally or in the IDE). How about making "average"
> lowercase?
>

Probably best to discuss this on a new thread. Also consider "mean"
since there is more than one average ;)

Peter



From p.j.a.cock at googlemail.com  Thu Mar  3 20:32:11 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:32:11 +0000
Subject: [Biopython-dev] Fwd: [Bosc] Bioinformatics Open Source Conference
 (BOSC 2011)--Call for Abstracts
In-Reply-To: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
References: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
Message-ID: <AANLkTimNQ=o6Unw461vjPPGUB4VKnB+Ww+qFhT-D2iXq@mail.gmail.com>

Dear Biopythoneers,

BOSC will be in Vienna, Austria this year.

Peter

---------- Forwarded message ----------
From: Nomi Harris <nlharris at lbl.gov>
Date: Thu, Mar 3, 2011 at 7:37 PM
Subject: [Bosc] Bioinformatics Open Source Conference (BOSC
2011)--Call for Abstracts
To: bosc-announce at lists.open-bio.org, members at open-bio.org, GMOD
Announcements List <gmod-announce at lists.sourceforge.net>, GMOD
Developers List <gmod-devel at lists.sourceforge.net>
Cc: Nomi Harris <nlharris at lbl.gov>


We invite you to submit an abstract to BOSC 2011! ?Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source
Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to
corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see
http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters. ?Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock,
Erwin Frise, Darin London, Ron Taylor


_______________________________________________
BOSC mailing list
BOSC at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bosc



From tiagoantao at gmail.com  Thu Mar  3 23:27:45 2011
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Thu, 3 Mar 2011 23:27:45 +0000
Subject: [Biopython-dev] buildbot failure in Biopython on Linux 64 -
	Jython 2.5.2
In-Reply-To: <201103032000.p23K0Fhp002513@testing.open-bio.org>
References: <201103032000.p23K0Fhp002513@testing.open-bio.org>
Message-ID: <AANLkTi=vQq+74CDaMQOUqxgJMRf-Qn34rSHsESGApgai@mail.gmail.com>

On Thu, Mar 3, 2011 at 8:00 PM,  <biopython-dev at biopython.org> wrote:
> ?http://testing.open-bio.org:8010/buildbotbuilders/Linux%2064%20-%20Jython%202.5.2/builds/61

Argh... these links are wrong. I will have a look.



From bugzilla-daemon at portal.open-bio.org  Mon Mar  7 15:48:56 2011
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 7 Mar 2011 10:48:56 -0500
Subject: [Biopython-dev] [Bug 2968] Modifications to Emboss eprimer3 parser
	and associated files
In-Reply-To: <bug-2968-42@http.bugzilla.open-bio.org/>
Message-ID: <201103071548.p27Fmum8005492@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2968





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2011-03-07 10:48 EST -------
I've committed some fixes based on Leighton's ideas,
https://github.com/biopython/biopython/commit/b550da19d1749bb160711d240074010ebbd7252f


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.


From komalsnehal1991 at gmail.com  Tue Mar  8 07:58:11 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Tue, 8 Mar 2011 13:28:11 +0530
Subject: [Biopython-dev] Biopython Projects
Message-ID: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>

Hi everyone,

I'm Komal, a Junior Undergraduate Student from India studying
Bioengineering. I'm a fan of Python and I love Computational Biology and I
plan to do my further studies in the same.
I went through the projects on the Biopython page. I was very much
interested in the RNA Structure project mentioned. Any contribution which I
make will help me a lot and the organisation too. In fact, I am currently
doing a project on RNA Editing. I'll be very happy to integrate my
knowledge.

Please help me on how I should proceed.

Komal


From komalsnehal1991 at gmail.com  Wed Mar  9 10:49:23 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Wed, 9 Mar 2011 02:49:23 -0800
Subject: [Biopython-dev] ::Biopython Project
Message-ID: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>

Hi everyone,

I'm Komal, a Junior Undergraduate Student from India
studying Bioengineering. I'm a fan of Python and I love Computational
Biology and I plan to do my further studies in the same.
I went through the projects on the Biopython page. I was very
much interested in the RNA Structure project mentioned. Any contribution
which I make will help me a lot and the organisation too. In fact, I am
currently doing a project on RNA Editing. I'll be very happy to integrate
my knowledge.

In fact, I have been trying to contact people on #obf-soc IRC. I think there
is no separate IRC for Biopython.

Please help me on how I should proceed.


Komal


From p.j.a.cock at googlemail.com  Wed Mar  9 10:58:33 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 9 Mar 2011 10:58:33 +0000
Subject: [Biopython-dev] Biopython Projects
In-Reply-To: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>
References: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>
Message-ID: <AANLkTi=e=x54B3yeu4VGZAO7MRtTJnEBuvdUA+Togq5z@mail.gmail.com>

On Tue, Mar 8, 2011 at 7:58 AM, Komal S <komalsnehal1991 at gmail.com> wrote:
> Hi everyone,
>
> I'm Komal, a Junior Undergraduate Student from India studying
> Bioengineering. I'm a fan of Python and I love Computational Biology and I
> plan to do my further studies in the same.
> I went through the projects on the Biopython page. I was very much
> interested in the RNA Structure project mentioned. Any contribution which I
> make will help me a lot and the organisation too. In fact, I am currently
> doing a project on RNA Editing. I'll be very happy to integrate my
> knowledge.
>
> Please help me on how I should proceed.
>
> Komal

Hi Kamal,

Since you expressed an interest in the RNA structure project list here,
http://www.biopython.org/wiki/Active_projects I was hoping Kristian
would comment. I have CC'd him on this email.

Peter

P.S. Are you interested in the Google Summer of Code, or in general?


From krother at rubor.de  Wed Mar  9 11:36:14 2011
From: krother at rubor.de (Kristian Rother)
Date: Wed, 9 Mar 2011 12:36:14 +0100
Subject: [Biopython-dev] [Biopython] ::Biopython Project
In-Reply-To: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
References: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
Message-ID: <d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>


Hi,

I'll take Peters hint to give a short summary what is going on on
RNA at biopython. Actually, there are three lines of development:

- Adding an extended sequence format that can handle modified RNA
nucleotides (works with preliminary tests done).
- Adding some simple parsers for common RNA 2D structure formats (Vienna,
Ct, Bpseq) (something already works).
- Adding the FCCD loop closer algorithm by Thomas Hamelryck (got the code
but needs to be contributed).

Basically all three require at the moment an independent person to take a
look at them and state 'yes, this is useful for me' (if so).

Komal, if you like to get involved could you write a little about what you
are working with (RNA editing). If we find something thats not too far off
for you we could get it moving.

Best regards,
    Kristian



> Hi everyone,
>
> I'm Komal, a Junior Undergraduate Student from India
> studying Bioengineering. I'm a fan of Python and I love Computational
> Biology and I plan to do my further studies in the same.
> I went through the projects on the Biopython page. I was very
> much interested in the RNA Structure project mentioned. Any contribution
> which I make will help me a lot and the organisation too. In fact, I am
> currently doing a project on RNA Editing. I'll be very happy to integrate
> my knowledge.
>
> In fact, I have been trying to contact people on #obf-soc IRC. I think
> there
> is no separate IRC for Biopython.
>
> Please help me on how I should proceed.
>
>
> Komal
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>



From komalsnehal1991 at gmail.com  Wed Mar  9 13:00:04 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Wed, 9 Mar 2011 05:00:04 -0800
Subject: [Biopython-dev] Biopython Projects
In-Reply-To: <AANLkTi=e=x54B3yeu4VGZAO7MRtTJnEBuvdUA+Togq5z@mail.gmail.com>
References: <AANLkTi=s_bjATb4qWbu1kP6kpULEjABJ+7HOdbfL6_ka@mail.gmail.com>
	<AANLkTi=e=x54B3yeu4VGZAO7MRtTJnEBuvdUA+Togq5z@mail.gmail.com>
Message-ID: <AANLkTikcWBA49RLx4R7DqJA8wxda9dCgYPx3txhHrNVE@mail.gmail.com>

Hi Peter,

Thanks a lot for your reply.

Well, both. I really don't know whether OBF has applied for GSOC this year
or not. If yes, GSOC will help me a lot. Nonetheless, I want to involve
myself in Computational Biology related projects so that they help me in the
future. I'm planning a PhD in Computational Biology in the next 2 years. I
want a good background and experience for that.

Komal


On Wed, Mar 9, 2011 at 2:58 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Mar 8, 2011 at 7:58 AM, Komal S <komalsnehal1991 at gmail.com> wrote:
> > Hi everyone,
> >
> > I'm Komal, a Junior Undergraduate Student from India studying
> > Bioengineering. I'm a fan of Python and I love Computational Biology and
> I
> > plan to do my further studies in the same.
> > I went through the projects on the Biopython page. I was very much
> > interested in the RNA Structure project mentioned. Any contribution which
> I
> > make will help me a lot and the organisation too. In fact, I am currently
> > doing a project on RNA Editing. I'll be very happy to integrate my
> > knowledge.
> >
> > Please help me on how I should proceed.
> >
> > Komal
>
> Hi Kamal,
>
> Since you expressed an interest in the RNA structure project list here,
> http://www.biopython.org/wiki/Active_projects I was hoping Kristian
> would comment. I have CC'd him on this email.
>
> Peter
>
> P.S. Are you interested in the Google Summer of Code, or in general?
>


From komalsnehal1991 at gmail.com  Wed Mar  9 13:18:00 2011
From: komalsnehal1991 at gmail.com (Komal S)
Date: Wed, 9 Mar 2011 05:18:00 -0800
Subject: [Biopython-dev] [Biopython] ::Biopython Project
In-Reply-To: <d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>
References: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
	<d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>
Message-ID: <AANLkTinqXqJQhizkJhWcpqkD_D8pffj_1V7mk7o_851G@mail.gmail.com>

Hi Kristian,

Well, my work is basically the construction of a database of RNA Editing.
I'm part of a team from UCC, Ireland. I joined this project around a month
ago.

I'm interested in this project and I'm ready to get involved.

Komal


On Wed, Mar 9, 2011 at 3:36 AM, Kristian Rother <krother at rubor.de> wrote:

>
> Hi,
>
> I'll take Peters hint to give a short summary what is going on on
> RNA at biopython. Actually, there are three lines of development:
>
> - Adding an extended sequence format that can handle modified RNA
> nucleotides (works with preliminary tests done).
> - Adding some simple parsers for common RNA 2D structure formats (Vienna,
> Ct, Bpseq) (something already works).
> - Adding the FCCD loop closer algorithm by Thomas Hamelryck (got the code
> but needs to be contributed).
>
> Basically all three require at the moment an independent person to take a
> look at them and state 'yes, this is useful for me' (if so).
>
> Komal, if you like to get involved could you write a little about what you
> are working with (RNA editing). If we find something thats not too far off
> for you we could get it moving.
>
> Best regards,
>    Kristian
>
>
>
> > Hi everyone,
> >
> > I'm Komal, a Junior Undergraduate Student from India
> > studying Bioengineering. I'm a fan of Python and I love Computational
> > Biology and I plan to do my further studies in the same.
> > I went through the projects on the Biopython page. I was very
> > much interested in the RNA Structure project mentioned. Any contribution
> > which I make will help me a lot and the organisation too. In fact, I am
> > currently doing a project on RNA Editing. I'll be very happy to integrate
> > my knowledge.
> >
> > In fact, I have been trying to contact people on #obf-soc IRC. I think
> > there
> > is no separate IRC for Biopython.
> >
> > Please help me on how I should proceed.
> >
> >
> > Komal
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
> >
>
>


From anaryin at gmail.com  Wed Mar  9 13:23:54 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Wed, 9 Mar 2011 14:23:54 +0100
Subject: [Biopython-dev] [Biopython] ::Biopython Project
In-Reply-To: <AANLkTinqXqJQhizkJhWcpqkD_D8pffj_1V7mk7o_851G@mail.gmail.com>
References: <AANLkTikDHtLdbyih7u3Jiy76Puvpr7Lh995-aBX-9jKu@mail.gmail.com>
	<d18d2fd8669f65b517a29211ae7a9ff0-EhVcX1xCQgFaRwICBxEAXR0wfgFLV15YQUBGAEFfUC9ZUFgWXVpyH1RXX0FdQU1tXlhQSV5SWA1YWw==-webmailer1@server05.webmailer.hosteurope.de>
	<AANLkTinqXqJQhizkJhWcpqkD_D8pffj_1V7mk7o_851G@mail.gmail.com>
Message-ID: <AANLkTi=ShGChKK=jDL=Q=+xD+gYmsOUtW_eZLAG5XEJb@mail.gmail.com>

Hello Komal,

I assume you're talking about this:
http://www.ncbi.nlm.nih.gov/pubmed/20547637.

Which features from the current Biopython RNA modules would fit your work
and how do you think you could improve them? Do you already have some ideas?

Cheers,

J


From p.j.a.cock at googlemail.com  Thu Mar 10 17:42:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 10 Mar 2011 17:42:58 +0000
Subject: [Biopython-dev] Bugzilla -> Redmine migration
Message-ID: <AANLkTi=VuX3+ymNEo34f2XY1N-OmSGJ1MPFp7TNbginn@mail.gmail.com>

Hi all,

Anyone who has tried to file a bug recently will have noticed a big
red message "Sorry, entering bugs into the product Biopython has been
disabled."

The reason for this is the OBF team are about to move us (and all the
other Bio* projects using Bugzilla) to a Redmine server instead.
See http://www.redmine.org/

I expect this to be completed in the next few days (with all the old
bugs and accounts carried across). Hopefully this will include
integration with our git repository as well.

We'll make an announcement once it is ready, in the mean time, any new
bugs could be emailed to the mailing list as a short term measure.

Peter


From updates at feedmyinbox.com  Sat Mar 12 09:11:34 2011
From: updates at feedmyinbox.com (Feed My Inbox)
Date: Sat, 12 Mar 2011 04:11:34 -0500
Subject: [Biopython-dev] 3/12 biopython Questions - BioStar
Message-ID: <59619d8d66b2e5c275645a69e1951352@74.63.51.88>

// Plotting DNA sequence traces
// March 11, 2011 at 11:00 AM

http://biostar.stackexchange.com/questions/6356/plotting-dna-sequence-traces
I have read/consulted these two threads here, the ABI file format document, the BioPython project, the R project, the BioConductor project and have searched extensively on the Internet, but I am not able to find an answer or explanation for what I would like to do.  

I would like to know how to interpret trace data from an ABI/AB1 trace file and how to plot this data. Ideally, I'd like to plot it on a web-page (in some format that allows for scrolling of course, but I haven't thought that much about this yet), but first I need to understand the trace data itself and how to plot it with Python and/or R.


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From updates at feedmyinbox.com  Fri Mar 18 13:05:29 2011
From: updates at feedmyinbox.com (Feed My Inbox)
Date: Fri, 18 Mar 2011 09:05:29 -0400
Subject: [Biopython-dev] 3/18 biopython Questions - BioStar
Message-ID: <aa2c8676d8752537ccfbac508cb3b969@74.63.51.88>

// Error translating genbank CDS using BioPython
// March 17, 2011 at 4:28 AM

http://biostar.stackexchange.com/questions/6560/error-translating-genbank-cds-using-biopython
Hi all,

I'm trying to translate the a genbank record using BioPython 1.53, ignoring the already given translation in the CDS feature. The code I've written to translate this is pretty straight forward:

...
for gb_record in SeqIO.parse(file_handle, 'genbank'):#Bio.GenBank.Record
    for gb_feature in gb_record.features:#Bio.SeqFeature
        #Skip any non coding sequence features
        if gb_feature.type != 'CDS':
            continue

        #Protein identifier is a property of the genbank feature
        protein_id = gb_feature.qualifiers['protein_id'][0]

        #Original sequence retrieved through BioPython 1.53+'s internal method 
        extracted_seq = gb_feature.extract(gb_record.seq)#Bio.Seq.Seq

        #Translation table is a property of the genbank feature
        transl_table = gb_feature.qualifiers['transl_table'][0]

        #Translate entire sequence as coding sequence using translation table
        #Additional CodonTables optionally available from Bio.Data.CodonTable
        try:
            protein_seq = extracted_seq.translate(table = transl_table, cds = True)
        except TranslationError, err:
            log.error('%s: Error in translating %s\n%s', gb_record.id, protein_id, extracted_seq)
            raise err

        #Write out fasta. Header format as requested: >genome_ac|protein_id
        _write_fasta_line(write_handle, '{0}|{1}'.format(gb_record.id, protein_id), str(protein_seq))


The translate line throws a TranslationError on the following feature:

 CDS             complement(2276255..2279302)
                 /locus_tag="ECBD_2165"
                 /EC_number="1.7.99.4"
                 /inference="protein motif:TFAM:TIGR01553"
                 /note="KEGG: ssn:SSON_1650 formate dehydrogenase-N,
                 nitrate-inducible, alpha subunit;
                 TIGRFAM: formate dehydrogenase, alpha subunit;
                 PFAM: molybdopterin oxidoreductase; molybdopterin
                 oxidoreductase Fe4S4 region; molydopterin
                 dinucleotide-binding region"
                 /codon_start=1
                 /transl_except=(pos:complement(2278715..2278717),aa:Sec)
                 /transl_table=11
                 /product="formate dehydrogenase, alpha subunit"
                 /protein_id="YP_003036386.1"
                 /db_xref="GI:253773555"
                 /db_xref="InterPro:IPR006311"
                 /db_xref="InterPro:IPR006443"
                 /db_xref="InterPro:IPR006655"
                 /db_xref="InterPro:IPR006656"
                 /db_xref="InterPro:IPR006657"
                 /db_xref="InterPro:IPR006963"
                 /db_xref="GeneID:8157271"
                 /translation="MDVSRRQFFKICAGGMAGTTVAALGFAPKQALAQARNYKLLRAK
                 EIRNTCTYCSVGCGLLMYSLGDGAKNAREAIYHIEGDPDHPVSRGALCPKGAGLLDYV
                 NSENRLRYPEYRAPGSDKWQRISWEEAFSRIAKLMKADRDANFIEKNEQGVTVNRWLS
                 TGMLCASGASNETGMLTQKFARSLGMLAVDNQARVUHGPTVASLAPTFGRGAMTNHWV
                 DIKNANVVMVMGGNAAEAHPVGFRWAMEAKNNNDATLIVVDPRFTRTASVADIYAPIR
                 SGTDITFLSGVLRYLIENNKINAEYVKHYTNASLLVRDDFAFEDGLFSGYDAEKRQYD
                 KSSWNYQFDENGYAKRDETLTHPRCVWNLLKEHVSRYTPDVVENICGTPKADFLKVCE
                 VLASTSAPDRTTTFLYALGWTQHTVGAQNIRTMAMIQLLLGNMGMAGGGVNALRGHSN
                 IQGLTDLGLLSTSLPGYLTLPSEKQVDLQSYLEANTPKATLADQVNYWSNYPKFFVSL
                 MKSFYGDAAQKENNWGYDWLPKWDQTYDVIKYFNMMDEGKVTGYFCQGFNPVASFPDK
                 NKVVSCLSKLKYMVVIDPLVTETSTFWQNHGESNDVDPASIQTEVFRLPSTCFAEEDG
                 SIANSGRWLQWHWKGQDAPGEARNDGEILAGIYHHLRELYQAEGGKGVEPLMKMSWNY
                 KQPHEPQSDEVAKENNGYALEDLYDANGVLIAKKGQLLSSFAHLRDDGTTASSCWIYT
                 GSWTEQGNQMANRDNSDPSGLGNTLGWAWAWPLNRRVLYNRASADINGKPWDPKRMLI
                 QWNGSKWTGNDIPDFGNAAPGTPTGPFIMQPEGMGRLFAINKMAEGPFPEHYEPIETP
                 LGTNPLHPNVVSNPVVRLYEQDALRMGKKEQFPYVGTTYRLTEHFHTWTKHALLNAIA
                 QPEQFVEISETLAAAKGINNGDRVTVSSKRGFIRAVAVVTRRLKPLNVNGQQVETVGI
                 PIHWGFEGVARKGYIANTLTPNVGDANSQTPEYKAFLVNIEKA"

root: ERROR: NC_012947.1: Error in translating YP_003036386.1
ATGGACGTCAGTCGCAGACAATTTTTTAAAATCTGCGCGGGCGGTATGGCTGGAACAACGGTAGCGGCATTGGGCTTTGCCCCGAAGCAAGCACTGGCTCAGGCGCGAAACTACAAATTATTACGCGCTAAAGAGATCCGTAACACCTGCACATACTGTTCCGTAGGTTGCGGGCTATTGATGTATAGCCTGGGTGATGGCGCGAAAAACGCCAGAGAAGCGATTTATCACATTGAAGGTGACCCGGATCATCCGGTAAGCCGTGGTGCGCTGTGCCCAAAAGGGGCCGGTTTGCTGGATTACGTCAACAGCGAAAACCGTCTGCGCTACCCGGAATATCGTGCGCCAGGTTCTGACAAATGGCAGCGCATTAGCTGGGAAGAAGCATTCTCCCGTATTGCAAAGCTGATGAAAGCTGACCGTGACGCTAACTTTATTGAAAAGAACGAGCAGGGCGTAACGGTAAACCGTTGGCTTTCTACCGGTATGCTGTGTGCCTCCGGTGCCAGCAACGAAACCGGGATGCTGACACAGAAATTTGCCCGCTCCCTCGGGATGCTGGCGGTAGACAACCAGGCGCGCGTCTGACACGGACCAACGGTAGCAAGTCTTGCTCCAACATTTGGTCGCGGTGCGATGACCAACCACTGGGTGGATATCAAAAACGCTAACGTCGTAATGGTAATGGGCGGTAACGCTGCTGAAGCGCATCCCGTCGGTTTCCGCTGGGCGATGGAAGCGAAAAACAACAACGATGCAACCTTGATCGTTGTCGATCCTCGTTTTACGCGTACCGCTTCTGTGGCGGATATTTACGCACCTATTCGTTCCGGTACGGACATTACGTTCCTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAACATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGCCTGTTCAGCGGTTATGACGCTGAAAAACGCCAGT
ACGACAAATCGTCCTGGAACTATCAGTTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGACTCATCCGCGCTGTGTGTGGAACCTGCTGAAAGAGCACGTTTCCCGCTACACGCCGGACGTCGTTGAAAACATCTGCGGTACGCCAAAAGCCGACTTCCTGAAAGTGTGTGAAGTGCTGGCCTCCACCAGCGCACCGGATCGCACAACCACCTTCCTGTACGCGCTGGGCTGGACGCAGCACACCGTGGGTGCGCAGAACATCCGTACTATGGCGATGATCCAGTTACTGCTCGGTAACATGGGTATGGCCGGTGGCGGCGTGAACGCATTGCGTGGTCACTCCAACATTCAGGGCCTGACTGACTTAGGTCTGCTCTCTACCAGCCTGCCAGGTTATCTGACGCTGCCGTCAGAAAAACAGGTTGATTTGCAGTCGTATCTGGAAGCGAACACGCCGAAAGCGACGCTGGCTGATCAGGTGAACTACTGGAGCAACTATCCGAAGTTCTTCGTTAGCCTGATGAAATCTTTCTATGGCGATGCCGCGCAGAAAGAGAACAACTGGGGCTATGACTGGCTGCCGAAGTGGGACCAGACCTACGACGTCATCAAGTATTTCAACATGATGGACGAAGGCAAAGTCACCGGTTATTTCTGCCAGGGCTTTAACCCGGTTGCGTCCTTCCCGGACAAAAACAAAGTGGTGAGCTGCCTGAGCAAGCTGAAGTACATGGTGGTTATCGATCCGCTGGTGACTGAAACCTCTACCTTCTGGCAGAACCACGGCGAGTCGAACGATGTCGATCCGGCGTCTATTCAGACTGAAGTATTCCGTCTGCCTTCGACCTGCTTTGCTGAAGAAGATGGTTCTATTGCTAACTCCGGTCGCTGGCTGCAGTGGCACTGGAAAGGTCAGGATGCGCCGGGCGAAGCGCGTAACGACGGTGAAATTCTGGCGGGTATCTACCATCACCTGCGCGAGCTGTACCA
GGCCGAAGGTGGTAAAGGCGTAGAACCGCTGATGAAGATGAGCTGGAACTACAAGCAGCCGCACGAACCGCAATCTGACGAAGTAGCTAAAGAGAACAACGGCTATGCGCTGGAAGATCTCTATGATGCTAATGGCGTGCTGATTGCGAAGAAAGGTCAGTTGCTGAGTAGCTTTGCGCATCTGCGTGATGACGGTACAACCGCATCTTCTTGCTGGATCTACACCGGTAGCTGGACAGAGCAGGGCAACCAGATGGCTAACCGCGATAACTCCGACCCGTCCGGTCTGGGGAATACGCTGGGATGGGCCTGGGCGTGGCCGCTCAACCGTCGCGTGCTGTACAACCGTGCTTCGGCGGATATCAACGGTAAACCGTGGGATCCGAAACGGATGCTGATCCAGTGGAACGGCAGCAAGTGGACGGGTAACGATATTCCTGACTTCGGCAATGCCGCACCGGGTACGCCAACCGGGCCGTTTATCATGCAGCCGGAAGGGATGGGACGCCTGTTTGCTATCAACAAAATGGCGGAAGGTCCGTTCCCGGAACACTACGAGCCGATTGAAACGCCGCTGGGCACTAACCCGCTGCATCCGAACGTGGTGTCTAACCCGGTTGTTCGTCTGTATGAACAAGACGCACTGCGGATGGGTAAAAAAGAGCAGTTCCCGTATGTGGGTACGACCTATCGTCTGACCGAGCACTTCCACACCTGGACCAAGCACGCATTGCTCAACGCAATTGCTCAGCCGGAACAGTTTGTGGAAATCAGCGAAACGCTGGCGGCGGCGAAAGGCATTAATAATGGCGATCGTGTCACTGTCTCAAGCAAGCGTGGCTTTATCCGCGCGGTGGCTGTGGTAACGCGTCGTCTGAAACCACTGAATGTAAATGGTCAGCAGGTTGAAACGGTGGGTATTCCAATCCACTGGGGCTTTGAGGGTGTCGCGCGTAAAGGTTATATCGCTAACACTCTGACGCCGAATGTCGGTGAT
GCAAACTCGCAAACGCCGGAATATAAAGCGTTCTTAGTCAACATCGAGAAGGCGTAA


Error:

Traceback (most recent call last):
  File "/usr/lib/python2.6/unittest.py", line 279, in run
    testMethod()
  File "/home/user/jenkins/workspace/Divergence/divergence/src/divergence/test/test_translate.py", line 33, in test_translate_ecoli_and_salmo
    fasta_file = translate_genbank_to_protein(genbank_file, ptt_file)
  File "/home/user/jenkins/workspace/Divergence/divergence/src/divergence/translate.py", line 73, in translate_genbank_to_protein
    raise err
TranslationError: Extra in frame stop codon found.


Now I'm guessing this has something to do with the /transl_except I'm seeing in the GenBank record, but I'm not (yet) sure. (The GenBank supplied translation contains a Selenocysteine.) But even if this is the cause: How would I properly handle this in my BioPython translation? I can't find any method to exclude certain sections from translation..

Can anyone help me fix the translation?

Best regards,
Tim

(Ps. Should anyone wonder why I'm not using the translation in the GenBank file directly: It's a requirement that I translate from the DNA sequence to protein myself...)


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From mnaik28 at gmail.com  Wed Mar 23 05:50:59 2011
From: mnaik28 at gmail.com (Medha Naik)
Date: Wed, 23 Mar 2011 00:50:59 -0500
Subject: [Biopython-dev] Project ideas for CS grad
Message-ID: <4D898A43.5010407@gmail.com>

Hi All,

I am a Computer Science Master's student from Texas with an inclination 
towards Bioinformatics. I love coding in Python and would like to 
contribute to some code development in Biopython. I do have basic 
understanding of the biology and genetics concepts in bioinformatics but 
I am primarily looking to work on the computational aspects like coding 
some algorithms, data structures or database interactions.

I read Dan Gusfield's book, 'Algorithms on Strings, Trees and 
Sequences', as part of my coursework and got interested in implementing 
an algorithm or two from the same using the sequence and tree classes 
already defined in Biopython.

Is there any open project that I could contribute to by doing the above? 
I do not want to independently begin something without some guidance 
from a person from the team.

I am open to all ideas/suggestions  and I hope that I can contribute 
something to this amazing module that integrates python, computer 
science concepts and biology!

Regards,
Medha Naik




From updates at feedmyinbox.com  Wed Mar 23 08:06:27 2011
From: updates at feedmyinbox.com (Feed My Inbox)
Date: Wed, 23 Mar 2011 04:06:27 -0400
Subject: [Biopython-dev] 3/23 active questions tagged biopython - Stack
	Overflow
Message-ID: <cb8d4903fb229180f66226d9544ec6e3@74.63.51.88>

// marking up mutation positions in a sequence with html in python
// March 22, 2011 at 7:03 AM

http://stackoverflow.com/questions/5390170/marking-up-mutation-positions-in-a-sequence-with-html-in-python
Hello,

I was wondering if there are any methods in python or biopython that allows one to markup a sequence in html.

I would like to mark positions on a sequence (ie colour bases differently) according to if that position is a known snp/indel etc 

Having a list of mutation positions in an array (read from a database) eg

mutation_position = [10,20,30,40]

I can change case for the affected base using something like:
seq = seq[0:b] + mutation_positions[b].lower() + seq[(b+1):len(seq)]

But is it possible to add some html code eg add the tag pos for each of the mutation positions. (when the html markup is added to the sequence, the length of the sequence is altered and so the mutation positions don't match to the newly marked up sequence during each iteration of the loop!)

I hope this makes sense!

Thanks.


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From p.j.a.cock at googlemail.com  Sun Mar 27 13:32:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sun, 27 Mar 2011 14:32:28 +0100
Subject: [Biopython-dev] New test_Phylo.py test on Python 3
Message-ID: <AANLkTin4vj27c6YRxY6Lf7CbdhgrOvg97a=20WnGxxuL@mail.gmail.com>

Hi Eric,

You'll need to handle None explicitly for the comparison to pass under
Python 3 (see below), or you get:

Traceback (most recent call last):
  ...
  File "/home/buildslave/BuildBot/lin3264/build/build/py3.2/Tests/test_Phylo.py",
line 280, in <lambda>
    tree.collapse_all(lambda c: c.branch_length < 0.1)
TypeError: unorderable types: NoneType() < float()

http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100/steps/shell/logs/stdio
http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.1/builds/179/steps/shell/logs/stdio

Regards,

Peter

---------- Forwarded message ----------
From:  <biopython-dev at biopython.org>
Date: Sun, Mar 27, 2011 at 4:12 AM
Subject: buildbot failure in Biopython on Linux 64 - Python 3.2
To: p.j.a.cock at googlemail.com, tiagoantao at gmail.com


The Buildbot has detected a new failure on builder Linux 64 - Python
3.2 while building Biopython.
Full details are available at:
?http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100

Buildbot URL: http://testing.open-bio.org/biopython/

Buildslave for this Build: peter_linux64

Build Reason: The Nightly scheduler named 'nightly' triggered this build
Build Source Stamp: HEAD
Blamelist:

BUILD FAILED: failed shell

sincerely,
?-The Buildbot



From p.j.a.cock at googlemail.com  Mon Mar 28 12:43:40 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 28 Mar 2011 13:43:40 +0100
Subject: [Biopython-dev] Fwd: [Biopython - Bug #3187] pip install biopython
In-Reply-To: <redmine.journal-14249.20110328123532@redmine.open-bio.org>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
Message-ID: <AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>

Hi Brad (et al),

It looks like automatic emails from Redmine to the biopython-dev list
are not working properly... anyway, could you take a look at Bug 3187?

https://redmine.open-bio.org/issues/3187

I suspect this is related to PIP issue 8, i.e. PIP doesn't like our
setup.py file.

https://github.com/pypa/pip/issues/8

Thanks,

Peter


---------- Forwarded message ----------
From:  <redmine at redmine.open-bio.org>
Date: Mon, Mar 28, 2011 at 1:35 PM
Subject: [Biopython - Bug #3187] pip install biopython
To: casbon at gmail.com
Cc: p.j.a.cock at googlemail.com


Issue #3187 has been updated by James Casbon.

File pip.log added

It's pretty much the same as the output I posted, but I have attached.

________________________________

Bug #3187: pip install biopython

Author: James Casbon
Status: New
Priority: Normal
Assignee:
Category: Main Distribution
Target version:
URL:

james at flapjack:/tmp$ virtualenv bp-pip
New python executable in bp-pip/bin/python
Installing setuptools............done.
james at flapjack:/tmp$ source /tmp/bp-pip/bin/activate
(bp-pip)james at flapjack:/tmp$ pip install biopython
Downloading/unpacking biopython
  Downloading biopython-1.56.tar.gz (6.9Mb): 6.9Mb downloaded
  Running setup.py egg_info for package biopython

    warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
    warning: no previously-included files found matching 'Tests/Graphics/*.eps'
    warning: no previously-included files found matching 'Tests/Graphics/*.svg'
    warning: no previously-included files found matching 'Tests/Graphics/*.png'
    warning: no previously-included files matching '*' found under
directory 'Tests/UnitTests'
    warning: no previously-included files matching '.cvsignore' found
under directory '*'
    warning: no previously-included files matching '.gitignore' found
under directory '*'
    warning: no previously-included files matching '*.pyc' found under
directory '*'
Installing collected packages: biopython
  Running setup.py install for biopython
    usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
       or: -c --help [cmd1 cmd2 ...]
       or: -c --help-commands
       or: -c cmd --help

    error: option --single-version-externally-managed not recognized
    Complete output from command /private/tmp/bp-pip/bin/python -c
"import setuptools;
__file__='/private/tmp/bp-pip/build/biopython/setup.py';
execfile('/private/tmp/bp-pip/build/biopython/setup.py')" install
--single-version-externally-managed --record
/var/folders/Gn/GneSaDeKGaGpZXx+hcopdU+++TI/-Tmp-/pip-slq1Hy-record/install-record.txt
--install-headers /private/tmp/bp-pip/bin/../include/site/python2.7:
    usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]

   or: -c --help [cmd1 cmd2 ...]

   or: -c --help-commands

   or: -c cmd --help

error: option --single-version-externally-managed not recognized

----------------------------------------
Command /private/tmp/bp-pip/bin/python -c "import setuptools;
__file__='/private/tmp/bp-pip/build/biopython/setup.py';
execfile('/private/tmp/bp-pip/build/biopython/setup.py')" install
--single-version-externally-managed --record
/var/folders/Gn/GneSaDeKGaGpZXx+hcopdU+++TI/-Tmp-/pip-slq1Hy-record/install-record.txt
--install-headers /private/tmp/bp-pip/bin/../include/site/python2.7
failed with error code 1
Storing complete log in /Users/james/.pip/pip.log

________________________________

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From chapmanb at 50mail.com  Mon Mar 28 13:36:39 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 28 Mar 2011 09:36:39 -0400
Subject: [Biopython-dev] Fwd: [Biopython - Bug #3187] pip install
	biopython
In-Reply-To: <AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
Message-ID: <20110328133639.GD26383@sobchak>

Peter;

[pip install problem]
> https://redmine.open-bio.org/issues/3187

Thanks for the heads up. I pushed a fix for this back in December,
which was unfortunately post-1.56:

https://github.com/biopython/biopython/commit/4e4c3aa1df3d6848afed4783c4e54186a751accd#setup.py

What is our timeline for 1.57? If it's a long way out we can
work on back-porting to 1.56 and re-upload. 

Brad



From p.j.a.cock at googlemail.com  Mon Mar 28 13:55:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 28 Mar 2011 14:55:58 +0100
Subject: [Biopython-dev] Fwd: [Biopython - Bug #3187] pip install
	biopython
In-Reply-To: <20110328133639.GD26383@sobchak>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
	<20110328133639.GD26383@sobchak>
Message-ID: <AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>

On Mon, Mar 28, 2011 at 2:36 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Peter;
>
> [pip install problem]
>> https://redmine.open-bio.org/issues/3187
>
> Thanks for the heads up. I pushed a fix for this back in December,
> which was unfortunately post-1.56:
>
> https://github.com/biopython/biopython/commit/4e4c3aa1df3d6848afed4783c4e54186a751accd#setup.py
>
> What is our timeline for 1.57? If it's a long way out we can
> work on back-porting to 1.56 and re-upload.

I was hoping for some more comments on the tutorial, and ideally fix
http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html
but other than that we're good to go. Do you want to do the honours?

Peter


From eric.talevich at gmail.com  Mon Mar 28 14:17:46 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Mon, 28 Mar 2011 10:17:46 -0400
Subject: [Biopython-dev] New test_Phylo.py test on Python 3
In-Reply-To: <AANLkTin4vj27c6YRxY6Lf7CbdhgrOvg97a=20WnGxxuL@mail.gmail.com>
References: <AANLkTin4vj27c6YRxY6Lf7CbdhgrOvg97a=20WnGxxuL@mail.gmail.com>
Message-ID: <AANLkTi=N51e+JUCHE_0nY0+SstpErW8MSVS+-q+R9iVm@mail.gmail.com>

Thanks, Peter. The build bot is pretty handy!

My fix was here, for the public record:
https://github.com/biopython/biopython/commit/8edd552b72a31179cd53eb1493ac5462f7fb8f7c

Lambda expressions like the one in test_Phylo.py are supposed to Just Work,
since manually handling all the edge cases for comparisons is tedious (or
impossible, since try/except statements aren't allowed in Python's lambda
expressions). So I fixed the way Bio.Phylo wraps lambda expressions,
instead.

-E

On Sun, Mar 27, 2011 at 9:32 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi Eric,
>
> You'll need to handle None explicitly for the comparison to pass under
> Python 3 (see below), or you get:
>
> Traceback (most recent call last):
>  ...
>  File
> "/home/buildslave/BuildBot/lin3264/build/build/py3.2/Tests/test_Phylo.py",
> line 280, in <lambda>
>    tree.collapse_all(lambda c: c.branch_length < 0.1)
> TypeError: unorderable types: NoneType() < float()
>
>
> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100/steps/shell/logs/stdio
>
> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.1/builds/179/steps/shell/logs/stdio
>
> Regards,
>
> Peter
>
> ---------- Forwarded message ----------
> From:  <biopython-dev at biopython.org>
> Date: Sun, Mar 27, 2011 at 4:12 AM
> Subject: buildbot failure in Biopython on Linux 64 - Python 3.2
> To: p.j.a.cock at googlemail.com, tiagoantao at gmail.com
>
>
> The Buildbot has detected a new failure on builder Linux 64 - Python
> 3.2 while building Biopython.
> Full details are available at:
>
> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.2/builds/100
>
> Buildbot URL: http://testing.open-bio.org/biopython/
>
> Buildslave for this Build: peter_linux64
>
> Build Reason: The Nightly scheduler named 'nightly' triggered this build
> Build Source Stamp: HEAD
> Blamelist:
>
> BUILD FAILED: failed shell
>
> sincerely,
>  -The Buildbot
>


From redmine at redmine.open-bio.org  Mon Mar 28 15:04:43 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 28 Mar 2011 15:04:43 +0000
Subject: [Biopython-dev] [Biopython - Bug #3188] Test bug, please ignore
References: <redmine.issue-3188.20110328134006@redmine.open-bio.org>
Message-ID: <redmine.journal-14252.20110328150443@redmine.open-bio.org>


Issue #3188 has been updated by Chris Fields.

Assignee set to Biopython Developer's

retesting with dev account
----------------------------------------
Bug #3188: Test bug, please ignore
https://redmine.open-bio.org/issues/3188

Author: Peter Cock
Status: New
Priority: Normal
Assignee: Biopython Developer's
Category: 
Target version: 
URL: 


The aim of this bug is to test the Redmine "Email on New Issue" option from the Newissuealerts module.

This issue should get emailed to the biopython-dev email list automatically...

Peter


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From chapmanb at 50mail.com  Tue Mar 29 12:05:32 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 29 Mar 2011 08:05:32 -0400
Subject: [Biopython-dev] 1.57 release plans
In-Reply-To: <AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>
References: <redmine.issue-3187.20110328105726@redmine.open-bio.org>
	<redmine.journal-14249.20110328123532@redmine.open-bio.org>
	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
	<20110328133639.GD26383@sobchak>
	<AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>
Message-ID: <20110329120532.GL26383@sobchak>

Peter;

> > What is our timeline for 1.57? 

> I was hoping for some more comments on the tutorial, and ideally fix
> http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html
> but other than that we're good to go. Do you want to do the honours?

For your fastq file examples, we could use the EBI short read
archive, which is staying around for a while longer:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000001/

I can do on the release, but probably later this week or over the
weekend. How do you normally get together the list of contributors?
That, and the list of new features, are the major two things I'm not
on top off.

Thanks,
Brad


From p.j.a.cock at googlemail.com  Tue Mar 29 12:26:21 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 29 Mar 2011 13:26:21 +0100
Subject: [Biopython-dev] 1.57 release plans
In-Reply-To: <20110329120532.GL26383@sobchak>
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	<AANLkTik3qiHZYPHGZrNSc+NhrRYYS73KEhgREGuzjGQc@mail.gmail.com>
	<20110328133639.GD26383@sobchak>
	<AANLkTim6AGDdn0+QKrnwEAxrWOhExnwC2HO65ZVGB0t6@mail.gmail.com>
	<20110329120532.GL26383@sobchak>
Message-ID: <AANLkTikSRaz_RDDwJvw2YKNwRicnYoOD0sURVUGOvTu0@mail.gmail.com>

On Tue, Mar 29, 2011 at 1:05 PM, Brad Chapman wrote:
> Peter;
>
>> > What is our timeline for 1.57?
>
>> I was hoping for some more comments on the tutorial, and ideally fix
>> http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html
>> but other than that we're good to go. Do you want to do the honours?
>
> For your fastq file examples, we could use the EBI short read
> archive, which is staying around for a while longer:
>
> ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000001/

Good plan - why didn't I think of that the other night when I was
looking at this? I may even be able to find the equivalent files to
the ones we used to use from the NCBI SRA. I'll try and sort
that today or tomorrow...

> I can do on the release, but probably later this week or over the
> weekend.

Cool. That suits me. You can trigger builds on the buildbot
manually (if you know the password...) and/or wait for the
nightly scheduled build. That is quite handy for a final test
just before tagging the repository and building the archives.
Also useful if you don't have a suitable Windows machine
handy - I can always do the Windows installers a day later
(well, not on weekends).

> How do you normally get together the list of contributors?
> That, and the list of new features, are the major two things
> I'm not on top off.

I try to make sure that the NEWS file is kept up to date as
we go along, so the "release announcement" is a prettified
version of that really. You can take a bit more space to talk
about new stuff, and really big bits of new code could even
warrant their blog post on news.open-bio.org to help raise
awareness. As usual circulating a draft release statement on
the dev list is a good way to avoid missing anything really
obvious :)

Thanks,

Peter