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Brad Chapman | 1 Apr 2011 12:37
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Re: GSoC: "Variant representation, parser, generator, and coordinate converter"

Maximiliano;
Thanks for the introduction and interest in the project. I'm cc'ing
in the mailing list and Reece, who is the primary mentor.

> >> My name is Maximiliano David Bustos, I am from La Rioja, Argentina. I am
> >> 20 years old, and currently studying Computer Science at "Facultad de
> >> Matemática Astronomía y Física" (Fa.M.A.F - UNC).
> >>
> >> I have read about your organization, in I like the projects that you are
> >> developing. I am really interested in contributing in the project
> >> "Variant representation, parser, generator, and coordinate converter",
> >> taken from your wiki.
> >>
> >> I want to read more about the topic before writing to the corresponding
> >> mailing list.

Great to hear. Could you provide some more background and details
about why you are interested in the project and what areas you would
like to read more on? It would be really helpful to understand how
comfortable you are with Python programming, with the Biopython
project, and with the biological concepts (variations, genes,
proteins).

Thanks again,
Brad
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Peter Cock | 1 Apr 2011 12:48
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Re: 1.57 release plans

On Tue, Mar 29, 2011 at 1:26 PM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
> 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...

Good news - the tutorial update is nearly done now.

Bad news - I updated to NCBI BLAST 2.2.25+ and the unit test is
complaining about some new switches like -db_hard_mask which
we'll need to add and then white-list in test_NCBI_BLAST_tools.py
(or just turn off this bit of the tests)

Peter
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Peter Cock | 1 Apr 2011 18:35
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Re: 1.57 release plans

On Fri, Apr 1, 2011 at 11:48 AM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
>
> Good news - the tutorial update is nearly done now.
>
> Bad news - I updated to NCBI BLAST 2.2.25+ and the unit test is
> complaining about some new switches like -db_hard_mask which
> we'll need to add and then white-list in test_NCBI_BLAST_tools.py
> (or just turn off this bit of the tests)
>

OK, I think both the SRA links in the Tutorial and the new
arguments added to the BLAST+ tools are done.

We are also all green on the buildbot (I just forced a set of
builds after making those commits):
http://testing.open-bio.org/biopython/grid

Ready when you are Brad, and if you'd like to wait until after
April 1st is over to avoid any jokes, that's OK with me ;)

Peter
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Brad Chapman | 1 Apr 2011 20:50
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Re: 1.57 release plans

Peter;
Thanks for fixing the BLAST+ issue and the tutorial. We'll plan for
a release later this evening or tomorrow morning, so everyone please
hold off commits until it's finished.

Below are the release notes and contributors list for the release.
Please let me know anything or anyone is missing; additionally if
anyone wants to clean up the text or add more flourishes of
brilliance, that would be very welcome.

Thanks everyone for all the hard work for the release,
Brad

In progress: Biopython 1.57 (not yet released).

Bio.SeqIO now includes an index_db() function which extends the existing
indexing functionality to allow indexing many files, and more importantly
this keeps the index on disk in a simple SQLite3 database rather than in
memory in a Python dictionary.

Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter
tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the
ability to run the BLAST tools and save the output as ASN.1 format, and then
convert this to any other supported BLAST ouput format (plain text, tabular,
XML, or HTML) with the blast_formatter tool. The wrappers were also updated
to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.

The SeqRecord object now has a reverse_complement method (similar to that of
the Seq object). This is most useful to reversing per-letter-annotation (such
as quality scores from FASTQ) or features (such as annotation from GenBank).
(Continue reading)

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Eric Talevich | 2 Apr 2011 00:08
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Re: 1.57 release plans

On Fri, Apr 1, 2011 at 2:50 PM, Brad Chapman <chapmanb <at> 50mail.com> wrote:

>
> Below are the release notes and contributors list for the release.
> Please let me know anything or anyone is missing; additionally if
> anyone wants to clean up the text or add more flourishes of
> brilliance, that would be very welcome.
>
> Thanks everyone for all the hard work for the release,
> Brad
>
>
> In progress: Biopython 1.57 (not yet released).
>
> Bio.SeqIO now includes an index_db() function which extends the existing
> indexing functionality to allow indexing many files, and more importantly
> this keeps the index on disk in a simple SQLite3 database rather than in
> memory in a Python dictionary.
>
> Bio.Blast.Applications now includes a wrapper for the BLAST+
> blast_formatter
> tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the
> ability to run the BLAST tools and save the output as ASN.1 format, and
> then
> convert this to any other supported BLAST ouput format (plain text,
> tabular,
> XML, or HTML) with the blast_formatter tool. The wrappers were also updated
> to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.
>
> The SeqRecord object now has a reverse_complement method (similar to that
(Continue reading)

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Feed My Inbox | 2 Apr 2011 10:09

4/2 active questions tagged biopython - Stack Overflow

// Bio.IUPAC problem in Biopython
// April 1, 2011 at 5:28 PM

http://stackoverflow.com/questions/5519081/bio-iupac-problem-in-biopython
i was testing this simple code

from Bio.Alphabet import IUPAC
from Bio import Seq
my_prot=Seq("AGTACACTGGT",IUPAC.protein)

and it gives me this error

TypeError: 'module' object is not callable

can anyone explain why this is happening?

PS: this is an Example from the BioPython's Cookbook

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Chen Wei | 2 Apr 2011 10:49
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Re: 4/2 active questions tagged biopython - Stack Overflow

On Sat, Apr 02, 2011 at 04:09:17AM -0400, Feed My Inbox wrote:
> from Bio.Alphabet import IUPAC
> from Bio import Seq
> my_prot=Seq("AGTACACTGGT",IUPAC.protein)
> 
> and it gives me this error
> 
> TypeError: 'module' object is not callable
> 
it is a namespace problem, Seq is a class lives inside module Seq. Take
a look at Bio/Seq.py.

u can either change the code to:
my_prot=Seq.Seq("AGTACACTGGT",IUPAC.protein)
or use:
from Bio.Seq import Seq

--

-- 
Chen Wei
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Peter Cock | 2 Apr 2011 15:43
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Re: 1.57 release plans

Thanks Brad :)

http://news.open-bio.org/news/2011/04/biopython-1-57-released/

I'll get the Windows installers done on Monday.

Peter
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redmine | 2 Apr 2011 16:25

[Biopython - Feature #3193] (New) Bio.Phylo.Applications support for MrBayes


Issue #3193 has been reported by Eric Talevich.

----------------------------------------
Feature #3193: Bio.Phylo.Applications support for MrBayes
https://redmine.open-bio.org/issues/3193

Author: Eric Talevich
Status: New
Priority: Normal
Assignee: Eric Talevich
Category: Main Distribution
Target version: Not Applicable
URL: 

MrBayes is a popular tool for inferring phylogenies, reasonably best-practice, open-source, and
packaged for Debian. Let's create a wrapper for it in Biopython.

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redmine | 2 Apr 2011 16:59

[Biopython - Feature #3194] (New) Bio.Phylo export to 'ape' via Rpy2


Issue #3194 has been reported by Eric Talevich.

----------------------------------------
Feature #3194: Bio.Phylo export to 'ape' via Rpy2
https://redmine.open-bio.org/issues/3194

Author: Eric Talevich
Status: New
Priority: Low
Assignee: Eric Talevich
Category: Main Distribution
Target version: Not Applicable
URL: 

There are many more packages for working with phylogenetic data in R, and most of these operate on the basic
tree object defined in the ape package. Let's support interoperability through Rpy2.

The trivial way to do this is serialize a tree to a Newick string, then feed that to the read.tree() function.
Maybe we can build the tree object in R directly and retain the tree annotations that Newick doesn't handle.

See:
http://ape.mpl.ird.fr/
http://rpy.sourceforge.net/rpy2.html

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Gmane