headers
Peter Cock | 1 Sep 2010 01:00
Gravatar

[Biopython] Biopython 1.55 released

Dear Biopythoneers,

After the beta earlier this month (thank you to everyone who
helped test this), we’ve just released Biopython 1.55 . For
full details see:

http://news.open-bio.org/news/2010/08/biopython-1-55-released/

Note we are phasing out support for Python 2.4. We will continue
to support it for at least one further release (i.e. Biopython 1.56).
This could be delayed given feedback from our users (e.g. if this
proves to be a problem in combination with other libraries or a
popular Linux distribution).

(At least) 12 people have contributed to this release, including
6 new people – thank you all:

    * Andres Colubri (first contribution)
    * Carlos Rios Vera (first contribution)
    * Claude Paroz (first contribution)
    * Cymon Cox
    * Eric Talevich
    * Frank Kauff
    * Joao Rodrigues (first contribution)
    * Konstantin Okonechnikov (first contribution)
    * Michiel de Hoon
    * Nathan Edwards (first contribution)
    * Peter Cock
    * Tiago Antao
(Continue reading)

Permalink | Reply | 0 comments |
headers
Peter | 1 Sep 2010 18:52
Picon
Picon

[Biopython] Deprecating Bio.GenBank.LocationParser and Bio.Parsers?

Hello all,

One of the improvements in Biopython 1.55 was a re-written location
parser for Bio.GenBank (which also covers EMBL parsing). This made
parsing much faster, and also meant Bio.GenBank.LocationParser
and the underlying Bio.Parsers and Bio.Parsers.spark modules were
obsolete. I'd like to mark these as deprecated in the next release:

* Bio.GenBank.LocationParser
* Bio.Parsers (including Bio.Parsers.spark)

Would this cause anyone a problem?

Thanks,

Peter
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
Permalink | Reply | 1 comment |
headers
John Reid | 3 Sep 2010 15:11
Picon

[Biopython] Wrong instance length bug in MEME parser

Hi,

The MEME parser in biopython 1.55 seems to incorrectly set the length of 
the first instance of a motif to 0. Here is an example:

#Sequence, start, length, site
Motif: E-value: 0.000010
      seq_3,   213,     0, AGGTGACAGAG
      seq_1,   146,    11, AGGTGACAGAG
      seq_0,   490,    11, AGGTGACAGAG
      seq_0,    83,    11, AGGTGACAGAG
      seq_0,   388,    11, AGGAAACAGAG
      seq_1,   422,    11, AGGGGACAGAG
      seq_1,    79,    11, TGGAGACAGAG
      seq_0,   281,    11, TGGGGACAGAG
      seq_0,    16,    11, TAGAGACAGAG
      seq_1,   228,    11, TTGTGACAGAG
      seq_4,   156,    11, AGGGGACAGGG
      seq_0,   348,    11, AGGAAAGAGAA
      seq_0,   374,    11, AGGAATGAGAG
      seq_5,    22,    11, GGGAAACTGAG
      seq_3,   486,    11, AAGGGAGTGAG

Here's the code that generated the above:

from Bio.Motif.Parsers.MEME import MEMEParser
import cStringIO

meme_output = cStringIO.StringIO("""
********************************************************************************
(Continue reading)

Permalink | Reply | 2 comments |
headers
Peter | 3 Sep 2010 15:44
Picon
Picon

Re: [Biopython] Wrong instance length bug in MEME parser

On Fri, Sep 3, 2010 at 2:11 PM, John Reid <j.reid <at> mail.cryst.bbk.ac.uk> wrote:
> Hi,
>
> The MEME parser in biopython 1.55 seems to incorrectly set the length of the
> first instance of a motif to 0. Here is an example:
> ...

Could you file a bug with all that useful information?
http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython

Thanks,

Peter
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
Permalink | Reply | 0 comments |
headers
Bartek Wilczynski | 3 Sep 2010 16:52
Gravatar

Re: [Biopython] Wrong instance length bug in MEME parser

On Fri, Sep 3, 2010 at 3:11 PM, John Reid <j.reid <at> mail.cryst.bbk.ac.uk>wrote:

> Hi,
>
> The MEME parser in biopython 1.55 seems to incorrectly set the length of
> the first instance of a motif to 0. Here is an example:
>
> /cut/
Hi,

Thanks for reporting the bug. It is fixed now in the main branch (small
change, you can see the diff here :
http://github.com/biopython/biopython/commit/102ad30a8c5d8bd87847000b33f771b40143e743

I'm closing the bug now, if you find anything else, please let us know.

thanks
Bartek
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
Permalink | Reply | 0 comments |
headers
xyz | 6 Sep 2010 15:24
Picon
Favicon

[Biopython] reading two fastq files at the same time

Hi,
How is it possible to read two fastq files at the same time in 
BioPython? I have the following BioRuby example:

require 'bio'

begin
   fq1 = Bio::FlatFile.open(Bio::Fastq, ARGV[2])
   fq2 = Bio::FlatFile.open(Bio::Fastq, ARGV[3])

   while (entry1 = fq1.next_entry) and (entry2 = fq2.next_entry)

     fastq_A1 = entry1.entry_id
     fastq_A2 = entry1.seq

     fastq_B1 = entry2.entry_id
     fastq_B2 = entry2.seq
   end

rescue => err
   raise "Exception: #{err}"
end

Thank you in advance.
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
Permalink | Reply | 1 comment |
headers
Peter | 6 Sep 2010 15:51
Picon
Picon

Re: [Biopython] reading two fastq files at the same time

On Mon, Sep 6, 2010 at 2:24 PM, xyz <mitlox <at> op.pl> wrote:
> Hi,
> How is it possible to read two fastq files at the same time in BioPython? I
> have the following BioRuby example:
>
> require 'bio'
>
> begin
>  fq1 = Bio::FlatFile.open(Bio::Fastq, ARGV[2])
>  fq2 = Bio::FlatFile.open(Bio::Fastq, ARGV[3])
>
>  while (entry1 = fq1.next_entry) and (entry2 = fq2.next_entry)
>
>    fastq_A1 = entry1.entry_id
>    fastq_A2 = entry1.seq
>
>    fastq_B1 = entry2.entry_id
>    fastq_B2 = entry2.seq
>  end
>
> rescue => err
>  raise "Exception: #{err}"
> end
>
> Thank you in advance.

Hi,

If you are using Python 2.6+ then probably itertools.izip_longest
would do what you want. You could use itertools.izip but this
(Continue reading)

Permalink | Reply | 0 comments |
headers
Peter | 9 Sep 2010 19:13
Picon
Picon

Re: [Biopython] Deprecating Bio.GenBank.LocationParser and Bio.Parsers?

On Wed, Sep 1, 2010 at 5:52 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
> Hello all,
>
> One of the improvements in Biopython 1.55 was a re-written location
> parser for Bio.GenBank (which also covers EMBL parsing). This made
> parsing much faster, and also meant Bio.GenBank.LocationParser
> and the underlying Bio.Parsers and Bio.Parsers.spark modules were
> obsolete. I'd like to mark these as deprecated in the next release:
>
> * Bio.GenBank.LocationParser
> * Bio.Parsers (including Bio.Parsers.spark)
>
> Would this cause anyone a problem?
>
> Thanks,

I've just added the deprecation warnings to the code, ready for
Biopython 1.56 - it is not too late to undo this is anyone is using
this code, but you need to tell us.

Peter
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
Permalink | Reply | 0 comments |
headers
mailing list | 10 Sep 2010 06:10
Picon

[Biopython] Added Biopython to my web tool

I made a web application (http://utilitymill.com) that lets people make
online utilities with Python.  I thought you guys might appreciate I added
Biopython as a built-in library users can use in their utilities.

Here's an example of a utility using Biopython:
http://utilitymill.com/utility/RNA_Transcription  (It's very simple, I just
wanted to try it out.)

I'm curious to know if it's useful to you guys.  And I'm also hoping I
installed everything correctly, so let me know if anything doesn't work.

-Greg
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
Permalink | Reply | 0 comments |
headers
Michiel de Hoon | 11 Sep 2010 07:29
Picon
Favicon

[Biopython] Parsing XML returned by efetch from the Journals database

Dear users,

The parser in Bio.Entrez can parse any XML returned by the Entrez E-utilities as long as the corresponding
DTD is available (which are included with each release of Biopython). One corner case is efetch results
from the Journals database. Officially, efetch from the Journals database does not generate output in
the XML format, but only plain text or HTML. However, when requesting XML explicitly from Entrez, in
practice it does return an XML-like output. Our parser in Bio.Entrez is able to parse this XML, but it
requires several hacks in the parser code.

To make the parser more stable for other XML documents, I'd like to remove these hacks. Currently is anybody
using Bio.Entrez to parse XML returned by efetch from the Journals database?

--Michiel.

      
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
Permalink | Reply | 0 comments |

Gmane