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bugzilla-daemon | 5 Feb 2008 14:36

[Bug 2443] New: Specifying the alphabet in Bio.SeqIO.parse()

http://bugzilla.open-bio.org/show_bug.cgi?id=2443

           Summary: Specifying the alphabet in Bio.SeqIO.parse()
           Product: Biopython
           Version: 1.44
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: biopython-bugzilla <at> maubp.freeserve.co.uk

Currently when reading sequences using Bio.SeqIO, unless the alphabet can be
determined from the file format, all the records have a generic alphabet.

This can be a handicap if later on you want to work with "strict" functions
which check for a particular alphabet (e.g. a gapped alphabet when working with
alignments), or perhaps the Bio.Translate module.

For an example of this, see Dalloliogm's question on the SeqIO wiki talk page,
http://biopython.org/wiki/Talk:SeqIO

Currently the user may need to use a tedious work around to override the
alphabet of each sequence, e.g.

from Bio import SeqIO
from Bio.Alphabet import generic_dna
records = list(SeqIO.parse(open("data.txt"), "fasta"))
(Continue reading)

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bugzilla-daemon | 5 Feb 2008 14:37

[Bug 2443] Specifying the alphabet in Bio.SeqIO.parse()

http://bugzilla.open-bio.org/show_bug.cgi?id=2443

------- Comment #1 from biopython-bugzilla <at> maubp.freeserve.co.uk  2008-02-05 08:37 EST -------
Created an attachment (id=853)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=853&action=view)
Path to Bio/SeqIO/__init__.py

One possible implementation which will use a format specific parser's optional
alphabet argument if defined, and if not simply override the alphabet of the
returned records.

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bugzilla-daemon | 5 Feb 2008 21:05

[Bug 2446] New: Comments in CT tags cause Bio.Sequencing.Ace.ACEParser to fail.

http://bugzilla.open-bio.org/show_bug.cgi?id=2446

           Summary: Comments in CT tags cause Bio.Sequencing.Ace.ACEParser
                    to fail.
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: dthomp325 <at> gmail.com

When parsing an ace file that contains CT tags with comments such as those
added by Polyphred 6.11, Bio.Sequencing.Ace.ACEParser appears to get stuck in
an infinite loop until it dies with a memory usage exception.

example CT tag with comment:
CT{
Contig36 polyPhredRank1 polyPhred 3608 3608 080205:125543
COMMENT{
99
C}
}

Parsing works correctly for the exact same ace file minus the COMMENTs.

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bugzilla-daemon | 6 Feb 2008 00:38

[Bug 2446] Comments in CT tags cause Bio.Sequencing.Ace.ACEParser to fail.

http://bugzilla.open-bio.org/show_bug.cgi?id=2446

------- Comment #1 from biopython-bugzilla <at> maubp.freeserve.co.uk  2008-02-05 18:38 EST -------
Could you supply an example input file [which we could use for a unit test] and
associated snippet of python code to load it, which shows the problem?  Thanks.

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Chris Lasher | 6 Feb 2008 04:27
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[BioPython] Biopython to begin transition to Subversion

Hello all Biopythonistas,

In the next upcoming weeks, Biopython will begin and complete its
transition from CVS to Subversion (SVN) as its revision control
system.

This transition will likely not affect end users of Biopython except
that to get the development version, a checkout with a Subversion
client, rather than a CVS client, will be necessary.

For developers, we will need to determine a suitable range of dates (a
week) during which we will "freeze" the CVS repository for its
transition to SVN. From the freeze and thereon, commits to the CVS
repository will no longer be possible. Instead, commits not placed in
during the freeze will need to take place in the Subversion repository
once we have it running. This week, we hope to have a "dry run" of the
Subversion repository available for the developers to poke around and
make sure the transition will include everything necessary. Following
that, we'll have the freeze and complete the transition.

If you have any questions, I'll be checking posts to the list, or you
may feel free contact me directly.

Best,
Chris
_______________________________________________
BioPython mailing list  -  BioPython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
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Chris Fields | 6 Feb 2008 04:33
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Re: [BioPython] Biopython to begin transition to Subversion

Let me know if you need any help.

chris

On Feb 5, 2008, at 9:27 PM, Chris Lasher wrote:

> Hello all Biopythonistas,
>
> In the next upcoming weeks, Biopython will begin and complete its
> transition from CVS to Subversion (SVN) as its revision control
> system.
>
> This transition will likely not affect end users of Biopython except
> that to get the development version, a checkout with a Subversion
> client, rather than a CVS client, will be necessary.
>
> For developers, we will need to determine a suitable range of dates (a
> week) during which we will "freeze" the CVS repository for its
> transition to SVN. From the freeze and thereon, commits to the CVS
> repository will no longer be possible. Instead, commits not placed in
> during the freeze will need to take place in the Subversion repository
> once we have it running. This week, we hope to have a "dry run" of the
> Subversion repository available for the developers to poke around and
> make sure the transition will include everything necessary. Following
> that, we'll have the freeze and complete the transition.
>
> If you have any questions, I'll be checking posts to the list, or you
> may feel free contact me directly.
>
> Best,
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bugzilla-daemon | 6 Feb 2008 17:25

[Bug 2446] Comments in CT tags cause Bio.Sequencing.Ace.ACEParser to fail.

http://bugzilla.open-bio.org/show_bug.cgi?id=2446

------- Comment #2 from dthomp325 <at> gmail.com  2008-02-06 11:25 EST -------
I tried to attach the file that causes the error, but it looks like it's too
big. I get this error from Bugzilla:
DBD::mysql::st execute failed: Got a packet bigger than 'max_allowed_packet'
bytes [for Statement "INSERT INTO attach_data
                           (id, thedata) VALUES (861, ?)" with ParamValues:
0='AS 2 1710

Would it be possible for me to e-mail the file directly to you?

(In reply to comment #1)
> Could you supply an example input file [which we could use for a unit test] and
> associated snippet of python code to load it, which shows the problem?  Thanks.
> 

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Peter | 6 Feb 2008 17:27
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Re: [BioPython] Biopython to begin transition to Subversion

> In the next upcoming weeks, Biopython will begin and complete its
> transition from CVS to Subversion (SVN) as its revision control
> system.

I gather that BioPerl and BioJava and BioSQL have all transitioned
fine, so its our turn now.

Michiel - do you think we should try and do another release before the
CVS freeze and migration?  We've had a lots little changes, plus
Tiago's PopGen work and my own efforts with BioSQL.  There are still a
few open issues, but I think a release soon would be reasonable
(depending on your time commitments of course).

> If you have any questions, I'll be checking posts to the list, or you
> may feel free contact me directly.

Will the existing developer accounts simply work on the new SVN repository?

Is there any issue with Unix/Windows newlines under SVN?  I recall
reading somewhere that like CVS, SVN can be setup to handle this
transparently for text files.  I may be worrying over nothing, but
given that we have developers using both Linux, Windows and MacOS this
seems worth checking.

Peter
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bugzilla-daemon | 6 Feb 2008 17:28

[Bug 2446] Comments in CT tags cause Bio.Sequencing.Ace.ACEParser to fail.

http://bugzilla.open-bio.org/show_bug.cgi?id=2446

------- Comment #3 from dthomp325 <at> gmail.com  2008-02-06 11:28 EST -------
The python code is simply:

from Bio.Sequencing import Ace
ace_parser = Ace.ACEParser()
ace_file = ace_parser.parse(open((in_file), 'r'))

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Tiago Antão | 6 Feb 2008 18:05
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Re: [BioPython] Biopython to begin transition to Subversion

Hi,

On Feb 6, 2008 4:27 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
> Michiel - do you think we should try and do another release before the
> CVS freeze and migration?  We've had a lots little changes, plus
> Tiago's PopGen work and my own efforts with BioSQL.  There are still a
> few open issues, but I think a release soon would be reasonable
> (depending on your time commitments of course).

Just FYI: As I noticed that the SVN move would be happening sooner or
later, I decided to put everything into a stable state and stop at
that point.
Hopefully all that there is PopGen related is stable and ready to move
(code, test, doc).
As soon as we move to SVN I will get back into committing (now the
really interesting stuff will start: statistics and maybe HapMap).

Tiago
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Gmane