From bugzilla-daemon at portal.open-bio.org Mon Dec 4 09:52:54 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 09:52:54 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041452.kB4Eqsou007413@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #2 from mdehoon at ims.u-tokyo.ac.jp 2006-12-04 09:52 -------
Can you use the XML parser instead of the plain text parser?
If not, why not?
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 11:15:03 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 11:15:03 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041615.kB4GF3Oj016652@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #3 from kael.fischer at gmail.com 2006-12-04 11:15 -------
The XML parser does not seem to handle queries with multiple FASTA records in
them properely with 2.2.14 XML output. I haven't looked at this in a while
(went back to 2.2.8, or using -m 8). If more testing is needed I can look at
it again.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 12:01:51 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 12:01:51 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041701.kB4H1pJK022107@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
kael.fischer at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |kael.fischer at gmail.com
------- Comment #4 from kael.fischer at gmail.com 2006-12-04 12:01 -------
I am running some tests with the XML parser and will submit the problems I am
observing as separate bugs. But there is at least one fundamental difference
between the parsers from the user's perspective (untested on blastall versions
< 2.2.14):
BlastParser: 1 Blast Record instance = 1 query sequence
XMLParser: 1 Blast Record instance = many query sequences
But this bug report is about the "BlastParser" I'll submit the XMLParser bugs
separately.
Is the BlastParser deprecated? That is the impression I am getting.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 12:45:32 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 12:45:32 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041745.kB4HjWde025936@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-04 12:45 -------
As you noted, please can we keep this bug for the plain text blast output
issues.
See Bug 2051 for XML parsing with multiple inputs using Blast 2.2.14 or later
(an open issue).
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 13:54:03 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 13:54:03 -0500
Subject: [Biopython-dev] [Bug 2157] New: Blast.NCBIXML looses query
information for queries 2-n
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2157
Summary: Blast.NCBIXML looses query information for queries 2-n
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: critical
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: kael.fischer at gmail.com
This is untested for blastall output versions other than 2.2.14-15 and I have
only looked at blastn.
XMLParser: 1 Blast Record instance = all submitted query sequences
Traditional BlastParser: 1 Blast Record instance = 1 query sequence
(for versions of BlastParser/blastall where it can parse)
The name of all the queries (after the first one) and their lengths is lost
during parsing. The data are in the XML output at the top level of each
. For the data structure to be isomorphus to the original
BlastParser and capture this important information, NCBIXML.parser should
return a list of records (one per XML ). Also, having some sort of
iterator/generator mechanism for the s would have the added benefit
of a smaller memory footprint for very large results.
It has been suggested that XMLParser be used in lieu of BlastParser, as
BlastParser is broken for new-ish versions of blastall (see bug 2090). All
code that uses record.query or record.query_letters, or in some other way
relies on the documented
(http://www.bioinformatics.org/bradstuff/bp/tut/images/BlastRecord.png) data
structure of 1 record per query is broken when using NCBIXML because of this
behavior.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 14:14:31 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:14:31 -0500
Subject: [Biopython-dev] [Bug 2158] New: NCBIXML Returns the union of all
the hits it has seen
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2158
Summary: NCBIXML Returns the union of all the hits it has seen
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: kael.fischer at gmail.com
If a BlastParser has already been used, it does not reset its _blast record.
Leading to man potential problems. This should at least be documented, or
better yet the "self._blast = Record.Blast()" moved to parse(self), and perhaps
setting it to None in __init__(self).
Alternately, if the parser was changed to yield separate records for each XML
, per the Blast Record documentation , this would all be rewritten
and would be moot.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 14:17:46 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:17:46 -0500
Subject: [Biopython-dev] [Bug 2157] Blast.NCBIXML looses query information
for queries 2-n
In-Reply-To:
Message-ID: <200612041917.kB4JHkoW032147@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2157
kael.fischer at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |RESOLVED
Resolution| |DUPLICATE
------- Comment #1 from kael.fischer at gmail.com 2006-12-04 14:17 -------
*** This bug has been marked as a duplicate of 2051 ***
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 14:17:47 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:17:47 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612041917.kB4JHlFU032155@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
kael.fischer at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |kael.fischer at gmail.com
------- Comment #5 from kael.fischer at gmail.com 2006-12-04 14:17 -------
*** Bug 2157 has been marked as a duplicate of this bug. ***
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 14:18:39 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:18:39 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612041918.kB4JIdsU032243@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #6 from kael.fischer at gmail.com 2006-12-04 14:18 -------
This is untested for blastall output versions other than 2.2.14-15 and I have
only looked at blastn.
XMLParser: 1 Blast Record instance = all submitted query sequences
Traditional BlastParser: 1 Blast Record instance = 1 query sequence
(for versions of BlastParser/blastall where it can parse)
The name of all the queries (after the first one) and their lengths is lost
during parsing. The data are in the XML output at the top level of each
. For the data structure to be isomorphus to the original
BlastParser and capture this important information, NCBIXML.parser should
return a list of records (one per XML ). Also, having some sort of
iterator/generator mechanism for the s would have the added benefit
of a smaller memory footprint for very large results.
It has been suggested that XMLParser be used in lieu of BlastParser, as
BlastParser is broken for new-ish versions of blastall (see bug 2090). All
code that uses record.query or record.query_letters, or in some other way
relies on the documented
(http://www.bioinformatics.org/bradstuff/bp/tut/images/BlastRecord.png) data
structure of 1 record per query is broken when using NCBIXML because of this
behavior.
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From bugzilla-daemon at portal.open-bio.org Tue Dec 5 05:28:51 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 5 Dec 2006 05:28:51 -0500
Subject: [Biopython-dev] [Bug 2158] NCBIXML Returns the union of all the
hits it has seen
In-Reply-To:
Message-ID: <200612051028.kB5ASpsL005573@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2158
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |RESOLVED
Resolution| |DUPLICATE
------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-05 05:28 -------
I'm pretty sure this is a duplicate of bug 1970 (which turned out to be more
complicated than I realised).
*** This bug has been marked as a duplicate of 1970 ***
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From bugzilla-daemon at portal.open-bio.org Fri Dec 8 14:50:01 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 8 Dec 2006 14:50:01 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612081950.kB8Jo1lj028728@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #7 from mdehoon at ims.u-tokyo.ac.jp 2006-12-08 14:50 -------
To get started on this patch, I committed the patch to NCBIStandalone to CVS.
Its changes seem to be independent of the other two patches.
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From bugzilla-daemon at portal.open-bio.org Tue Dec 12 07:40:04 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 12 Dec 2006 07:40:04 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612121240.kBCCe4fP025879@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-12 07:40 -------
I see, regarding comment 7, that was revision 1.64 to
Bio/Blast/NCBIStandalone.py and added support for the command line option
"oldengine"
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py.diff?r1=1.63&r2=1.64&cvsroot=biopython
Jacob Joseph's patch on comment 1 also included changes to Bio/Blast/Record.py
and Bio/Blast/NCBIXML.py - some of his suggestions also appear in bug 1970
comment 2
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From bugzilla-daemon at portal.open-bio.org Tue Dec 12 07:56:33 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 12 Dec 2006 07:56:33 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612121256.kBCCuXX4027025@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |ASSIGNED
------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-12 07:56 -------
Karl,
Could you attach a couple of small example "plain text" output files from
running standalone blast 2.2.14 and/or 2.2.15 please?
I'll try and have a go at fixing this - and I would like to include the
example(s) in the test suite.
Thanks
Peter
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From bugzilla-daemon at portal.open-bio.org Wed Dec 13 11:53:55 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 11:53:55 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612131653.kBDGrtow019262@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-13 11:53 -------
I've been working with the plain text from BLASTP 2.2.15 (online).
The good news is I think I have something that seems to work for single
queries.
The bad news is that the behaviour for multiple queries has REALLY changed.
The first line header, here "BLASTP 2.2.15 [Oct-15-2006]" plus the other stuff
like the database reference IS NOT REPEATED before each query line.
i.e. We need to do the split on the "Query=" line for this version...
This is very much like the issue I had with RPS-BLAST 2.2.10 plain text output
discussed on bug 1715 comment 9. That nasty code was never committed in favour
of pushing XML parsing instead.
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From bugzilla-daemon at portal.open-bio.org Wed Dec 13 12:06:34 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 12:06:34 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612131706.kBDH6YV4019964@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
AssignedTo|biopython-dev at biopython.org |biopython-
| |bugzilla at maubp.freeserve.co.
| |uk
------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-13 12:06 -------
Created an attachment (id=520)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=520&action=view)
Patch for Bio/Blast/NCBIStandalone.py
test_NCBIStandalone.py still passes with this patch.
It seems to work for BLASTP 2.2.15 (online) but I would like to see some
examples from the standalone 2.2.15 as well please Frank.
Reading your comments, it sounds like 2.2.14 might also be slightly different
too - again, if you have some examples output files please attach them.
Even with this patch, it WILL NOT WORK with multiple input queries on 2.2.15
(unsure about other recent versions).
(I know we want to push the BLAST XML output by default, but that currently has
issues too...)
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From bugzilla-daemon at portal.open-bio.org Thu Dec 14 18:48:37 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 14 Dec 2006 18:48:37 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612142348.kBENmbZf001062@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |ASSIGNED
------- Comment #9 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-14 18:48 -------
I've just checked in a fairly big change to Bio/Blast/NCBIXML.py (see revision
1.8), see bug 1970 comment 15.
NOTE: While it still reads an entire XML file in one go,
NCBIXML.BlastParser.parse() now returns a list of records - not a single record
as before.
This SHOULD address most of this bug (the unusable with multiple queries bit
anyway).
Some of Jacob's suggestions in comment 1 have been included (e.g. the
expectation threshold parameter is dealt with more sensibly) but not all...
Could you test the new code please Jacob, and point out any outstanding issues.
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From bugzilla-daemon at portal.open-bio.org Thu Dec 14 19:09:22 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 14 Dec 2006 19:09:22 -0500
Subject: [Biopython-dev] [Bug 1950] addition of element, SSBOND, OBSLTE,
CAVEAT fields to PDB
In-Reply-To:
Message-ID: <200612150009.kBF09MTg002106@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=1950
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
AssignedTo|biopython-dev at biopython.org |thamelry at binf.ku.dk
------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-14 19:09 -------
Looking at the patch, one minor point is that the change is to the __init__
method of the class Atom is not backwards compatible:
Old:
def __init__(self, ..., altloc, fullname, serial_number):
Suggested:
def __init__(self, ..., altloc, fullname, element, serial_number):
Anyway, assigning this one to Thomas
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From bugzilla-daemon at portal.open-bio.org Mon Dec 18 06:47:26 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 18 Dec 2006 06:47:26 -0500
Subject: [Biopython-dev] [Bug 1751] Not a bug: testing attachments to
bugzilla
In-Reply-To:
Message-ID: <200612181147.kBIBlQsT012255@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=1751
------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-18 06:47 -------
Created an attachment (id=523)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=523&action=view)
Text file to test a bug in bugzilla
Seeing if a Bugzilla Internal Error this happens for me... please ignore.
This seems to be a problem with Firefox 1.5.0.8 on Windows XP. IE6 works.
(Seemed better to reuse this old bug than create another "attachment test"
bug.)
>> Bugzilla Version 2.20.3
>> Internal Error
>>
>> Bugzilla has suffered an internal error. Please save this page and send
>> it to root-l at open-bio.org with details of
>> what you were doing at the
>> time this message appeared.
>>
>> URL: http://bugzilla.open-bio.org/attachment.cgi
>> undef error - Undefined subroutine Fh::slice at
>> data/template/template/en/default/global/hidden-fields.html.tmpl line 58
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From jig.parikh at gmail.com Tue Dec 19 13:46:07 2006
From: jig.parikh at gmail.com (Jignesh Parikh)
Date: Tue, 19 Dec 2006 13:46:07 -0500
Subject: [Biopython-dev] py2exe module import problems
Message-ID: <6af1ed1c0612191046v191d3b73xe7a2d51804ed9660@mail.gmail.com>
Hi,
I am using python 2.4, biopython 1.42, and py2exe 0.6.5
When I run python setup py2exe, it cannot find the following modules:
The following modules appear to be missing
['Bio.db', 'TextTools', '_ssl', 'bsddb3', 'dtds.pvsystem',
'mxTextTools.__version__', 'xml.parsers.xmlproc.dtdparser']
In my program I import GenBank in order to get and parse GenBank files by
using:
from Bio import GenBank
My executable will not run and fails trying to import db:
Traceback (most recent call last):
File "keywordFilter2.py", line 52, in ?
File "Bio\GenBank\__init__.pyc", line 47, in ?
ImportError: cannot import name db
I cannot even find the Bio.db module. Can you think of how I can ensure that
these modules get imported? Please help!
Thanks,
Jignesh Parikh
Dana-Farber Cancer Institute
Boston, MA
From bugzilla-daemon at portal.open-bio.org Fri Dec 22 10:54:01 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 22 Dec 2006 10:54:01 -0500
Subject: [Biopython-dev] [Bug 2169] New: 'close' method is missing for
ReseekFile wrapper
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2169
Summary: 'close' method is missing for ReseekFile wrapper
Product: Biopython
Version: 1.24
Platform: All
OS/Version: Mac OS
Status: NEW
Severity: normal
Priority: P2
Component: Other
AssignedTo: biopython-dev at biopython.org
ReportedBy: sunhwanj at gmail.com
ReseekFile class doesn't have close method.
While I tried to read PDB file after I download pdb file using Bio.db,
PDBParser complains that it can't close pdbfile.
>>> from Bio.PDB.PDBParser import PDBParser
>>> from Bio import db
>>>
>>> p = PDBParser()
>>> p.get_structure('1kdx', db['pdb']['1kdx'])
Traceback (most recent call last):
File "", line 1, in
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/PDB/PDBParser.py",
line 67, in get_structure
file.close()
AttributeError: ReseekFile instance has no attribute 'close'
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From tiagoantao at gmail.com Fri Dec 22 13:19:26 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Fri, 22 Dec 2006 18:19:26 +0000
Subject: [Biopython-dev] Population Genetics code
Message-ID: <6d941f120612221019g400af87enfb81fd04a1a3b69c@mail.gmail.com>
Hi!
During the last few months I have developed a lot of code in Python
around the topic of Population Genetics. Things from parsers (GenePop,
fdist2, Arlequin), to invoking other programs (simcoal2, fdist2), to
statistics (Fst, expected heterozygosity, ...), to data structures
representing population relationships, to HapMap data analysis,
currently I am developing code to interact with UCSC table browser...
Some of this code is used from Jython, by the way.
I am now in the process of consolidating the mess that I have done (I
have sometimes, several implementations of the same thing, just
because I was too lazy to do proper reuse). I was thinking that I
could do that in the context of BioPython, ie contributing the code.
Especially because BioPython seems to lack Population Genetics code.
Code quality varies a lot, from highly tested - under heavy use, to
one offs that were used a single time. But, even things that are poor
quality can easily be upgraded. The biggest issue is that some code
dealing with representation of molecular markers is still not matured
enough, ie, I believe that even good code it will have change quite a
lot in the future, breaking interfaces...
Anyway, I was thinking in starting with an easy task, namely
converting my parsers of GenePop and fdist2 to BioPython. These are 2
absolutely trivial formats.
Any comments on this? Would there be an interest in population
genetics oriented code?
Regards,
Tiago
--
The right to offend is far more important than the right not to be
offended - Rowan Atkinson
From tiagoantao at gmail.com Wed Dec 27 07:04:04 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Wed, 27 Dec 2006 12:04:04 +0000
Subject: [Biopython-dev] GenePop parser code
Message-ID: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
Hi!
I have finalized converting my code to parse GenePop(*) files into
BioPython. I would like to know if there would be interest in adding
it to BioPython?
After reading the instructions, I suppose, as this is not strictly a
patch, that it makes no sense to submit it through Bugzilla? More, as
this is my first contribution to BioPython, I would bet its full of
small problems typical from a newbie...
I also have test code, but its still in my own ad-hoc format (I will
convert it to the BioPython standard in case it gets accepted).
I have truckloads more of Population Genetics code that I would be
willing to convert to Biopython (more or less things along the lines
of BioPerls's Bio::PopGen). I decided to start with a small/simple
thing to see how it goes...
Is there any interest? If so, how do I submit this?
(*)GenePop: http://wbiomed.curtin.edu.au/genepop/
--
The right to offend is far more important than the right not to be
offended - Rowan Atkinson
From biopython-dev at maubp.freeserve.co.uk Wed Dec 27 13:40:03 2006
From: biopython-dev at maubp.freeserve.co.uk (Peter (BioPython Dev))
Date: Wed, 27 Dec 2006 18:40:03 +0000
Subject: [Biopython-dev] GenePop parser code
In-Reply-To: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
References: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
Message-ID: <4592BE03.8030609@maubp.freeserve.co.uk>
Tiago Ant?o wrote:
> Hi!
>
> I have finalized converting my code to parse GenePop(*) files into
> BioPython. I would like to know if there would be interest in adding
> it to BioPython?
>
> (*)GenePop: http://wbiomed.curtin.edu.au/genepop/
>
I think someone asked about Population genetics on a mailing list in the
last year or so, and there was some interest out there.
Check Feb 2006 on the discussion list, look for a thread on "PopGen"
started by Ralph Haygood. He had written a Python module for computing
a variety of population-genetic statistics from DNA sequences.
Does this overlap with your plans at all?
> After reading the instructions, I suppose, as this is not strictly a
> patch, that it makes no sense to submit it through Bugzilla? More, as
> this is my first contribution to BioPython, I would bet its full of
> small problems typical from a newbie...
I would suggest creating an enhancement bug for "Adding a GenPop file
format parser" or something like that, and then attach your code to it.
Sending attachments on mailing lists is asking for trouble.
> I also have test code, but its still in my own ad-hoc format (I will
> convert it to the BioPython standard in case it gets accepted).
Have a look at the existing Tests directory - basically you have a
script that produces some output, and the expected output in the
"output" subdirectory. Avoid things like printing floating point
numbers or filenames in any print statements - they make running the
test suite on different platforms tricky. Most parser tests have a few
sample input files too (held in subdirectories again).
> I have truckloads more of Population Genetics code that I would be
> willing to convert to Biopython (more or less things along the lines
> of BioPerls's Bio::PopGen). I decided to start with a small/simple
> thing to see how it goes...
That sounds sensible - unless there is some generic object structure you
want to introduce for handling population data? I don't know enough
about this to comment.
> Is there any interest? If so, how do I submit this?
To recap: yes there is some interest, and I would suggest creating an
enhancement "bug" on bugzilla and attaching files/patches there.
Peter
From tiagoantao at gmail.com Wed Dec 27 19:11:22 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Thu, 28 Dec 2006 00:11:22 +0000
Subject: [Biopython-dev] GenePop parser code
In-Reply-To: <4592BE03.8030609@maubp.freeserve.co.uk>
References: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
<4592BE03.8030609@maubp.freeserve.co.uk>
Message-ID: <6d941f120612271611p268cebaci7dc80c49806d1308@mail.gmail.com>
Hi!
On 12/27/06, Peter (BioPython Dev) wrote:
> That sounds sensible - unless there is some generic object structure you
> want to introduce for handling population data? I don't know enough
> about this to comment.
Well, this has been floating around my mind... In fact I would need to
introduce, sooner or later, notions like population, individual,
marker... What I currently have is enough for me, but I am pretty much
aware that its not generic enough. One good example of this is Ralph
Haygood's messages that you talk about, where he uses mainly sequence
data statistics (I work more with SNP and microsatellite data), as
such I suppose my data structures would not be enough for his work
(and vice-versa).
I propose the following strategy:
1. I will try to contact him (maybe he still reads this list? Are you
there? ;) )
2. I will have a much more closer look at Bio::PopGen from BioPerl.
3. Wait for any more comments on this list
Let see where this leads to...
In the mean time I have some less problematic code: mainly code to
work with Mark Beaumont's fdist program, parser and code to control
it. The problem here is that fdist is such a niche program, that I
don't think it deserves to be at top level Bio (but my suggestion is
for it to be supported, as is clearly used in population genetics). I
think it would make more sense to be Bio.PopGen.FDist rather than
Bio.FDist, just to not to make Bio too "noisy". Does this make sense?
Thanks,
Tiago
PS - Tomorrow I will submit GenePop code as you suggested
--
The right to offend is far more important than the right not to be
offended - Rowan Atkinson
From solymosi.norbert at gmail.com Thu Dec 28 02:45:03 2006
From: solymosi.norbert at gmail.com (Solymosi Norbert)
Date: Thu, 28 Dec 2006 08:45:03 +0100
Subject: [Biopython-dev] py2exe module import problems
Message-ID: <459375FF.5070903@gmail.com>
Hi,
I have the same problem and no solution.
If anybody has idea, please tell me
Thanks,
Norbert Solymosi
From bugzilla-daemon at portal.open-bio.org Thu Dec 28 07:07:43 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 07:07:43 -0500
Subject: [Biopython-dev] [Bug 2170] New: Adding a GenPop file format parser
and simple utilities
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2170
Summary: Adding a GenPop file format parser and simple utilities
Product: Biopython
Version: Not Applicable
Platform: PC
OS/Version: Linux
Status: NEW
Severity: enhancement
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: tiagoantao at gmail.com
This is a bug entry to submit GenePop related code (including some tests)
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From bugzilla-daemon at portal.open-bio.org Thu Dec 28 07:12:05 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 07:12:05 -0500
Subject: [Biopython-dev] [Bug 2170] Adding a GenPop file format parser and
simple utilities
In-Reply-To:
Message-ID: <200612281212.kBSCC5Xc013879@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2170
tiagoantao at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
AssignedTo|biopython-dev at biopython.org |tiagoantao at gmail.com
Status|NEW |ASSIGNED
------- Comment #1 from tiagoantao at gmail.com 2006-12-28 07:12 -------
Created an attachment (id=525)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=525&action=view)
Parser/Utils and test for GenePop code
This is my first submission to BioPython, most probably full of problems... Any
suggestions are more than welcome...
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From tiagoantao at gmail.com Thu Dec 28 07:14:49 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Thu, 28 Dec 2006 12:14:49 +0000
Subject: [Biopython-dev] GenePop parser code
In-Reply-To: <4592BE03.8030609@maubp.freeserve.co.uk>
References: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
<4592BE03.8030609@maubp.freeserve.co.uk>
Message-ID: <6d941f120612280414p13b5c4c5u345ae3701eb4bfed@mail.gmail.com>
On 12/27/06, Peter (BioPython Dev) wrote:
> To recap: yes there is some interest, and I would suggest creating an
> enhancement "bug" on bugzilla and attaching files/patches there.
I have just submitted the code on bugzilla (assigned it to myself,
don't know if that is correct).
As this is my first submission, this is probably a big piece of crap
;) . I am more than willing to correct things...
Regards,
Tiago
From bugzilla-daemon at portal.open-bio.org Thu Dec 28 15:25:25 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 15:25:25 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612282025.kBSKPPaI029719@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #10 from jmjoseph at andrew.cmu.edu 2006-12-28 15:25 -------
Thanks for your work. I have had a chance to work with the CVS
NCBIXML parser. I have not tested with output other than that from
blastall 2.2.13 and 2.2.15, so many of my suggestions may not be
acceptable for compatibility reasons. Regardless, I do still see a
number of inconsistencies. I did address some of these in my previous
patches, but it's not worth the effort of starting with them. Now,
though:
In Record.py, HSP.identities, HSP.gaps, and HSP.positives are still
defined as (None,None) tuples. However, in NCBIXML.py, these
variables are set as integers. I don't see a point of a tuple at all,
at least for NCBIXML. (I realize it is used in NCBIStandalone.py).
Most importantly, the inconsistency makes it difficult to handle cases
when the parameter is not set. It seems easiest, though, to just
retain the tuple format.
In the past, I worried that the order of tuple building for
self._blast.gap_penalties or ka_params could cause the tuple to have
an incorrect ordering. I seem to remember hitting an issue where the
tuple was built with the wrong length, but I can't be specific. In
general, it remains odd to me to not just use a list and set each
element respectively. If necessary, one could convert to a tuple when
finished or use some other approach that does not rely upon order.
Why not use query_len, as defined in the XML file, or query_length
instead of query_letters as a variable name? In
BlastParser._end_Iteration, self._blast.query_letters is set. This is
not defined/documented in the Parameters class in Record.py. Rather,
query_length is defined there. In the Header class, though, the name
query_letters is used. There also seems to be some confusion between
num_letters_in_database, num_sequences_in_database, database_letters,
and database_sequences. Note that even if this naming is not
corrected, NCBIXML.py:186 is wrong with "self._blast_query_letters"
rather than "self._blast.query_letters".
Similarly, why store the bit score and E-value as 'bits' and
'_hsp.expect'/'descr.e' rather than just using bit_score and
evalue, as in the blast XML ouput?
I make use of in 2.2.13. This value missing
entirely.
The parsing of and is confusing. For example,
1
gnl|BL_ORD_ID|0
3377250
...
results in _hit.title set to "gnl|BL_ORD_ID|0 3377250". I would
rather they remain separate (or both methods be used).
This is certainly not an exhaustive list. I'm happy to provide
another patch correcting many of these inconsistencies. At the
very least, the variable names defined in Record.py should be
used in NCBIXML.py. May I modify at least the above names to
correspond more closely to the names used in the XML? I know
I've found this particularly confusing.
-Jacob
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From bugzilla-daemon at portal.open-bio.org Thu Dec 28 15:26:52 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 15:26:52 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612282026.kBSKQqAe029798@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #11 from jmjoseph at andrew.cmu.edu 2006-12-28 15:26 -------
Created an attachment (id=526)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=526&action=view)
Patch to record.py
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From bugzilla-daemon at portal.open-bio.org Thu Dec 28 15:27:22 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 15:27:22 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612282027.kBSKRM3v029844@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #12 from jmjoseph at andrew.cmu.edu 2006-12-28 15:27 -------
Created an attachment (id=527)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=527&action=view)
Patch to NCBIXML.py
These patches to NCBIXML and Record:
* replace query_letters with query_length,
* use tuples for _hsp.identities, positives, and gaps
* store _hsp.align_length
* separate the hit id and hit def elements. title is retained
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 14:52:54 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 09:52:54 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041452.kB4Eqsou007413@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #2 from mdehoon at ims.u-tokyo.ac.jp 2006-12-04 09:52 -------
Can you use the XML parser instead of the plain text parser?
If not, why not?
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 16:15:03 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 11:15:03 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041615.kB4GF3Oj016652@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #3 from kael.fischer at gmail.com 2006-12-04 11:15 -------
The XML parser does not seem to handle queries with multiple FASTA records in
them properely with 2.2.14 XML output. I haven't looked at this in a while
(went back to 2.2.8, or using -m 8). If more testing is needed I can look at
it again.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 17:01:51 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 12:01:51 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041701.kB4H1pJK022107@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
kael.fischer at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |kael.fischer at gmail.com
------- Comment #4 from kael.fischer at gmail.com 2006-12-04 12:01 -------
I am running some tests with the XML parser and will submit the problems I am
observing as separate bugs. But there is at least one fundamental difference
between the parsers from the user's perspective (untested on blastall versions
< 2.2.14):
BlastParser: 1 Blast Record instance = 1 query sequence
XMLParser: 1 Blast Record instance = many query sequences
But this bug report is about the "BlastParser" I'll submit the XMLParser bugs
separately.
Is the BlastParser deprecated? That is the impression I am getting.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 17:45:32 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 12:45:32 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612041745.kB4HjWde025936@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-04 12:45 -------
As you noted, please can we keep this bug for the plain text blast output
issues.
See Bug 2051 for XML parsing with multiple inputs using Blast 2.2.14 or later
(an open issue).
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 18:54:03 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 13:54:03 -0500
Subject: [Biopython-dev] [Bug 2157] New: Blast.NCBIXML looses query
information for queries 2-n
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2157
Summary: Blast.NCBIXML looses query information for queries 2-n
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: critical
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: kael.fischer at gmail.com
This is untested for blastall output versions other than 2.2.14-15 and I have
only looked at blastn.
XMLParser: 1 Blast Record instance = all submitted query sequences
Traditional BlastParser: 1 Blast Record instance = 1 query sequence
(for versions of BlastParser/blastall where it can parse)
The name of all the queries (after the first one) and their lengths is lost
during parsing. The data are in the XML output at the top level of each
. For the data structure to be isomorphus to the original
BlastParser and capture this important information, NCBIXML.parser should
return a list of records (one per XML ). Also, having some sort of
iterator/generator mechanism for the s would have the added benefit
of a smaller memory footprint for very large results.
It has been suggested that XMLParser be used in lieu of BlastParser, as
BlastParser is broken for new-ish versions of blastall (see bug 2090). All
code that uses record.query or record.query_letters, or in some other way
relies on the documented
(http://www.bioinformatics.org/bradstuff/bp/tut/images/BlastRecord.png) data
structure of 1 record per query is broken when using NCBIXML because of this
behavior.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 19:14:31 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:14:31 -0500
Subject: [Biopython-dev] [Bug 2158] New: NCBIXML Returns the union of all
the hits it has seen
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2158
Summary: NCBIXML Returns the union of all the hits it has seen
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: kael.fischer at gmail.com
If a BlastParser has already been used, it does not reset its _blast record.
Leading to man potential problems. This should at least be documented, or
better yet the "self._blast = Record.Blast()" moved to parse(self), and perhaps
setting it to None in __init__(self).
Alternately, if the parser was changed to yield separate records for each XML
, per the Blast Record documentation , this would all be rewritten
and would be moot.
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 19:17:46 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:17:46 -0500
Subject: [Biopython-dev] [Bug 2157] Blast.NCBIXML looses query information
for queries 2-n
In-Reply-To:
Message-ID: <200612041917.kB4JHkoW032147@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2157
kael.fischer at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |RESOLVED
Resolution| |DUPLICATE
------- Comment #1 from kael.fischer at gmail.com 2006-12-04 14:17 -------
*** This bug has been marked as a duplicate of 2051 ***
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 19:17:47 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:17:47 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612041917.kB4JHlFU032155@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
kael.fischer at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |kael.fischer at gmail.com
------- Comment #5 from kael.fischer at gmail.com 2006-12-04 14:17 -------
*** Bug 2157 has been marked as a duplicate of this bug. ***
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From bugzilla-daemon at portal.open-bio.org Mon Dec 4 19:18:39 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 4 Dec 2006 14:18:39 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612041918.kB4JIdsU032243@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #6 from kael.fischer at gmail.com 2006-12-04 14:18 -------
This is untested for blastall output versions other than 2.2.14-15 and I have
only looked at blastn.
XMLParser: 1 Blast Record instance = all submitted query sequences
Traditional BlastParser: 1 Blast Record instance = 1 query sequence
(for versions of BlastParser/blastall where it can parse)
The name of all the queries (after the first one) and their lengths is lost
during parsing. The data are in the XML output at the top level of each
. For the data structure to be isomorphus to the original
BlastParser and capture this important information, NCBIXML.parser should
return a list of records (one per XML ). Also, having some sort of
iterator/generator mechanism for the s would have the added benefit
of a smaller memory footprint for very large results.
It has been suggested that XMLParser be used in lieu of BlastParser, as
BlastParser is broken for new-ish versions of blastall (see bug 2090). All
code that uses record.query or record.query_letters, or in some other way
relies on the documented
(http://www.bioinformatics.org/bradstuff/bp/tut/images/BlastRecord.png) data
structure of 1 record per query is broken when using NCBIXML because of this
behavior.
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From bugzilla-daemon at portal.open-bio.org Tue Dec 5 10:28:51 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 5 Dec 2006 05:28:51 -0500
Subject: [Biopython-dev] [Bug 2158] NCBIXML Returns the union of all the
hits it has seen
In-Reply-To:
Message-ID: <200612051028.kB5ASpsL005573@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2158
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |RESOLVED
Resolution| |DUPLICATE
------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-05 05:28 -------
I'm pretty sure this is a duplicate of bug 1970 (which turned out to be more
complicated than I realised).
*** This bug has been marked as a duplicate of 1970 ***
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From bugzilla-daemon at portal.open-bio.org Fri Dec 8 19:50:01 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 8 Dec 2006 14:50:01 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612081950.kB8Jo1lj028728@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #7 from mdehoon at ims.u-tokyo.ac.jp 2006-12-08 14:50 -------
To get started on this patch, I committed the patch to NCBIStandalone to CVS.
Its changes seem to be independent of the other two patches.
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From bugzilla-daemon at portal.open-bio.org Tue Dec 12 12:40:04 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 12 Dec 2006 07:40:04 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612121240.kBCCe4fP025879@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-12 07:40 -------
I see, regarding comment 7, that was revision 1.64 to
Bio/Blast/NCBIStandalone.py and added support for the command line option
"oldengine"
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py.diff?r1=1.63&r2=1.64&cvsroot=biopython
Jacob Joseph's patch on comment 1 also included changes to Bio/Blast/Record.py
and Bio/Blast/NCBIXML.py - some of his suggestions also appear in bug 1970
comment 2
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From bugzilla-daemon at portal.open-bio.org Tue Dec 12 12:56:33 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 12 Dec 2006 07:56:33 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612121256.kBCCuXX4027025@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |ASSIGNED
------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-12 07:56 -------
Karl,
Could you attach a couple of small example "plain text" output files from
running standalone blast 2.2.14 and/or 2.2.15 please?
I'll try and have a go at fixing this - and I would like to include the
example(s) in the test suite.
Thanks
Peter
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From bugzilla-daemon at portal.open-bio.org Wed Dec 13 16:53:55 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 11:53:55 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612131653.kBDGrtow019262@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-13 11:53 -------
I've been working with the plain text from BLASTP 2.2.15 (online).
The good news is I think I have something that seems to work for single
queries.
The bad news is that the behaviour for multiple queries has REALLY changed.
The first line header, here "BLASTP 2.2.15 [Oct-15-2006]" plus the other stuff
like the database reference IS NOT REPEATED before each query line.
i.e. We need to do the split on the "Query=" line for this version...
This is very much like the issue I had with RPS-BLAST 2.2.10 plain text output
discussed on bug 1715 comment 9. That nasty code was never committed in favour
of pushing XML parsing instead.
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From bugzilla-daemon at portal.open-bio.org Wed Dec 13 17:06:34 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 12:06:34 -0500
Subject: [Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails
with blastall 2.2.14
In-Reply-To:
Message-ID: <200612131706.kBDH6YV4019964@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2090
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
AssignedTo|biopython-dev at biopython.org |biopython-
| |bugzilla at maubp.freeserve.co.
| |uk
------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-13 12:06 -------
Created an attachment (id=520)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=520&action=view)
Patch for Bio/Blast/NCBIStandalone.py
test_NCBIStandalone.py still passes with this patch.
It seems to work for BLASTP 2.2.15 (online) but I would like to see some
examples from the standalone 2.2.15 as well please Frank.
Reading your comments, it sounds like 2.2.14 might also be slightly different
too - again, if you have some examples output files please attach them.
Even with this patch, it WILL NOT WORK with multiple input queries on 2.2.15
(unsure about other recent versions).
(I know we want to push the BLAST XML output by default, but that currently has
issues too...)
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From bugzilla-daemon at portal.open-bio.org Thu Dec 14 23:48:37 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 14 Dec 2006 18:48:37 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612142348.kBENmbZf001062@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |ASSIGNED
------- Comment #9 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-14 18:48 -------
I've just checked in a fairly big change to Bio/Blast/NCBIXML.py (see revision
1.8), see bug 1970 comment 15.
NOTE: While it still reads an entire XML file in one go,
NCBIXML.BlastParser.parse() now returns a list of records - not a single record
as before.
This SHOULD address most of this bug (the unusable with multiple queries bit
anyway).
Some of Jacob's suggestions in comment 1 have been included (e.g. the
expectation threshold parameter is dealt with more sensibly) but not all...
Could you test the new code please Jacob, and point out any outstanding issues.
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From bugzilla-daemon at portal.open-bio.org Fri Dec 15 00:09:22 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 14 Dec 2006 19:09:22 -0500
Subject: [Biopython-dev] [Bug 1950] addition of element, SSBOND, OBSLTE,
CAVEAT fields to PDB
In-Reply-To:
Message-ID: <200612150009.kBF09MTg002106@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=1950
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
AssignedTo|biopython-dev at biopython.org |thamelry at binf.ku.dk
------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-14 19:09 -------
Looking at the patch, one minor point is that the change is to the __init__
method of the class Atom is not backwards compatible:
Old:
def __init__(self, ..., altloc, fullname, serial_number):
Suggested:
def __init__(self, ..., altloc, fullname, element, serial_number):
Anyway, assigning this one to Thomas
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From bugzilla-daemon at portal.open-bio.org Mon Dec 18 11:47:26 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 18 Dec 2006 06:47:26 -0500
Subject: [Biopython-dev] [Bug 1751] Not a bug: testing attachments to
bugzilla
In-Reply-To:
Message-ID: <200612181147.kBIBlQsT012255@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=1751
------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk 2006-12-18 06:47 -------
Created an attachment (id=523)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=523&action=view)
Text file to test a bug in bugzilla
Seeing if a Bugzilla Internal Error this happens for me... please ignore.
This seems to be a problem with Firefox 1.5.0.8 on Windows XP. IE6 works.
(Seemed better to reuse this old bug than create another "attachment test"
bug.)
>> Bugzilla Version 2.20.3
>> Internal Error
>>
>> Bugzilla has suffered an internal error. Please save this page and send
>> it to root-l at open-bio.org with details of
>> what you were doing at the
>> time this message appeared.
>>
>> URL: http://bugzilla.open-bio.org/attachment.cgi
>> undef error - Undefined subroutine Fh::slice at
>> data/template/template/en/default/global/hidden-fields.html.tmpl line 58
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From jig.parikh at gmail.com Tue Dec 19 18:46:07 2006
From: jig.parikh at gmail.com (Jignesh Parikh)
Date: Tue, 19 Dec 2006 13:46:07 -0500
Subject: [Biopython-dev] py2exe module import problems
Message-ID: <6af1ed1c0612191046v191d3b73xe7a2d51804ed9660@mail.gmail.com>
Hi,
I am using python 2.4, biopython 1.42, and py2exe 0.6.5
When I run python setup py2exe, it cannot find the following modules:
The following modules appear to be missing
['Bio.db', 'TextTools', '_ssl', 'bsddb3', 'dtds.pvsystem',
'mxTextTools.__version__', 'xml.parsers.xmlproc.dtdparser']
In my program I import GenBank in order to get and parse GenBank files by
using:
from Bio import GenBank
My executable will not run and fails trying to import db:
Traceback (most recent call last):
File "keywordFilter2.py", line 52, in ?
File "Bio\GenBank\__init__.pyc", line 47, in ?
ImportError: cannot import name db
I cannot even find the Bio.db module. Can you think of how I can ensure that
these modules get imported? Please help!
Thanks,
Jignesh Parikh
Dana-Farber Cancer Institute
Boston, MA
From bugzilla-daemon at portal.open-bio.org Fri Dec 22 15:54:01 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 22 Dec 2006 10:54:01 -0500
Subject: [Biopython-dev] [Bug 2169] New: 'close' method is missing for
ReseekFile wrapper
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2169
Summary: 'close' method is missing for ReseekFile wrapper
Product: Biopython
Version: 1.24
Platform: All
OS/Version: Mac OS
Status: NEW
Severity: normal
Priority: P2
Component: Other
AssignedTo: biopython-dev at biopython.org
ReportedBy: sunhwanj at gmail.com
ReseekFile class doesn't have close method.
While I tried to read PDB file after I download pdb file using Bio.db,
PDBParser complains that it can't close pdbfile.
>>> from Bio.PDB.PDBParser import PDBParser
>>> from Bio import db
>>>
>>> p = PDBParser()
>>> p.get_structure('1kdx', db['pdb']['1kdx'])
Traceback (most recent call last):
File "", line 1, in
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/PDB/PDBParser.py",
line 67, in get_structure
file.close()
AttributeError: ReseekFile instance has no attribute 'close'
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From tiagoantao at gmail.com Fri Dec 22 18:19:26 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Fri, 22 Dec 2006 18:19:26 +0000
Subject: [Biopython-dev] Population Genetics code
Message-ID: <6d941f120612221019g400af87enfb81fd04a1a3b69c@mail.gmail.com>
Hi!
During the last few months I have developed a lot of code in Python
around the topic of Population Genetics. Things from parsers (GenePop,
fdist2, Arlequin), to invoking other programs (simcoal2, fdist2), to
statistics (Fst, expected heterozygosity, ...), to data structures
representing population relationships, to HapMap data analysis,
currently I am developing code to interact with UCSC table browser...
Some of this code is used from Jython, by the way.
I am now in the process of consolidating the mess that I have done (I
have sometimes, several implementations of the same thing, just
because I was too lazy to do proper reuse). I was thinking that I
could do that in the context of BioPython, ie contributing the code.
Especially because BioPython seems to lack Population Genetics code.
Code quality varies a lot, from highly tested - under heavy use, to
one offs that were used a single time. But, even things that are poor
quality can easily be upgraded. The biggest issue is that some code
dealing with representation of molecular markers is still not matured
enough, ie, I believe that even good code it will have change quite a
lot in the future, breaking interfaces...
Anyway, I was thinking in starting with an easy task, namely
converting my parsers of GenePop and fdist2 to BioPython. These are 2
absolutely trivial formats.
Any comments on this? Would there be an interest in population
genetics oriented code?
Regards,
Tiago
--
The right to offend is far more important than the right not to be
offended - Rowan Atkinson
From tiagoantao at gmail.com Wed Dec 27 12:04:04 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Wed, 27 Dec 2006 12:04:04 +0000
Subject: [Biopython-dev] GenePop parser code
Message-ID: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
Hi!
I have finalized converting my code to parse GenePop(*) files into
BioPython. I would like to know if there would be interest in adding
it to BioPython?
After reading the instructions, I suppose, as this is not strictly a
patch, that it makes no sense to submit it through Bugzilla? More, as
this is my first contribution to BioPython, I would bet its full of
small problems typical from a newbie...
I also have test code, but its still in my own ad-hoc format (I will
convert it to the BioPython standard in case it gets accepted).
I have truckloads more of Population Genetics code that I would be
willing to convert to Biopython (more or less things along the lines
of BioPerls's Bio::PopGen). I decided to start with a small/simple
thing to see how it goes...
Is there any interest? If so, how do I submit this?
(*)GenePop: http://wbiomed.curtin.edu.au/genepop/
--
The right to offend is far more important than the right not to be
offended - Rowan Atkinson
From biopython-dev at maubp.freeserve.co.uk Wed Dec 27 18:40:03 2006
From: biopython-dev at maubp.freeserve.co.uk (Peter (BioPython Dev))
Date: Wed, 27 Dec 2006 18:40:03 +0000
Subject: [Biopython-dev] GenePop parser code
In-Reply-To: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
References: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
Message-ID: <4592BE03.8030609@maubp.freeserve.co.uk>
Tiago Ant?o wrote:
> Hi!
>
> I have finalized converting my code to parse GenePop(*) files into
> BioPython. I would like to know if there would be interest in adding
> it to BioPython?
>
> (*)GenePop: http://wbiomed.curtin.edu.au/genepop/
>
I think someone asked about Population genetics on a mailing list in the
last year or so, and there was some interest out there.
Check Feb 2006 on the discussion list, look for a thread on "PopGen"
started by Ralph Haygood. He had written a Python module for computing
a variety of population-genetic statistics from DNA sequences.
Does this overlap with your plans at all?
> After reading the instructions, I suppose, as this is not strictly a
> patch, that it makes no sense to submit it through Bugzilla? More, as
> this is my first contribution to BioPython, I would bet its full of
> small problems typical from a newbie...
I would suggest creating an enhancement bug for "Adding a GenPop file
format parser" or something like that, and then attach your code to it.
Sending attachments on mailing lists is asking for trouble.
> I also have test code, but its still in my own ad-hoc format (I will
> convert it to the BioPython standard in case it gets accepted).
Have a look at the existing Tests directory - basically you have a
script that produces some output, and the expected output in the
"output" subdirectory. Avoid things like printing floating point
numbers or filenames in any print statements - they make running the
test suite on different platforms tricky. Most parser tests have a few
sample input files too (held in subdirectories again).
> I have truckloads more of Population Genetics code that I would be
> willing to convert to Biopython (more or less things along the lines
> of BioPerls's Bio::PopGen). I decided to start with a small/simple
> thing to see how it goes...
That sounds sensible - unless there is some generic object structure you
want to introduce for handling population data? I don't know enough
about this to comment.
> Is there any interest? If so, how do I submit this?
To recap: yes there is some interest, and I would suggest creating an
enhancement "bug" on bugzilla and attaching files/patches there.
Peter
From tiagoantao at gmail.com Thu Dec 28 00:11:22 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Thu, 28 Dec 2006 00:11:22 +0000
Subject: [Biopython-dev] GenePop parser code
In-Reply-To: <4592BE03.8030609@maubp.freeserve.co.uk>
References: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
<4592BE03.8030609@maubp.freeserve.co.uk>
Message-ID: <6d941f120612271611p268cebaci7dc80c49806d1308@mail.gmail.com>
Hi!
On 12/27/06, Peter (BioPython Dev) wrote:
> That sounds sensible - unless there is some generic object structure you
> want to introduce for handling population data? I don't know enough
> about this to comment.
Well, this has been floating around my mind... In fact I would need to
introduce, sooner or later, notions like population, individual,
marker... What I currently have is enough for me, but I am pretty much
aware that its not generic enough. One good example of this is Ralph
Haygood's messages that you talk about, where he uses mainly sequence
data statistics (I work more with SNP and microsatellite data), as
such I suppose my data structures would not be enough for his work
(and vice-versa).
I propose the following strategy:
1. I will try to contact him (maybe he still reads this list? Are you
there? ;) )
2. I will have a much more closer look at Bio::PopGen from BioPerl.
3. Wait for any more comments on this list
Let see where this leads to...
In the mean time I have some less problematic code: mainly code to
work with Mark Beaumont's fdist program, parser and code to control
it. The problem here is that fdist is such a niche program, that I
don't think it deserves to be at top level Bio (but my suggestion is
for it to be supported, as is clearly used in population genetics). I
think it would make more sense to be Bio.PopGen.FDist rather than
Bio.FDist, just to not to make Bio too "noisy". Does this make sense?
Thanks,
Tiago
PS - Tomorrow I will submit GenePop code as you suggested
--
The right to offend is far more important than the right not to be
offended - Rowan Atkinson
From solymosi.norbert at gmail.com Thu Dec 28 07:45:03 2006
From: solymosi.norbert at gmail.com (Solymosi Norbert)
Date: Thu, 28 Dec 2006 08:45:03 +0100
Subject: [Biopython-dev] py2exe module import problems
Message-ID: <459375FF.5070903@gmail.com>
Hi,
I have the same problem and no solution.
If anybody has idea, please tell me
Thanks,
Norbert Solymosi
From bugzilla-daemon at portal.open-bio.org Thu Dec 28 12:07:43 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 07:07:43 -0500
Subject: [Biopython-dev] [Bug 2170] New: Adding a GenPop file format parser
and simple utilities
Message-ID:
http://bugzilla.open-bio.org/show_bug.cgi?id=2170
Summary: Adding a GenPop file format parser and simple utilities
Product: Biopython
Version: Not Applicable
Platform: PC
OS/Version: Linux
Status: NEW
Severity: enhancement
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: tiagoantao at gmail.com
This is a bug entry to submit GenePop related code (including some tests)
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From bugzilla-daemon at portal.open-bio.org Thu Dec 28 12:12:05 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 07:12:05 -0500
Subject: [Biopython-dev] [Bug 2170] Adding a GenPop file format parser and
simple utilities
In-Reply-To:
Message-ID: <200612281212.kBSCC5Xc013879@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2170
tiagoantao at gmail.com changed:
What |Removed |Added
----------------------------------------------------------------------------
AssignedTo|biopython-dev at biopython.org |tiagoantao at gmail.com
Status|NEW |ASSIGNED
------- Comment #1 from tiagoantao at gmail.com 2006-12-28 07:12 -------
Created an attachment (id=525)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=525&action=view)
Parser/Utils and test for GenePop code
This is my first submission to BioPython, most probably full of problems... Any
suggestions are more than welcome...
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From tiagoantao at gmail.com Thu Dec 28 12:14:49 2006
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Thu, 28 Dec 2006 12:14:49 +0000
Subject: [Biopython-dev] GenePop parser code
In-Reply-To: <4592BE03.8030609@maubp.freeserve.co.uk>
References: <6d941f120612270404wcfd83c9jc9d4a00bc11baf92@mail.gmail.com>
<4592BE03.8030609@maubp.freeserve.co.uk>
Message-ID: <6d941f120612280414p13b5c4c5u345ae3701eb4bfed@mail.gmail.com>
On 12/27/06, Peter (BioPython Dev) wrote:
> To recap: yes there is some interest, and I would suggest creating an
> enhancement "bug" on bugzilla and attaching files/patches there.
I have just submitted the code on bugzilla (assigned it to myself,
don't know if that is correct).
As this is my first submission, this is probably a big piece of crap
;) . I am more than willing to correct things...
Regards,
Tiago
From bugzilla-daemon at portal.open-bio.org Thu Dec 28 20:25:25 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 15:25:25 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612282025.kBSKPPaI029719@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #10 from jmjoseph at andrew.cmu.edu 2006-12-28 15:25 -------
Thanks for your work. I have had a chance to work with the CVS
NCBIXML parser. I have not tested with output other than that from
blastall 2.2.13 and 2.2.15, so many of my suggestions may not be
acceptable for compatibility reasons. Regardless, I do still see a
number of inconsistencies. I did address some of these in my previous
patches, but it's not worth the effort of starting with them. Now,
though:
In Record.py, HSP.identities, HSP.gaps, and HSP.positives are still
defined as (None,None) tuples. However, in NCBIXML.py, these
variables are set as integers. I don't see a point of a tuple at all,
at least for NCBIXML. (I realize it is used in NCBIStandalone.py).
Most importantly, the inconsistency makes it difficult to handle cases
when the parameter is not set. It seems easiest, though, to just
retain the tuple format.
In the past, I worried that the order of tuple building for
self._blast.gap_penalties or ka_params could cause the tuple to have
an incorrect ordering. I seem to remember hitting an issue where the
tuple was built with the wrong length, but I can't be specific. In
general, it remains odd to me to not just use a list and set each
element respectively. If necessary, one could convert to a tuple when
finished or use some other approach that does not rely upon order.
Why not use query_len, as defined in the XML file, or query_length
instead of query_letters as a variable name? In
BlastParser._end_Iteration, self._blast.query_letters is set. This is
not defined/documented in the Parameters class in Record.py. Rather,
query_length is defined there. In the Header class, though, the name
query_letters is used. There also seems to be some confusion between
num_letters_in_database, num_sequences_in_database, database_letters,
and database_sequences. Note that even if this naming is not
corrected, NCBIXML.py:186 is wrong with "self._blast_query_letters"
rather than "self._blast.query_letters".
Similarly, why store the bit score and E-value as 'bits' and
'_hsp.expect'/'descr.e' rather than just using bit_score and
evalue, as in the blast XML ouput?
I make use of in 2.2.13. This value missing
entirely.
The parsing of and is confusing. For example,
1
gnl|BL_ORD_ID|0
3377250
...
results in _hit.title set to "gnl|BL_ORD_ID|0 3377250". I would
rather they remain separate (or both methods be used).
This is certainly not an exhaustive list. I'm happy to provide
another patch correcting many of these inconsistencies. At the
very least, the variable names defined in Record.py should be
used in NCBIXML.py. May I modify at least the above names to
correspond more closely to the names used in the XML? I know
I've found this particularly confusing.
-Jacob
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From bugzilla-daemon at portal.open-bio.org Thu Dec 28 20:26:52 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 15:26:52 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612282026.kBSKQqAe029798@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #11 from jmjoseph at andrew.cmu.edu 2006-12-28 15:26 -------
Created an attachment (id=526)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=526&action=view)
Patch to record.py
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From bugzilla-daemon at portal.open-bio.org Thu Dec 28 20:27:22 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 15:27:22 -0500
Subject: [Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple
queries and recent (2.2.13) blast - patch attached
In-Reply-To:
Message-ID: <200612282027.kBSKRM3v029844@portal.open-bio.org>
http://bugzilla.open-bio.org/show_bug.cgi?id=2051
------- Comment #12 from jmjoseph at andrew.cmu.edu 2006-12-28 15:27 -------
Created an attachment (id=527)
--> (http://bugzilla.open-bio.org/attachment.cgi?id=527&action=view)
Patch to NCBIXML.py
These patches to NCBIXML and Record:
* replace query_letters with query_length,
* use tuples for _hsp.identities, positives, and gaps
* store _hsp.align_length
* separate the hit id and hit def elements. title is retained
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