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