From bogus@does.not.exist.com Sat Mar 5 14:42:50 2005 From: bogus@does.not.exist.com () Date: Sat Mar 5 14:42:52 2005 Subject: No subject Message-ID: also be backcompatible with python 1.5.2 with PyXML installed (well, once the 0.6.1 release comes out, that is), so I think I'll go ahead and check in the necessary changes to the Clustalw stuff to make it work with 2.0b2 alone. > I haven't sat down with the new Python distro to see what's changed. > Again, that will wait until after I get this 0.3 release out. Okay, sounds good. I think I'm starting to undestand what is going on with PyXML and python2.0 XML (well, as much as it is possible to understand :-), so I can let you know how the new stuff works. [fasta parser] > So the "yes" part means, go ahead and write a parser for FASTA which > produces Biopython data structures. However, it will likely change > for the future. Okay, I'll look at doing this, and then maybe this can tell us how nicely Martel will play with the current parser setup. Brad From bogus@does.not.exist.com Sat Mar 5 14:42:50 2005 From: bogus@does.not.exist.com () Date: Sat Mar 5 14:43:11 2005 Subject: No subject Message-ID: of data generated by sparse coding. I am not sure python is suitable for this but we can always give it a try. Worst case scenario is to use it for translating biological data to fit the input and translating the output back to biological data. The actual calculation can then be done by a C based engine. Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From bugzilla-daemon at portal.open-bio.org Fri Mar 4 06:48:13 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:44:00 2005 Subject: [Biopython-dev] [Bug 1756] Tutorial patch Message-ID: <200503041148.j24BmDEQ023162@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1756 ------- Additional Comments From ybastide@irisa.fr 2005-03-04 06:48 ------- Created an attachment (id=196) --> (http://bugzilla.open-bio.org/attachment.cgi?id=196&action=view) Aforementionned spelling fixes ------- 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 Mar 4 06:46:37 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:44:00 2005 Subject: [Biopython-dev] [Bug 1756] New: Tutorial patch Message-ID: <200503041146.j24Bkb9c023150@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1756 Summary: Tutorial patch Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: minor Priority: P2 Component: Documentation AssignedTo: biopython-dev@biopython.org ReportedBy: ybastide@irisa.fr Hi, I've got a patch to Doc/Tutorial.tex: mostly spelling fixes, and some doc on ExPASy.sprot_search_(de|ful) ------- 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 Mar 4 06:53:48 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:44:00 2005 Subject: [Biopython-dev] [Bug 1757] New: Doc/images and Doc/Tutorial.pdf not included in the tarball Message-ID: <200503041153.j24Brmnr023255@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1757 Summary: Doc/images and Doc/Tutorial.pdf not included in the tarball Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: ybastide@irisa.fr Hi, biopython-1.40b.tar.gz doesn't include the Doc/images directory; the tutorial is therefore hard to compile. Moreover, I suppose it (Tutorial.pdf) should be included in the distribution Regards, yves ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From jhackney at stanford.edu Fri Mar 4 18:23:18 2005 From: jhackney at stanford.edu (Jason A. Hackney) Date: Sat Mar 5 14:44:00 2005 Subject: [Biopython-dev] MEME parser Message-ID: <303961c81c0e97a1d8cc9edf92950d96@stanford.edu> Hi all, I have written a simple parser for both meme and mast text output. I am currently finishing up test cases and documenting my source, and I would like to submit the finished code to biopython. I've already read the Contributing to... on the website, but would like some more info as to how to submit my code. Thanks, Jason Jason A. Hackney Postdoctoral Scholar Department of Microbiology and Immunology Stanford University From mdehoon at ims.u-tokyo.ac.jp Mon Mar 7 06:19:28 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Mon Mar 7 06:16:00 2005 Subject: [Biopython-dev] Removing spam from the biopython-dev archives Message-ID: <422C38C0.6060300@ims.u-tokyo.ac.jp> Dear Biopythoneers, I have good news and bad news for you. The good news is that the biopython-dev mailing list archives are now spam-free. See http://www.biopython.org/pipermail/biopython-dev/ If you sent a message to biopython-dev during the past couple of days, it may be missing in the archives. If you find out that a message you sent is missing, please send it again to make sure that it is preserved for future generations of Biopythoneers. The bad news is that when the biopython-dev archive was replaced on the biopython.org webserver, the source file for the biopython archive was accidentally overwritten. The biopython archive is still there, but the source file from which the archives are generated is not. There is a backup file until about March 2004, but for messages between March 2004 and early March 2005 we no longer have the source file. If you happen to have a copy of these messages, please let us know. --Michiel. From hoffman at ebi.ac.uk Mon Mar 7 06:23:43 2005 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Mon Mar 7 06:18:45 2005 Subject: [Biopython-dev] Removing spam from the biopython-dev archives In-Reply-To: <422C38C0.6060300@ims.u-tokyo.ac.jp> References: <422C38C0.6060300@ims.u-tokyo.ac.jp> Message-ID: > The bad news is that when the biopython-dev archive was replaced on > the biopython.org webserver, the source file for the biopython > archive was accidentally overwritten. The biopython archive is still > there, but the source file from which the archives are generated is > not. There is a backup file until about March 2004, but for messages > between March 2004 and early March 2005 we no longer have the source > file. If you happen to have a copy of these messages, please let us > know. I should have copies of most of these messages. -- Michael Hoffman European Bioinformatics Institute From hoffman at ebi.ac.uk Mon Mar 7 06:25:38 2005 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Mon Mar 7 06:20:28 2005 Subject: [Biopython-dev] Removing spam from the biopython-dev archives In-Reply-To: References: <422C38C0.6060300@ims.u-tokyo.ac.jp> Message-ID: On Mon, 7 Mar 2005, Michael Hoffman wrote: >> The bad news is that when the biopython-dev archive was replaced on >> the biopython.org webserver, the source file for the biopython >> archive was accidentally overwritten. > > I should have copies of most of these messages. Oops, I thought you meant biopython-dev. Anyway, the biopython stuff is on gmane going back to September 2002. -- Michael Hoffman European Bioinformatics Institute From mdehoon at ims.u-tokyo.ac.jp Mon Mar 7 06:30:11 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Mon Mar 7 06:25:14 2005 Subject: [Biopython-dev] Removing spam from the biopython-dev archives In-Reply-To: References: <422C38C0.6060300@ims.u-tokyo.ac.jp> Message-ID: <422C3B43.80903@ims.u-tokyo.ac.jp> Michael Hoffman wrote: >> The bad news is that when the biopython-dev archive was replaced on >> the biopython.org webserver, the source file for the biopython >> archive was accidentally overwritten. The biopython archive is still >> there, but the source file from which the archives are generated is >> not. There is a backup file until about March 2004, but for messages >> between March 2004 and early March 2005 we no longer have the source >> file. If you happen to have a copy of these messages, please let us >> know. > > > I should have copies of most of these messages. Great! Could you put them somewhere on the web where I can download them? --Michiel. From bugzilla-daemon at portal.open-bio.org Tue Mar 8 13:05:10 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 8 13:28:42 2005 Subject: [Biopython-dev] [Bug 1756] Tutorial patch Message-ID: <200503081805.j28I5ASI002706@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1756 ybastide@irisa.fr changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #196 is|0 |1 obsolete| | ------- Additional Comments From ybastide@irisa.fr 2005-03-08 13:05 ------- Created an attachment (id=197) --> (http://bugzilla.open-bio.org/attachment.cgi?id=197&action=view) Patch, iteration #2 The previous patch mentioned a way to retrieve SwissProt IDs from sprot-search-{de,ful} html results. Unfortunatly, the regex provided doesn't work when a single result is returned. Here's an extended version... Bye, yves ------- 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 Mar 8 16:16:44 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 8 16:28:49 2005 Subject: [Biopython-dev] [Bug 1758] New: genbank parser chokes on /transl_except Message-ID: <200503082116.j28LGisr004671@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1758 Summary: genbank parser chokes on /transl_except Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Martel/Mindy AssignedTo: biopython-dev@biopython.org ReportedBy: mkersz@ccr.jussieu.fr Genbank records such as Drosophila 2L chromosome contains lines about translation exceptions, such as /transl_except=(pos:2489262..2489264,aa:OTHER) It seems that the biopython genbank parser does not successfully parse these. ------- 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 Mar 8 17:19:21 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 8 17:28:49 2005 Subject: [Biopython-dev] [Bug 1758] genbank parser chokes on /transl_except Message-ID: <200503082219.j28MJLLu005234@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1758 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2005-03-08 17:19 ------- You can test this with accession NT_033779 available here: ftp://ftp.ncbi.nih.gov/genomes/Drosophila_melanogaster/CHR_2/NT_033779.gbk I think the problem is that the /transl_except=... entry spans multiple lines, but is not wrapped in quotes (as done normally for multi-line entries). Due to bug 1747 I haven't tried loading this with the current GenBank parser as I don't have enough RAM. However, for the record, even my personal GenBank parser (patch on bug 1747) doesn't yet cope with the /transl_except=... entry. Is this file and others like it are "wrong", and should it quote the entry? Or we need to cope with this as well (not sure how painful that would be!)? Snippet from the file: CDS complement(join(18108857..18109603,18109665..18110692, 18111046..18111608,18111671..18112909,18113657..18114058, 18115560..18116014)) /gene="kel" /locus_tag="CG7210" /codon_start=1 /transl_except=(pos:complement(18111697..18111699), aa:OTHER) /protein_id="NP_476589.4" /db_xref="GI:45549017" /db_xref="FLYBASE:FBgn0001301" /db_xref="GeneID:35084" /translation="MIALSALLTKYTIGIMSNLSNGNSNNNNQQQQQQQQGQNPQQPA QNEGGAGAEFVAPPPGLGAAVGVAAMQQRNRLLQQQQQQHHHHQNPAAEGSGLERGSC LLRYASQNSLDESSQKHVQRPNGKERGTVGQYSNEQHTARSFDAMNEMRKQKQLCDVI LVADDVEIHAHRMVLASCSPYFYAMFTSFEESRQARITLQSVDARALELLIDYVYTAT VEVNEDNVQVLLTAANLLQLTDVRDACCDFLQTQLDASNCLGIREFADIHACVELLNY AETYIEQHFNEVIQFDEFLNLSHEQVISLIGNDRISVPNEERVYECVIAWLRYDVPMR EQFTSLLMEHVRLPFLSKEYITQRVDKEILLEGNIVCKNLIIEALTYHLLPTETKSAR TVPRKPVGMPKILLVIGGQAPKAIRSVEWYDLREEKWYQAAEMPNRRCRSGLSVLGDK VYAVGGFNGSLRVRTVDVYDPATDQWANCSNMEARRSTLGVAVLNGCIYAVGGFDGTT GLSSAEMYDPKTDIWRFIASMSTRRSSVGVGVVHGLLYAVGGYDGFTRQCLSSVERYN PDTDTWVNVAEMSSRRSGAGVGVLNNILYAVGGHDGPMVRRSVEAYDCETNSWRSVAD MSYCRRNAGVVAHDGLLYVVGGDDGTSNLASVEVYCPDSDSWRILPALMTIGRSYAGV CMIDKPMXMEEQGALARQAASLAIALLDDENSQAEGTMEGAIGGAIYGNLAPAGGAAA AAAPAAPAQAPQPNHPHYENIYAPIGQPSNNNNNSGSNSNQAAAIANANAPANAEEIQ QQQQPAPTEPNANNNPQPPTAAAPAPSQQQQQQQAQPQQPQRILPMNNYRNDLYDRSA AGGVCSAYDVPRAVRSGLGYRRNFRIDMQNGNRCGSGLRCTPLYTNSRSNCQRQRSFD DTESTDGYNLPYAGAGTMRYENIYEQIRDEPLYRTSAANRVPLYTRLDVLGHGIGRIE RHLSSSCGNIDHYNLGGHYAVLGHSHFGTVGHIRLNANGSGVAAPGVAGTGTCNVPNC QGYMTAAGSTVPVEYANVKVPVKNSASSFFSCLHGENSQSMTNIYKTSGTAAAMAAHN SPLTPNVSMERASRSASAGAAGSAAAAVEEHSAADSIPSSSNINANRTTGAIPKVKTA NKPAKESGGSSTAASPILDKTTSTGSGKSVTLAKKTSTAAARSSSSGDTNGNGTLNRI SKSSLQWLLVNKWLPLWIGQGPDCKVIDFNFMFSRDCVSCDTASVASQMSNPYGTPRL SGLPQDMVRFQSSCAGACAAAGAASTIRRDANASARPLHSTLSRLRNGEKRNPNRVAG NYQYEDPSYENVHVQWQNGFEFGRSRDYDPNSTYHQQRPLLQRARSESPTFSNQQRRL QRQGAQAQQQSQQPKPPGSPDPYKNYKLNADNNTFKPKPIAADELEGAVGGAVAEIAL PEVDIEVVDPVSLSDNETETTSSQNNLPSTTNSNNLNEHND" ------- 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 Mar 8 17:25:51 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 8 17:28:51 2005 Subject: [Biopython-dev] [Bug 1758] genbank parser chokes on /transl_except Message-ID: <200503082225.j28MPpl3005358@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1758 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2005-03-08 17:25 ------- Created an attachment (id=199) --> (http://bugzilla.open-bio.org/attachment.cgi?id=199&action=view) Test case - a reduced version of NT_033779.gbk Confirms bug exists in BioPython 1.30 / CVS version of Bio/GenBank/__init__.py as follows. The attchement is an reduced version of NT_033779.gbk with only a few features and only a fraction of the full sequence. Traceback (most recent call last): File "C:\TEMP\genbank\test004.py", line 52, in ? cur_record = gb_iterator.next() File "C:\Python23\lib\site-packages\Bio\GenBank\__init__.py", line 129, in next return self._parser.parse(File.StringHandle(data)) File "C:\Python23\lib\site-packages\Bio\GenBank\__init__.py", line 240, in parse self._scanner.feed(handle, self._consumer) File "C:\Python23\lib\site-packages\Bio\GenBank\__init__.py", line 1264, in feed self._parser.parseFile(handle) File "C:\Python23\lib\site-packages\Martel\Parser.py", line 332, in parseFile self.parseString(fileobj.read()) File "C:\Python23\lib\site-packages\Martel\Parser.py", line 360, in parseString self._err_handler.fatalError(result) File "C:\Python23\lib\xml\sax\handler.py", line 38, in fatalError raise exception ParserPositionException: error parsing at or beyond character 6841 ------- 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 Mar 8 16:59:34 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 8 17:28:51 2005 Subject: [Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files Message-ID: <200503082159.j28LxY9K004987@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1747 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2005-03-08 16:59 ------- See also Andrew Dalke's comment on this bug: http://www.biopython.org/pipermail/biopython-dev/2005-February/001910.html I wrote: > I filed bug 1747 as "major" and feel it renders the GenBank parser > effectively useless for large genomes. Andrew replied: I saw that bug report when it came in a couple weeks ago but I was busy at a client site. One of the fundamental problems with this implementation of Martel is that it parses a record in memory and uses about 4x as much memory as the record. The slowness for large records comes from hitting swap. It can't be fixed without some non-trivial changes to Martel; basically a rewrite. If anyone wants to tackle rewriting a regex engine I have some comments about what needs to be done. As for me I haven't touched the code in years because I haven't needed that capability and other tasks (including paying work) keep me busy. ------- 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 Mar 8 17:04:21 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 8 17:28:52 2005 Subject: [Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files Message-ID: <200503082204.j28M4LZR005103@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1747 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2005-03-08 17:04 ------- Created an attachment (id=198) --> (http://bugzilla.open-bio.org/attachment.cgi?id=198&action=view) Patch to the class _Scanner in Bio/GenBank/__init__.py The following patch seems to pass all existing GenBank tests, and my own testing. The only change is to the class _Scanner in Bio/GenBank/__init__.py This is a patch created on Windows XP with the Cygwin diff command against file revision 1.53 (as shipped with BioPython 1.30 and 1.40b): diff my_version.py vcs_version.py > patch.txt Instead of using Martel to parse entire genbank records, it is only used to parse the "header section" from the LOCUS line to the FEATURES line. The features themselves, and the nucleotide sequences, are parsed with new python code. i.e. Rather than rewriting Martel, I re-wrote the GenBank scanner. It should be possible to go further and not use Martel at all, probably another afternoon's work for me. Updates timings to follow, but in general both time taken and memory required are more than halved - which is nice! ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Tue Mar 8 23:53:02 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Tue Mar 8 23:47:51 2005 Subject: [Biopython-dev] Re: [BioPython] Removing spam from the biopython-dev archives In-Reply-To: <422C38C0.6060300@ims.u-tokyo.ac.jp> References: <422C38C0.6060300@ims.u-tokyo.ac.jp> Message-ID: <422E812E.1010903@ims.u-tokyo.ac.jp> > The bad news is that when the biopython-dev archive was replaced on the > biopython.org webserver, the source file for the biopython archive was > accidentally overwritten. The biopython archive is still there, but the > source file from which the archives are generated is not. There is a > backup file until about March 2004, but for messages between March 2004 > and early March 2005 we no longer have the source file. If you happen to > have a copy of these messages, please let us know. Bartek Wilczynski sent me his copy of the Biopython messages since mid August 2004, which allowed me to recover all messages since then except for one message in September. From March 2004 to mid August 2004, there is still a gap. So if you have saved some of those messages, please let me know. Note that Netscape and Mozilla don't actually delete a message from the source file until you compact the mail folders. So if you delete biopython messages but don't compact the mail folders, you probably still have those messages even if they don't show up in Netscape. --Michiel From bugzilla-daemon at portal.open-bio.org Wed Mar 9 05:32:39 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Mar 9 06:31:19 2005 Subject: [Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files Message-ID: <200503091032.j29AWdRO013677@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1747 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2005-03-09 05:32 ------- The following times and memory usage figures are on Windows 2000, Python 2.3.3 using the GenBank Iterator (script running from Idle). The computer was a 2.26 GHz Intel Pentium 4, with 735 MB RAM:- BioPython 1.30 using Martel:- NC_003065.gbk 480 kb, 4 seconds, 28 MB RAM NC_003064.gbk 1,217 kb, 11 seconds, 56 MB RAM NC_000854.gbk 3,391 kb, 45 seconds, 165 MB RAM NC_003063.gbk 4,725 kb, 55 seconds, 195 MB RAM NC_003062.gbk 6,574 kb, 88 seconds, 268 MB RAM NC_005966.gbk 8,858 kb, 139 seconds, 372 MB RAM NC_000913.gbk 10,267 kb, 171 seconds, 409 MB RAM NC_000962.gbk 11,010 kb, 200 seconds, 486 MB RAM NC_003997.gbk 12,026 kb, 228 seconds, 496 MB RAM NC_002678.gbk 15,120 kb, 306 seconds, 586 MB RAM NC_005027.gbk 18,211 kb, not enough RAM NC_004463.gbk 19,500 kb, not enough RAM NC_003888.gbk 24,390 kb, not enough RAM NC_004354.gbk 33,139 kb, not enough RAM NC_003074.gbk 42,281 kb, not enough RAM NC_003070.gbk 55,149 kb, not enough RAM BioPython 1.30 with this patch:- NC_003065.gbk 480 kb, 1 seconds, 13 MB RAM NC_003064.gbk 1,217 kb, 4 seconds, 16 MB RAM NC_000854.gbk 3,391 kb, 16 seconds, 25 MB RAM NC_003063.gbk 4,725 kb, 17 seconds, 26 MB RAM NC_003062.gbk 6,574 kb, 27 seconds, 33 MB RAM NC_005966.gbk 8,858 kb, 33 seconds, 40 MB RAM NC_000913.gbk 10,267 kb, 43 seconds, 45 MB RAM NC_000962.gbk 11,010 kb, 41 seconds, 45 MB RAM NC_003997.gbk 12,026 kb, 55 seconds, 52 MB RAM NC_002678.gbk 15,120 kb, 71 seconds, 61 MB RAM NC_005027.gbk 18,211 kb, 88 seconds, 68 MB RAM NC_004463.gbk 19,500 kb, 95 seconds, 74 MB RAM NC_003888.gbk 24,390 kb, 146 seconds, 95 MB RAM NC_004354.gbk 33,139 kb, 156 seconds, 121 MB RAM NC_003074.gbk 42,281 kb, 302 seconds, 193 MB RAM NC_003070.gbk 55,149 kb, 436 seconds, 250 MB RAM The last three (really big) files are from Drosophila and Arabidopsis, the rest are bacteria. Times recorded by the test script, memory usage recorded by hand using Task Manager. In summary, with the patch parsing is nearly four times faster, and uses almost a tenth of the memory - quite an improvement. The details of implementation for this approach could be improved, I have had some thoughts about this over night. ------- 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 Mar 9 11:34:45 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Mar 9 12:28:43 2005 Subject: [Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files Message-ID: <200503091634.j29GYjNP017049@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1747 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #198 is|0 |1 obsolete| | ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2005-03-09 11:34 ------- Created an attachment (id=200) --> (http://bugzilla.open-bio.org/attachment.cgi?id=200&action=view) Patch to the class _Scanner in Bio/GenBank/__init__.py This version of the patch completely replaces the Martel code in the class _Scanner. The feature parsing code has (in my opinion) been simplified (since the previous patch). However, with all the new code added to deal with the "GenBank header section", the feed function is probably ripe for splitting up into sub functions. This has been fully tested with the Tests/test_GenBank.py as shipped with Biopython 1.40b. As before, patch created on Windows XP with the Cygwin diff command against Bio/GenBank/__init__.py revision 1.53 (shipped with BioPython 1.30 and 1.40b): diff my_version.py vcs_version.py > patch.txt ------- 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 Mar 9 21:39:47 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Mar 9 22:28:39 2005 Subject: [Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files Message-ID: <200503100239.j2A2dlM1022941@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1747 ------- Additional Comments From dalke@dalkescientific.com 2005-03-09 21:39 ------- I think the history has shown that the idea of Martel, while interesting, has had problems in its implementation. It could only be fixed with a lot of effort. Hand-written code to do the same parsing doesn't have the purity to it but is easier to maintain, and easier to understand by a wider number of people. I think also that the Martel grammers I developed were too nit-picky and there are places where perhaps it should have been a bit looser. So I have no qualms with getting rid of Martel as the patcher suggests. >From an email I wrote recently on the topic, included here for the record Martel hasn't panned out as well as I had hoped. I think I know the reasons: - regexps are hard to write and debug Could be improved with some sort of development/ testing environment - Martel's grammars are hard to edit When a grammar changes it's not possible to say "the new format is the old format but change this one bottom level node". I'm actually considering switching over to a DOM-style description of the tree so I can use XSLT as the editing language. Except that I think XSLT's grammar is clumsy and ugly. - Martel needs everything in memory I implemented a hack to parse a record at a time but it's a hack and fails (except on large memory machines) for people who want to read a chromosome at a time. I would also like it to be feed based instead of pull based. ------- 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 Mar 10 04:52:59 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Mar 10 05:31:38 2005 Subject: [Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files Message-ID: <200503100952.j2A9qxI7027005@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1747 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2005-03-10 04:52 ------- While "working" with the GenBank parser and this patch, I think I got a rough idea of how Martel is intended to work - and very clever it is too. Its a pity it does not scale well. I agree with Andrews point that any Martel parser is much harder to get to grips with than a format specific hand writen parser (e.g. the BLAST parser). P.S. Timings and memory needs with the first patch (#198 - still using Martel for the "header section") and the second patch (#200 - no Martel dependance) are more or less the same. If anyone interested in testing this, and could produce some memory footprint information automatically, that would be welcome. ------- 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 Mar 10 22:14:53 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Mar 10 22:29:00 2005 Subject: [Biopython-dev] [Bug 1760] Test - ignore Message-ID: <200503110314.j2B3ErQa005832@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1760 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |INVALID ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-10 22:14 ------- OK, got it. ------- 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 Mar 10 22:13:24 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Mar 10 22:29:02 2005 Subject: [Biopython-dev] [Bug 1760] New: Test - ignore Message-ID: <200503110313.j2B3DOw4005809@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1760 Summary: Test - ignore Product: Biopython Version: Not Applicable Platform: All OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Other AssignedTo: biopython-dev@biopython.org ReportedBy: mdehoon@ims.u-tokyo.ac.jp Just trying to find out how to submit a patch. ------- 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 Mar 14 07:04:10 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Mar 14 07:29:16 2005 Subject: [Biopython-dev] [Bug 1761] New: BLAST not returning final results Message-ID: <200503141204.j2EC4ANE021948@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1761 Summary: BLAST not returning final results Product: Biopython Version: Not Applicable Platform: PC OS/Version: Windows XP Status: NEW Severity: normal Priority: P2 Component: Other AssignedTo: biopython-dev@biopython.org ReportedBy: genesniffer@hotmail.com Hi, I'm just trying to run BLAST at NCBI using NCBIWWW using the script below. The request seems to be sent fine, but the returned page ends with "This page will automatically be updated...." ie the final results are not being returned. The module doesn't not seem to be polling for the final result. Is this a bug in the program or am I doing something wrong? I look forward to hearing from you... Kate from Bio.Blast import NCBIWWW blast_results = NCBIWWW.blast('blastp', 'nr', protein_seq, entrez_query="Homo sapiens [ORGN]") blast_results = blast_results.readlines() print blast_results ------- 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 Mar 14 09:27:56 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Mar 14 09:29:16 2005 Subject: [Biopython-dev] [Bug 1762] Bio.GenBank.FeatureParser dislikes valid accessions and locus lines Message-ID: <200503141427.j2EERuEH024230@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1762 ------- Additional Comments From jtk@cmp.uea.ac.uk 2005-03-14 09:27 ------- Created an attachment (id=201) --> (http://bugzilla.open-bio.org/attachment.cgi?id=201&action=view) patch to fix the two issues mentioned in the bug report The patch addresses the locus line problem by making the parts that are missing in seqret generated files optional in the regexp, and the accession issue by allowing the "-" character in accession numbers. The patch only modifies the Bio/expressions/genbank.py file. Changes are marked by comments containing "JTK" The patch allows me to work with the files in question and does not introduce new problems or regression test failures. I haven't checked whether missing division / length / DNA/RNA/protein / circular/linear information results in appropriate defaults in the objects created by parsing. As long as the corresponding members are not used, there should not be any problem. Regarding the accession, it seems to me that a proper representation of things like "AE000111-AE000510" might even necessitate a more differentiated approach to representing accessions (introducing something like ranges), but again, as long as the accessions are not used for further computation, there should not be a problem. ------- 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 Mar 14 09:28:12 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Mar 14 09:29:19 2005 Subject: [Biopython-dev] [Bug 1762] Bio.GenBank.FeatureParser dislikes valid accessions and locus lines Message-ID: <200503141428.j2EESClL024240@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1762 ------- Additional Comments From jtk@cmp.uea.ac.uk 2005-03-14 09:28 ------- Created an attachment (id=202) --> (http://bugzilla.open-bio.org/attachment.cgi?id=202&action=view) patch to fix the two issues mentioned in the bug report The patch addresses the locus line problem by making the parts that are missing in seqret generated files optional in the regexp, and the accession issue by allowing the "-" character in accession numbers. The patch only modifies the Bio/expressions/genbank.py file. Changes are marked by comments containing "JTK" The patch allows me to work with the files in question and does not introduce new problems or regression test failures. I haven't checked whether missing division / length / DNA/RNA/protein / circular/linear information results in appropriate defaults in the objects created by parsing. As long as the corresponding members are not used, there should not be any problem. Regarding the accession, it seems to me that a proper representation of things like "AE000111-AE000510" might even necessitate a more differentiated approach to representing accessions (introducing something like ranges), but again, as long as the accessions are not used for further computation, there should not be a problem. ------- 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 Mar 14 09:18:00 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Mar 14 09:29:20 2005 Subject: [Biopython-dev] [Bug 1762] New: Bio.GenBank.FeatureParser dislikes valid accessions and locus lines Message-ID: <200503141418.j2EEI0LN024112@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1762 Summary: Bio.GenBank.FeatureParser dislikes valid accessions and locus lines Product: Biopython Version: Not Applicable Platform: PC URL: n/a OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: jtk@cmp.uea.ac.uk Parsing a file with the locus line LOCUS U00096 without the further information, as in LOCUS U00096 4639675 bp DNA circular BCT leads to an exception. EMBOSS seqret (and probably other EMBOSS programs) don't write the additional stuff, so allowing such "truncated" locus lines would be convenient. Likewise, the line ACCESSION U00096 AE000111-AE000510 also results in an exception because the parser doesn't accept the "-". ------- 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 Mar 14 09:35:14 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Mar 14 10:31:06 2005 Subject: [Biopython-dev] [Bug 1762] Bio.GenBank.FeatureParser dislikes valid accessions and locus lines Message-ID: <200503141435.j2EEZEd6024445@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1762 jtk@cmp.uea.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #201|patch to fix the two issues |duplicate, please remove description|mentioned in the bug report | Attachment #201 is|0 |1 obsolete| | ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Mon Mar 14 22:03:12 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Mon Mar 14 21:57:41 2005 Subject: [Biopython-dev] cvs access problems Message-ID: <42365070.2050003@ims.u-tokyo.ac.jp> Hi everybody, I was planning to go through some biopython patches but I've been unable to checkout biopython from cvs. I'm getting the following error: [mdehoon@portal ~]$ cvs -d :ext:mdehoon@pub.open-bio.org:/home/repository/biopython checkout biopython pub.open-bio.org: Connection refused cvs [checkout aborted]: end of file from server (consult above messages if any) Is anybody else getting this error or is it just me? --Michiel. From hoffman at ebi.ac.uk Tue Mar 15 03:03:38 2005 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Tue Mar 15 02:58:08 2005 Subject: [Biopython-dev] cvs access problems In-Reply-To: <42365070.2050003@ims.u-tokyo.ac.jp> References: <42365070.2050003@ims.u-tokyo.ac.jp> Message-ID: On Tue, 15 Mar 2005, Michiel Jan Laurens de Hoon wrote: > [mdehoon@portal ~]$ cvs -d > :ext:mdehoon@pub.open-bio.org:/home/repository/biopython checkout biopython > pub.open-bio.org: Connection refused > cvs [checkout aborted]: end of file from server (consult above messages if > any) > > Is anybody else getting this error or is it just me? Worksforme. hoffman@damiana ~/src/biopython $ cu P Bio/PDB/PDBIO.py hoffman@damiana ~/src/biopython $ less CVS/Root :ext:grouse@pub.open-bio.org:/home/repository/biopython -- Michael Hoffman European Bioinformatics Institute From bugzilla-daemon at portal.open-bio.org Tue Mar 15 12:42:42 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 15 13:29:10 2005 Subject: [Biopython-dev] [Bug 1763] Bio.Fasta.RecordParser chokes on empty records Message-ID: <200503151742.j2FHggOx010826@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1763 ------- Additional Comments From ybastide@irisa.fr 2005-03-15 12:42 ------- Created an attachment (id=203) --> (http://bugzilla.open-bio.org/attachment.cgi?id=203&action=view) Patch: Bio.Fasta.RecordParser vs. empty sequences ------- 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 Mar 15 12:40:26 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Mar 15 13:29:12 2005 Subject: [Biopython-dev] [Bug 1763] New: Bio.Fasta.RecordParser chokes on empty records Message-ID: <200503151740.j2FHeQAW010800@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1763 Summary: Bio.Fasta.RecordParser chokes on empty records Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: ybastide@irisa.fr Hi, As per the summary: a Fasta record without a sequence breaks the parser. Patch follows. Regards, yves ------- 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 Mar 16 21:14:37 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Mar 16 21:29:14 2005 Subject: [Biopython-dev] [Bug 1756] Tutorial patch Message-ID: <200503170214.j2H2Eakd029655@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1756 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-16 21:14 ------- Patch accepted, thanks. ------- 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 Mar 16 22:22:23 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Mar 16 22:29:18 2005 Subject: [Biopython-dev] [Bug 1757] Doc/images and Doc/Tutorial.pdf not included in the tarball Message-ID: <200503170322.j2H3MNv5030111@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1757 ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-16 22:22 ------- Given that the Tutorial.pdf can be downloaded from the Biopython website, is there still a need to compile it? Since the tarball is rather large already, it may be better to leave it out. What do the other developers think? --Michiel. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Thu Mar 17 00:17:44 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Thu Mar 17 00:14:41 2005 Subject: [Biopython-dev] scanner in Bio.Fasta Message-ID: <423912F8.5000301@ims.u-tokyo.ac.jp> There used to be a _Scanner class in Bio.Fasta. It was removed about a year ago when Bio.Fasta started using Martel. As a result, the fasta_consumer.py example in Doc/examples no longer works (this example is also in the tutorial); see also bug 1741. The goal of the example can be achieved also by loading the Fasta file as a dictionary, so there is an easy way to fix this. However, in the section "General Parser Design" in the documentation, it says """ All of the parsers have two components: 1. Scanner - The part of the parser that actually does the work or going through the file and extracting useful information. This useful information is converted into Events. 2. Consumer - The consumer does the job of processing the useful information and spitting it out in a format that the programmer can use. The consumer does this by receiving the events created by the scanner. """ So is this no longer true? Or was the Fasta _Scanner removed by mistake? Anybody knows what's going on here? --Michiel. From bugzilla-daemon at portal.open-bio.org Thu Mar 17 04:06:50 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Mar 17 04:31:08 2005 Subject: [Biopython-dev] [Bug 1757] Doc/images and Doc/Tutorial.pdf not included in the tarball Message-ID: <200503170906.j2H96oqG001410@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1757 ------- Additional Comments From ybastide@irisa.fr 2005-03-17 04:06 ------- Good point. What do others projects do? You're right, the pdf doesn't need to be in the .tar.gz. However, it seems to me that the tutorial is the primary documentation for many users. (Anyway, the main bug is in the missing images) yves ------- 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 Mar 17 22:33:18 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Mar 17 23:29:27 2005 Subject: [Biopython-dev] [Bug 1757] Doc/images and Doc/Tutorial.pdf not included in the tarball Message-ID: <200503180333.j2I3XIot026910@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1757 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-17 22:33 ------- Python includes the source for the documentation in its distribution. So I think we should do the same. I have added the doc/images/*.png to the list of files to be included in the tarball. ------- 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 Mar 17 23:53:45 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Mar 18 00:29:46 2005 Subject: [Biopython-dev] [Bug 1740] change in GenBank.NCBIDictionary() Message-ID: <200503180453.j2I4rjo6027554@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1740 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-17 23:53 ------- This was fixed in CVS as part of patch 1756. See tutorial.tex version 1.40. ------- 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 Mar 17 23:58:46 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Mar 18 00:29:49 2005 Subject: [Biopython-dev] [Bug 1761] BLAST not returning final results Message-ID: <200503180458.j2I4wkhH027582@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1761 ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-17 23:58 ------- Which protein sequence were you using for protein_seq? Just so I can replicate this bug. ------- 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 Sun Mar 20 04:11:53 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sun Mar 20 04:30:24 2005 Subject: [Biopython-dev] [Bug 1764] New: Bio.Application _Option class Message-ID: <200503200911.j2K9BqvX031057@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1764 Summary: Bio.Application _Option class Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: minor Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: gvg500@york.ac.uk CC: gvg500@york.ac.uk When building a commandline from the sub-classed abstractcommandline: if more than one advanced options are parsed and they do not have a value, they appear on the commandline with no space separating them. | V hmmbuild -F --amino--archpri=0.5 --binary A | if they have an associated value then a space is inserted correctly I have modified __str__ in the _Options class in the following manner: def __str__(self): """Return the value of this option for the commandline. """ # first deal with long options if self.names[0].find("--") >= 0: output = "%s" % self.names[0] if self.value is not None: output += "=%s " % self.value else: <<<< output += " " <<<< ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Mon Mar 21 04:51:40 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Mon Mar 21 04:46:13 2005 Subject: [Biopython-dev] Bouncing non-member posts Message-ID: <423E992C.7050104@ims.u-tokyo.ac.jp> The biopython-dev mailing list has been receiving more and more spam messages from non-members. These messages are held for approval by the list managers, which means that they have to go in once a day or so and delete the spam messages. Since there are so many of these, I'm proposing to bounce all non-member messages by setting the generic_nonmember_action option to "Reject" instead of "Hold". Any objections? --Michiel. From bugzilla-daemon at portal.open-bio.org Mon Mar 21 04:35:39 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Mar 21 05:33:55 2005 Subject: [Biopython-dev] [Bug 1764] Bio.Application _Option class Message-ID: <200503210935.j2L9ZdbF018185@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1764 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-21 04:35 ------- Fixed in CVS, thanks. Would you be willing to write some documentation for Bio.Application? I don't think we have any documentation for this module. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From dalke at dalkescientific.com Mon Mar 21 14:25:29 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Mon Mar 21 14:20:36 2005 Subject: [Biopython-dev] Bouncing non-member posts In-Reply-To: <423E992C.7050104@ims.u-tokyo.ac.jp> References: <423E992C.7050104@ims.u-tokyo.ac.jp> Message-ID: <21f83cc3f4a38a65124fb6d851ef3bef@dalkescientific.com> Michiel: > I'm proposing to bounce all non-member messages by setting the > generic_nonmember_action option to "Reject" instead of "Hold". Any > objections? Not from me. Andrew dalke@dalkescientific.com From bugzilla-daemon at portal.open-bio.org Fri Mar 25 00:49:25 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Mar 25 01:29:57 2005 Subject: [Biopython-dev] [Bug 1763] Bio.Fasta.RecordParser chokes on empty records Message-ID: <200503250549.j2P5nPHo025378@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1763 ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-25 00:49 ------- Can you give a code example where Bio.Fasta.RecordParser chokes? (I don't use Bio.Fasta myself). ------- 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 Mar 25 03:21:16 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Mar 25 03:30:33 2005 Subject: [Biopython-dev] [Bug 1763] Bio.Fasta.RecordParser chokes on empty records Message-ID: <200503250821.j2P8LGep027813@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1763 ------- Additional Comments From ybastide@irisa.fr 2005-03-25 03:21 ------- A simple testcase: /tmp$ cat a.fasta >seq /tmp$ python Python 2.3.5 (#2, Feb 9 2005, 00:38:15) [GCC 3.3.5 (Debian 1:3.3.5-8)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from Bio import Fasta >>> f_iterator = Fasta.Iterator(file("a.fasta")) >>> f_iterator.next() Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.3/site-packages/Bio/Fasta/__init__.py", line 79, in next rec = parser.convert_lax(result) File "/usr/lib/python2.3/site-packages/Bio/Fasta/__init__.py", line 116, in convert_lax rec.sequence = "".join(result['bioformat:sequence']) KeyError: 'bioformat:sequence' >>> yves ------- 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 Sat Mar 26 02:17:00 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 26 02:30:25 2005 Subject: [Biopython-dev] [Bug 1763] Bio.Fasta.RecordParser chokes on empty records Message-ID: <200503260717.j2Q7GxjO011883@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1763 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-26 02:16 ------- Accepted in CVS, thanks. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Sat Mar 26 23:58:33 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 26 23:47:55 2005 Subject: [Biopython-dev] Re: forward for an error message In-Reply-To: <000601c53249$45430a30$14b2a8c0@Toedi> References: <000601c53249$45430a30$14b2a8c0@Toedi> Message-ID: <42463D79.4050203@ims.u-tokyo.ac.jp> How did you run into this bug? Recently, I changed the option of non-members messages from "Hold" to "Reject", but in either case you shouldn't get an error message. --Michiel. Axel Rasche wrote: > I'm sorry, It seems that I found a bug... > > ------------------------------------------------------------------------ > > > Bug in Mailman version 2.1.5 > > > We're sorry, we hit a bug! > > If you would like to help us identify the problem, please email a copy > of this page to the webmaster for this site with a description of what > happened. Thanks! > > > Traceback: > > Traceback (most recent call last): > File "/home/mailman/scripts/driver", line 87, in run_main > main() > File "/home/mailman/Mailman/Cgi/confirm.py", line 116, in main > subscription_confirm(mlist, doc, cookie, cgidata) > File "/home/mailman/Mailman/Cgi/confirm.py", line 345, in subscription_confirm > userdesc = mlist.pend_confirm(cookie, expunge=False)[1] > TypeError: unsubscriptable object > > > > ------------------------------------------------------------------------ > > > Python information: > > Variable Value > sys.version 2.2.2 (#1, Feb 24 2003, 19:13:11) [GCC 3.2.2 20030222 (Red > Hat Linux 3.2.2-4)] > sys.executable /usr/bin/python > sys.prefix /usr > sys.exec_prefix /usr > sys.path /usr > sys.platform linux2 > > ------------------------------------------------------------------------ > > > Environment variables: > > Variable Value > PATH_INFO /biopython-announce > CONTENT_LENGTH 123 > CONTENT_TYPE application/x-www-form-urlencoded > HTTP_REFERER > http://biopython.org/mailman/confirm/biopython-announce/6e78f840c071ac8dc254693baf975831b7beee97 > > SCRIPT_FILENAME /home/mailman/cgi-bin/confirm > PYTHONPATH /home/mailman > SERVER_SOFTWARE Apache/2.0.40 (Red Hat Linux) > SERVER_ADMIN root-l@open-bio.org > SCRIPT_NAME /mailman/confirm > SCRIPT_URI http://biopython.org/mailman/confirm/biopython-announce > SERVER_SIGNATURE > Apache/2.0.40 Server at biopython.org Port 80 > > REQUEST_METHOD POST > HTTP_HOST biopython.org > SCRIPT_URL /mailman/confirm/biopython-announce > SERVER_PROTOCOL HTTP/1.1 > QUERY_STRING > HTTP_CACHE_CONTROL no-cache > REQUEST_URI /mailman/confirm/biopython-announce > HTTP_ACCEPT image/gif, image/x-xbitmap, image/jpeg, image/pjpeg, > application/vnd.ms-powerpoint, application/vnd.ms-excel, > application/msword, application/x-shockwave-flash, */* > PATH_TRANSLATED > /home/websites/biopython.org/biopython.cgi/biopython-announce > HTTP_USER_AGENT Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1; > NetCaptor 7.2.2) > HTTP_CONNECTION Keep-Alive > SERVER_NAME biopython.org > REMOTE_ADDR 217.231.146.148 > REMOTE_PORT 62311 > HTTP_ACCEPT_LANGUAGE de-ch > UNIQUE_ID oNIXO0H2u7AAAFX4XrkAAAAC > SERVER_PORT 80 > GATEWAY_INTERFACE CGI/1.1 > HTTP_ACCEPT_ENCODING gzip, deflate > SERVER_ADDR 65.246.187.176 > DOCUMENT_ROOT /home/websites/biopython.org/ > -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From bugzilla-daemon at portal.open-bio.org Mon Mar 28 03:49:45 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Mar 28 04:30:07 2005 Subject: [Biopython-dev] [Bug 1746] Again with the "Unexpected end of stream" when parsing Blast results Message-ID: <200503280849.j2S8nigq017153@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1746 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-28 03:49 ------- I fixed www_blast.py in CVS to use NCBIWWW.qblast instead of NCBIWWW.blast, which has been deprecated. With this fix, the script runs correctly. Thanks for reporting this bug. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Mon Mar 28 06:37:02 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Mon Mar 28 06:26:39 2005 Subject: [Biopython-dev] NCBIWWW.qblast Message-ID: <4247EC5E.3010007@ims.u-tokyo.ac.jp> Hi everybody, In Blast.NCBIWWW, I noticed that qblast does not have all the options that blast (which is deprecated) has. Is that simply because qblast isn't finished yet, or is there some deeper reason that the options are different? I'm trying to solve bug # 1761, which (I think) needs the entrez_query argument, which is in blast but not in qblast. I don't use Blast.NCBIWWW myself, so I thought I'd ask before changes things around. --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From jhackney at stanford.edu Wed Mar 30 13:20:50 2005 From: jhackney at stanford.edu (Jason A. Hackney) Date: Wed Mar 30 13:16:32 2005 Subject: [Biopython-dev] MEME parser announcement Message-ID: <11823506a07ed0e612f97cddd9f5cc7f@stanford.edu> Hi All, I've written and submitted a basic parser for both MEME and MAST formats. The internal documentation is bare at the moment, though only a couple of internal functions do anything out of the ordinary. For most uses, the examples in the documentation should suffice. Both MEME and MAST parsers only work on text output, though HTML output parsing is in the long-term plans. The parsers are available in the current biopython CVS. Yours, Jason Jason A. Hackney Postdoctoral Scholar Department of Microbiology and Immunology Stanford University From bugzilla-daemon at portal.open-bio.org Wed Mar 30 22:37:07 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Mar 30 23:11:50 2005 Subject: [Biopython-dev] [Bug 1761] BLAST not returning final results Message-ID: <200503310337.j2V3b7CB009095@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1761 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2005-03-30 22:37 ------- I have added the entrez_query to NCBIWWW.qblast. The code fragment now works using qblast instead of blast. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.