From Peter.Bienstman at rug.ac.be Thu Jan 2 07:32:52 2003 From: Peter.Bienstman at rug.ac.be (Peter Bienstman) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Genbank has_header Message-ID: <200301021332.52925.Peter.Bienstman@rug.ac.be> Hi all, I'm working on improving the GenBank parser, and one of the things that's fairly easy to do is to ignore the 'has_header' argument and automatically check if a header is present. Jeff suggested that I asked around here to see if anyone else has another use for this flag that we didn't anticipate. Otherwise, I'll go ahead and implement this simplification. Cheers, Peter From gec at threeplusone.com Tue Jan 7 14:02:54 2003 From: gec at threeplusone.com (Gavin Crooks) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] biopython and fink Message-ID: I have submitted biopython 1.10 to fink, the unix package manager for Mac OS X. You can track the excitement at http://sourceforge.net/tracker/ index.php?func=detail&aid=663898&group_id=17203&atid=414256 Gavin -- Gavin E. Crooks Postdoctoral Fellow tel: (510) 642-9614 461 Koshland Hall fax: (413) 280-7813 University of California http://threeplusone.com/ Berkeley, CA 94720-3102, USA gec@compbio.berkeley.edu From biopython-bugs at bioperl.org Thu Jan 9 19:50:10 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/114 Message-ID: <200301100050.h0A0oASQ019775@pw600a.bioperl.org> JitterBug notification new message incoming/114 Message summary for PR#114 From: s.saubern@chem.csiro.au Subject: KDTree missing _KDTreec? Date: Thu, 9 Jan 2003 19:50:08 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From s.saubern@chem.csiro.au Thu Jan 9 19:50:09 2003 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0A0o8SQ019765 for ; Thu, 9 Jan 2003 19:50:09 -0500 Date: Thu, 9 Jan 2003 19:50:08 -0500 Message-Id: <200301100050.h0A0o8SQ019765@pw600a.bioperl.org> From: s.saubern@chem.csiro.au To: biopython-bugs@bioperl.org Subject: KDTree missing _KDTreec? X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Full_Name: Simon Saubern Module: KDTree Version: 1.10 OS: Win2K, Solaris 5.8 Submission from: cache.vic.csiro.au (138.194.15.102) Hi. I wanted to try out your KDTree module, but the file _KDTree.py tries to import _KDtreec (line 2). This is not in the Win distribution, nor does it show up when I build biopython from the CVS under Solaris. Am I missing something obvious? Thanks, Simon From biopython-bugs at bioperl.org Fri Jan 10 16:47:11 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/115 Message-ID: <200301102147.h0ALlBSQ028553@pw600a.bioperl.org> JitterBug notification new message incoming/115 Message summary for PR#115 From: Thomas Hamelryck Subject: Re: [Biopython-dev] Notification: incoming/114 Date: Fri, 10 Jan 2003 22:54:09 0100 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From thamelry@vub.ac.be Fri Jan 10 16:47:10 2003 Received: from riker.skynet.be (riker.skynet.be [195.238.3.89]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0ALl8SQ028546 for ; Fri, 10 Jan 2003 16:47:09 -0500 Received: from there (165.137-200-80.adsl.skynet.be [80.200.137.165]) by riker.skynet.be (8.11.6/8.11.6/Skynet-OUT-2.20) with SMTP id h0ALlnI23093 for ; Fri, 10 Jan 2003 22:47:49 +0100 (MET) (envelope-from ) Message-Id: <200301102147.h0ALlnI23093@riker.skynet.be> Content-Type: text/plain; charset="iso-8859-1" From: Thomas Hamelryck Organization: Vrije Universiteit Brussel To: biopython-bugs@bioperl.org Subject: Re: [Biopython-dev] Notification: incoming/114 Date: Fri, 10 Jan 2003 22:54:09 +0100 X-Mailer: KMail [version 1.3.2] References: <200301100050.h0A0oASQ019775@pw600a.bioperl.org> In-Reply-To: <200301100050.h0A0oASQ019775@pw600a.bioperl.org> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) > Hi. I wanted to try out your KDTree module, but the file _KDTree.py tries > to import _KDtreec (line 2). > > This is not in the Win distribution, nor does it show up when I build > biopython from the CVS under Solaris. > > Am I missing something obvious? I don't know about the Win distribution. Most likely the KDTree module simply wasn't included. Anyone? Under Solaris, there is some kind of problem with building the module, most likely due to some bug in Distutils (as far as I could see it's a problem with the compilation flags during the creation of the shared library). So the module isn't built, and you get an import error. Unfortunately, I do not have access to Solaris, so I cannot look into it. Could you send me the compilation output? Mmmrrh, I suddenly realize that the problem is quite likely that the C++ module is being compled with gcc and not g++. gcc assumes preprocessed (.i) files are C and assumes C style linking. g++ assumes preprocessed (.i) files are C++ and assumes C++ style linking. -Thomas --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From thamelry at vub.ac.be Mon Jan 13 07:36:39 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Manual Message-ID: <200301131150.MAA18663@mach.vub.ac.be> Hi guys, It's high time to update the manual. I've added a lot of stuff about the PDB code, but apparantly that is still not present in the downloadable document and I'm getting complaints about that :-) Shall I make new PS and PDF versions of the manual from the CVS version? Cheers, -Thomas --- Thomas Hamelryck COMO-ULTR Vrije Universiteit Brussel (VUB) Belgium http://homepages.vub.ac.be/~thamelry From biopython-bugs at bioperl.org Tue Jan 14 10:37:26 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/116 Message-ID: <200301141537.h0EFbQSQ002367@pw600a.bioperl.org> JitterBug notification new message incoming/116 Message summary for PR#116 From: Andreas Kuntzagk Subject: Re: [Biopython-dev] Notification: incoming/109 Date: 14 Jan 2003 16:38:28 0100 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From andreas.kuntzagk@mdc-berlin.de Tue Jan 14 10:37:25 2003 Received: from server1.bbb2.mdc-berlin.de (root@server1.bbb2.mdc-berlin.de [141.80.34.10]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0EFbNSQ002360 for ; Tue, 14 Jan 2003 10:37:24 -0500 Received: from sulawesi.bioinf.mdc-berlin.de (sulawesi.bioinf.mdc-berlin.de [141.80.80.60]) by server1.bbb2.mdc-berlin.de (8.11.4/8.11.4) with ESMTP id h0EFcAt22512; Tue, 14 Jan 2003 16:38:11 +0100 (MET) Subject: Re: [Biopython-dev] Notification: incoming/109 From: Andreas Kuntzagk To: biopython-bugs@bioperl.org Cc: BioPython Mailing List In-Reply-To: <200212121344.gBCDiYSQ009955@pw600a.bioperl.org> References: <200212121344.gBCDiYSQ009955@pw600a.bioperl.org> Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.8 Date: 14 Jan 2003 16:38:28 +0100 Message-Id: <1042558708.28387.16.camel@sulawesi> Mime-Version: 1.0 X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) > > >From andreas.kuntzagk@mdc-berlin.de Tue Dec 10 12:31:46 2002 > [...] > > > > While parsing the recent GenBank-Release, I got followin error: > > > > > > >>> from Bio import GenBank > > >>> f=file("gbest1.seq") > > > > >>> GenBank.Iterator(f,has_header=1) > > Traceback (most recent call last): > > File "", line 1, in ? > > File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 171, in > > __init__ > > self._reader = RecordReader.StartsWith(handle, "LOCUS") > > File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 133, in > > __init__ > > self.tagtable) > > File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 92, in > > _find_begin_positions > > raise ReaderError("invalid format starting with %s" % repr(text[:50])) > > Martel.RecordReader.ReaderError: invalid format starting with 'DEFINITION > > zd84h07.s1 Soares_fetal_heart_NbHH19W ' > > > > Problems seems, that in this file there is only one empty line after the > > "...reported sequences" instead of the expected two lines. > > > > I would suggest the following patch. This reads all text from the handle > into a string (which can consume quit some memory :-( ) and skips to the > first LOCUS. All remaining text is the turned into a StrinIO (would > cStringIO better?) [patch deleted] Answering myself again. Here is a better patch (against the biopython-1.10). Using cStringIO only when the handle doesn't have a seek, I read to the first "LOCUS" and then 'unread' the last line. This gives also more flexibility for the structure of the header. Is there anybody else there working with full GenBank-Releases and can confirm this patch? ---patch--- # diff GenBank/__init__.py ~/biopython-1.10/Bio/GenBank/ 162,166d161 < try: < handle.__getattribute__("seek") #Need seek to place file-position back after reading "LOCUS" < except: < import cStringIO #if there is no seek, we read all into a string and use a StringIO < handle=cStringIO.StringIO(handle.read()) 169,170c164 < if cur_line.startswith("LOCUS") or cur_line=="": < handle.seek(-len(cur_line),1) --- > if cur_line.find("reported sequences") >= 0: 171a166,169 > > # read off two more lines and we are ready to go > handle.readline() > handle.readline() From Y.Benita at pharm.uu.nl Fri Jan 17 02:33:30 2003 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Compiling for MacPython Message-ID: Hi All, I have been trying to compile version 1.10 for MacPython. While most extensions compiled with no problem, I still can't compile the trie extension. The output of codewarrior is below, any ideas? Error : illegal string constant triemodule.c line 606 " Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 608 lookup of a string in a dictionary, where M is the length of the\n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 609 string. It also supports approximate matches.\n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 610 \n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 611 Functions:\n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : ';' expected triemodule.c line 611 Functions:\n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 613 save Save a trie to a handle.\n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 614 load Load a trie from a handle.\n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 615 \n\ Project: trie.mcp, Target: trie, Source File: triemodule.c Error : illegal string constant triemodule.c line 616 "; Project: trie.mcp, Target: trie, Source File: triemodule.c Error : declaration syntax error triemodule.c line 616 void Project: trie.mcp, Target: trie, Source File: triemodule.c Error : illegal implicit conversion from 'int' to 'unsigned char *' trie.c line 95 if(!(new_suffix = strdup(key))) Project: trie.mcp, Target: trie, Source File: trie.c Error : illegal implicit conversion from 'int' to 'unsigned char *' trie.c line 156 if(!(new_suffix2 = strdup(suffix+chars_shared))) Project: trie.mcp, Target: trie, Source File: trie.c Error : illegal implicit conversion from 'int' to 'unsigned char *' trie.c line 700 if(!(transition->suffix = strdup(KEY))) Project: trie.mcp, Target: trie, Source File: trie.c From adalke at mindspring.com Fri Jan 17 02:44:03 2003 From: adalke at mindspring.com (Andrew Dalke) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Compiling for MacPython In-Reply-To: References: Message-ID: <20030117004403.490b7646.adalke@mindspring.com> Yair Benita: > Hi All, > I have been trying to compile version 1.10 for MacPython. While most > extensions compiled with no problem, I still can't compile the trie > extension. The output of codewarrior is below, any ideas? > > Error : illegal string constant > triemodule.c line 606 " > Project: trie.mcp, Target: trie, Source File: triemodule.c Starting with line 605 it looks like static char trie__doc__[] = " This module implements a trie data structure. This allows an O(M)\n\ Put a backslash character - \ - at the end of line 605, so it looks like static char trie__doc__[] = "\ This module implements a trie data structure. This allows an O(M)\n\ What's there now isn't valid C, I think. Andrew dalke@dalkescientific.com From piet at clondiag.com Fri Jan 17 12:47:14 2003 From: piet at clondiag.com (Peter Slickers) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] function Bio.utils.count_monomers() is broken Message-ID: <3E2841A2.2090600@clondiag.com> Here is an example code to demonstrate an error caused by function 'Bio.utils.count_monomers()': #!/usr/bin/python import string def my_count_monomers(seq): """ Fixed version of 'Bio.utils.count_monomers()' """ dict = {} ##s = buffer(seq.data) # works for strings and array.arrays s = seq.data for c in seq.alphabet.letters: dict[c] = string.count(s, c) return dict import Bio.Seq import Bio.utils import Bio.Alphabet.IUPAC seqObj = Bio.Seq.Seq("ACGCAGATAGCAGAT", \ Bio.Alphabet.IUPAC.unambiguous_dna ) print print my_count_monomers(seqObj) print print Bio.utils.count_monomers(seqObj) ------------------------------------------------------------------- Here is my output from this script: {'A': 6, 'C': 3, 'T': 2, 'G': 4} Traceback (most recent call last): File "count_monomers.py", line 31, in ? print Bio.utils.count_monomers(seqObj) File "/usr/local/lib/python2.2/site-packages/Bio/utils.py", line 63, in count_monomers dict[c] = string.count(s, c) File "/usr/local/lib/python2.2/string.py", line 161, in count return s.count(*args) AttributeError: 'buffer' object has no attribute 'count' ------------------------------------------------------------------- The error is caused by the usage of the buffer() function within 'Bio/utils.py'. Just removing the buffer() function fixes the problem. This is demonstrated by my modified version of the function, which is defined at the top of the script. (I have no idee why the buffer function is used in count_monomers().) Just in case, I have python 2.2.2 and biopython 1.10 installed. -- Peter ------------------------------------------------------------------- Peter Slickers piet@clondiag.com Clondiag Chip Technologies http://www.clondiag.com/ L?bstedter Str. 105 07749 Jena Germany Fon: 03641/5947-65 Fax: 03641/5947-20 ------------------------------------------------------------------- From jchang at smi.stanford.edu Fri Jan 17 17:35:12 2003 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Compiling for MacPython In-Reply-To: <20030117004403.490b7646.adalke@mindspring.com> References: <20030117004403.490b7646.adalke@mindspring.com> Message-ID: <20030117223512.GE25827@springfield.stanford.edu> Oops, that is an error that didn't cause my compiler to complain. Andrew's fix is correct. I've fixed the version in CVS. Jeff On Fri, Jan 17, 2003 at 12:44:03AM -0700, Andrew Dalke wrote: > Yair Benita: > > Hi All, > > I have been trying to compile version 1.10 for MacPython. While most > > extensions compiled with no problem, I still can't compile the trie > > extension. The output of codewarrior is below, any ideas? > > > > Error : illegal string constant > > triemodule.c line 606 " > > Project: trie.mcp, Target: trie, Source File: triemodule.c > > Starting with line 605 it looks like > > > static char trie__doc__[] = > " > This module implements a trie data structure. This allows an O(M)\n\ > > > Put a backslash character - \ - at the end of line 605, so it looks > like > > static char trie__doc__[] = > "\ > This module implements a trie data structure. This allows an O(M)\n\ > > What's there now isn't valid C, I think. > > Andrew > dalke@dalkescientific.com > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From katel at worldpath.net Fri Jan 17 21:46:00 2003 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] cvs finally works Message-ID: <000701c2be9b$bdc667a0$39c07f3f@pcklindner> Chris said I may have a path problem so I finally loaded LL_block with a fully qualified path. Cayte From biopython-bugs at bioperl.org Fri Jan 17 20:17:54 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/117 Message-ID: <200301180117.h0I1HsSQ010171@pw600a.bioperl.org> JitterBug notification new message incoming/117 Message summary for PR#117 From: Jeffrey Chang Subject: Re: [BioPython] Re: [Biopython-dev] Notification: incoming/109 Date: Fri, 17 Jan 2003 17:17:43 -0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From jchang@springfield.stanford.edu Fri Jan 17 20:17:54 2003 Received: from springfield.stanford.edu (springfield.Stanford.EDU [128.12.147.41]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0I1HqSQ010164 for ; Fri, 17 Jan 2003 20:17:53 -0500 Received: (from jchang@localhost) by springfield.stanford.edu (8.11.6/8.11.6) id h0I1Hh426816; Fri, 17 Jan 2003 17:17:43 -0800 (PST) (envelope-from jchang) Date: Fri, 17 Jan 2003 17:17:43 -0800 From: Jeffrey Chang To: Andreas Kuntzagk Cc: biopython-bugs@bioperl.org, BioPython Mailing List Subject: Re: [BioPython] Re: [Biopython-dev] Notification: incoming/109 Message-ID: <20030118011743.GK25827@springfield.stanford.edu> Mail-Followup-To: Andreas Kuntzagk , biopython-bugs@bioperl.org, BioPython Mailing List References: <200212121344.gBCDiYSQ009955@pw600a.bioperl.org> <1042558708.28387.16.camel@sulawesi> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <1042558708.28387.16.camel@sulawesi> User-Agent: Mutt/1.4i X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Hi Andreas, > Answering myself again. Here is a better patch (against the > biopython-1.10). Using cStringIO only when the handle doesn't have a > seek, I read to the first "LOCUS" and then 'unread' the last line. > This gives also more flexibility for the structure of the header. > > Is there anybody else there working with full GenBank-Releases and can > confirm this patch? Peter Bienstman has been working on validating the parser against all of GenBank. He has submitted a patch that will correctly read the blank lines in the header file by using an UndoHandle to suck up all the lines before the first LOCUS. It is available in the most recent CVS. Jeff From Y.Benita at pharm.uu.nl Sat Jan 18 07:51:12 2003 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Compiling for MacPython In-Reply-To: <20030117223512.GE25827@springfield.stanford.edu> Message-ID: on 17/1/2003 23:35, Jeffrey Chang at jchang@smi.stanford.edu wrote: >> static char trie__doc__[] = >> " >> This module implements a trie data structure. This allows an O(M)\n\ >> >> >> Put a backslash character - \ - at the end of line 605, so it looks >> like >> >> static char trie__doc__[] = >> "\ OK, that is done and it works fine. My other problem is in the trie.c file: Error : illegal implicit conversion from 'int' to 'unsigned char *' trie.c line 95 if(!(new_suffix = strdup(key))) Error : illegal implicit conversion from 'int' to 'unsigned char *' trie.c line 156 if(!(new_suffix2 = strdup(suffix+chars_shared))) Error : illegal implicit conversion from 'int' to 'unsigned char *' trie.c line 700 if(!(transition->suffix = strdup(KEY))) Yair From biopython-bugs at bioperl.org Tue Jan 21 10:22:25 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/118 Message-ID: <200301211522.h0LFMPSQ015807@pw600a.bioperl.org> JitterBug notification new message incoming/118 Message summary for PR#118 From: kawagash@affrc.go.jp Subject: PRIVATE: KEGG Enzyme Parser doesn't work Date: Tue, 21 Jan 2003 10:22:22 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From kawagash@affrc.go.jp Tue Jan 21 10:22:23 2003 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0LFMMSQ015801 for ; Tue, 21 Jan 2003 10:22:23 -0500 Date: Tue, 21 Jan 2003 10:22:22 -0500 Message-Id: <200301211522.h0LFMMSQ015801@pw600a.bioperl.org> From: kawagash@affrc.go.jp To: biopython-bugs@bioperl.org Subject: PRIVATE: KEGG Enzyme Parser doesn't work X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Full_Name: Nobuyuki Kawagashira Module: KEGG.Enzyme.__init__.py Version: 1.5 OS: Solaris 8 64bit Submission from: cytosine.abr.affrc.go.jp (150.26.151.213) I tried parsing as following program: Bio/KEGG/Enzyme/__init__.py and Martel/Parser.py error occured. from Bio.KEGG import Enzyme def make_enzyme(phase, file): parser = Enzyme.Parser() handler = open(file) iterator = Enzyme.Iterator(handler, parser) while 1: e = iterator.next() if e is None: break print e break ############################################################################# make_enzyme(1,'/db/kegg/enzyme') From idoerg at burnham.org Fri Jan 24 14:04:05 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Blast table parser Message-ID: <3E318E25.6090704@burnham.org> Hi, Do we have a Blast table parser? I mean the output from running: blastpgp [lots of silly arguments] -m 9 version 2.2.5 has this kind of output. If not, I'll be happy to add one. Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo From jchang at smi.stanford.edu Fri Jan 24 14:14:09 2003 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Blast table parser In-Reply-To: <3E318E25.6090704@burnham.org> References: <3E318E25.6090704@burnham.org> Message-ID: <20030124191408.GB55833@springfield.stanford.edu> On Fri, Jan 24, 2003 at 11:04:05AM -0800, Iddo Friedberg wrote: > Do we have a Blast table parser? I mean the output from running: > > blastpgp [lots of silly arguments] -m 9 > > version 2.2.5 has this kind of output. Not in the Biopython distribution. It parses -m 6 (master-slave output), but not -m 9. Is this new? > If not, I'll be happy to add one. Have at it! :) Jeff From idoerg at burnham.org Mon Jan 27 12:43:45 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] PSI-BLAST parsing & processing code snippets, please? Message-ID: <3E356FD1.9080808@burnham.org> Hi all, If anyone has written any cool PSI-BLAST parsing/processing code and does not mind having them displayed in a talk, I would very much like to have it. The talk will be in the O'Reilly BioCon2003, and of course credit shall be given where credit is due. Best, I. -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo From idoerg at burnham.org Wed Jan 29 06:24:03 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Blast table parser References: <3E318E25.6090704@burnham.org> <20030124191408.GB55833@springfield.stanford.edu> <3E319581.8000802@burnham.org> <20030124194523.GC55833@springfield.stanford.edu> <3E319E02.7080606@burnham.org> <20030124224234.GB56787@springfield.stanford.edu> <3E31C3A3.8040302@burnham.org> <20030124230702.GC56787@springfield.stanford.edu> <3E31CAC3.8020000@burnham.org> <20030129063451.GH77175@springfield.stanford.edu> Message-ID: <3E37B9D3.6060909@burnham.org> Jeffrey Chang wrote: >>The blast table parser is pretty much ready, should it go in >>NCBIStandalone.py, or should I set up a different file for it under >>Bio/Blast? > > > What does it do? Does it parse things into a Bio/Blast/Record > structure, or something different? How much code is it? It parses a BLAST output table (formatted through "blastpgp -m 9"). Since this table does not contain a sequence alignments, and it does contain other stuff, I don't think that the Bio/Blast/Record object is suitable, so I created two new classes, BlastTableRec, which can have 0 or more BlastTableEntry(s) in it. Actually, I already commited it (sorry...) so you can have a look. Let me know how you would like me to modify it. If you think I can do this with the Bio/Blast/Record let me know, I will make an effort. There isn't a lot of code, about 100 lines. The file is ParseBlastTable.py Tangentially related: do we have a way of _easily_ taking an MSA from PSI-BLAST and putting in the multiple sequence alignment class? I. > > It should go into NCBIStandalone, unless there's a lot of code, or > it's structurally different from the rest of the code in there. > > Jeff > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo From jchang at SMI.Stanford.EDU Wed Jan 29 15:04:56 2003 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Blast table parser In-Reply-To: <3E37B9D3.6060909@burnham.org> References: <20030124191408.GB55833@springfield.stanford.edu> <3E319581.8000802@burnham.org> <20030124194523.GC55833@springfield.stanford.edu> <3E319E02.7080606@burnham.org> <20030124224234.GB56787@springfield.stanford.edu> <3E31C3A3.8040302@burnham.org> <20030124230702.GC56787@springfield.stanford.edu> <3E31CAC3.8020000@burnham.org> <20030129063451.GH77175@springfield.stanford.edu> <3E37B9D3.6060909@burnham.org> Message-ID: <20030129200456.GD80229@springfield.stanford.edu> On Wed, Jan 29, 2003 at 03:24:03AM -0800, Iddo Friedberg wrote: [Iddo announces new code] > It parses a BLAST output table (formatted through "blastpgp -m 9"). > Since this table does not contain a sequence alignments, and it does > contain other stuff, I don't think that the Bio/Blast/Record object is > suitable, so I created two new classes, BlastTableRec, which can have 0 > or more BlastTableEntry(s) in it. Actually, I already commited it > (sorry...) so you can have a look. Let me know how you would like me to > modify it. If you think I can do this with the Bio/Blast/Record let me > know, I will make an effort. Great! Probably not necessary to make it work with Bio/Blast/Record. Someone can do it later if they really need it. Jeff From Peter.Bienstman at rug.ac.be Thu Jan 30 08:34:23 2003 From: Peter.Bienstman at rug.ac.be (Peter Bienstman) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Genbank bug fixes Message-ID: <200301301334.23205.Peter.Bienstman@rug.ac.be> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, Just a quick note to let you know that the Genbank code has been updated to parse the entire Genbank database correctly now. Patches are already commited to CVS. Enjoy, Peter -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQE+OSnf4dgPAIjyquoRAiKoAKDJyuMJMcha0U0xj016Hhd4O6sdXACfY94X UJ2cm68I4L1qr5PrVnMMif0= =Ysc0 -----END PGP SIGNATURE----- From biopython-bugs at bioperl.org Thu Jan 30 08:36:33 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/119 Message-ID: <200301301336.h0UDaX7E011156@pw600a.bioperl.org> JitterBug notification new message incoming/119 Message summary for PR#119 From: djaeggi@imim.es Subject: Bug in Pathway/Rep/MultiGraph.py Date: Thu, 30 Jan 2003 08:36:32 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From djaeggi@imim.es Thu Jan 30 08:36:32 2003 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0UDaW7E011150 for ; Thu, 30 Jan 2003 08:36:32 -0500 Date: Thu, 30 Jan 2003 08:36:32 -0500 Message-Id: <200301301336.h0UDaW7E011150@pw600a.bioperl.org> From: djaeggi@imim.es To: biopython-bugs@bioperl.org Subject: Bug in Pathway/Rep/MultiGraph.py X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Full_Name: Daniel Jaeggi Module: Pathway/Rep/MultiGraph.py Version: OS: Submission from: (NULL) (193.146.190.216) Hi There's a variable naming problem in the two subroutines: bf_search and df_search. The argument "graph" is passed to both subroutines but is no longer referenced... the variable "g" is used instead. This is fixed by a simple renaming of "graph" to "g" in the argument list. Thanks! From biopython-bugs at bioperl.org Thu Jan 30 14:28:03 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/120 Message-ID: <200301301928.h0UJS37E014052@pw600a.bioperl.org> JitterBug notification new message incoming/120 Message summary for PR#120 From: ognen@kc.rr.com Subject: biopython fails to compile on tru64 Date: Thu, 30 Jan 2003 14:28:02 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From ognen@kc.rr.com Thu Jan 30 14:28:02 2003 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0UJS27E014046 for ; Thu, 30 Jan 2003 14:28:02 -0500 Date: Thu, 30 Jan 2003 14:28:02 -0500 Message-Id: <200301301928.h0UJS27E014046@pw600a.bioperl.org> From: ognen@kc.rr.com To: biopython-bugs@bioperl.org Subject: biopython fails to compile on tru64 X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Full_Name: Ognen Duzlevski Module: KDTree Version: 1.1 OS: tru64 Submission from: (NULL) (204.56.6.63) Using Compaq CC 6.4 on a Tru64 5.1 alpha system. Python 2.2.2 was compiled using the same compiler (it would not compile using gcc 3.1 on the same machine). Doing python setup.py build produced the following output: ld -shared -expect_unresolved * build/temp.osf1-V5.1-alpha-2.2/_KDTree.o build/temp.osf1-V5.1-alpha-2.2/_KDTree.swig.o -lstdc++ -o build/lib.osf1-V5.1-alpha-2.2/Bio/KDTree/_KDTreecmodule.so ld: Can't open: build/temp.osf1-V5.1-alpha-2.2/_KDTree.o (No such file or directory) error: command 'ld' failed with exit status 1 I worked around this by manually executing the following two lines: gcc -DNDEBUG -O -I/usr/local/Python-2.2.2/include/python2.2 -c Bio/KDTree/_KDTree.C gcc -DNDEBUG -O -O -I/usr/local/Python-2.2.2/include/python2.2 -c Bio/KDTree/_KDTree.swig.C and then copying the resulting .o files into build/temp.. You will notice that the biopython was compiled with Compaq C but these two modules I had to compile with gcc and hopefully the mix will work ;)