From jhessel at u.washington.edu Mon Sep 1 13:35:57 2003 From: jhessel at u.washington.edu (Jay Hesselberth) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] Python GO database interface development Message-ID: <20030901173557.GA31040@hal.icmb.utexas.edu> Greetings, I was wondering if there is any ongoing development of a Python based interface to the GO (Gene Ontology) database. I'm in need of one, and don't particularly want to reinvent the wheel for this. If not, I was thinking of basing my code off of the Perl API with only some of the core functionality, e.g. an interface to a local database and perhaps an interface to AMIGO, though I'm not sure I'll be needing that. Does anyone have experience with the Perl API? Are there features that are lacking / could be improved in a newer, Python based interface? Jay -- _______________________________________________________________ Jay Hesselberth jhessel@u.washington.edu University of Washington Department of Genome Sciences Health Sciences Building K-222 / Box 357730 Seattle, WA 98195 From bartek at rezolwenta.eu.org Tue Sep 2 07:51:16 2003 From: bartek at rezolwenta.eu.org (Bartek Wilczynski) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] Python GO database interface development In-Reply-To: <20030901173557.GA31040@hal.icmb.utexas.edu> References: <20030901173557.GA31040@hal.icmb.utexas.edu> Message-ID: <1062503476.3f548434d1e84@imp.rezolwenta.eu.org> Hi, Some time ago (in July, I believe), I've posted similar question on this list. It appeared that Bertrand Frottier have written some code for his own use, and we started to develop it to the stage that it would be general enough to be incorporated to the biopython. (Also Arnaud von Cortenbosch was involved in that effort) The project sort of died, mostly because of lack of time, but I still would like to work on it. As for now, there's some of the old code contributed by Bertrand (mostly for xml and www interface to GO) and some newer stuff that can do very basic things with mysql GO database. If anyone is interested in helping with development, that would be just great (however I have to admit, that I'll probably not be able to work on it this week). You can find the sources at http://rezolwenta.eu.org/cgi-bin/cvsweb/pygo/ -- regards Bartek Wilczy?ski Quoting Jay Hesselberth : > Greetings, > > I was wondering if there is any ongoing development of a Python based > interface to the GO (Gene Ontology) database. I'm in need of one, and > don't particularly want to reinvent the wheel for this. > > If not, I was thinking of basing my code off of the Perl API with only > some of the core functionality, e.g. an interface to a local database and > perhaps an interface to AMIGO, though I'm not sure I'll be needing that. > > Does anyone have experience with the Perl API? Are there features that > are lacking / could be improved in a newer, Python based interface? > > Jay > > -- > _______________________________________________________________ > Jay Hesselberth jhessel@u.washington.edu > > University of Washington > Department of Genome Sciences > Health Sciences Building K-222 / Box 357730 > Seattle, WA 98195 > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > ------------------------------ > Scanned for viruses by MKS_Vir > Last update: > ------------------------------ > From Yves.Bastide at irisa.fr Tue Sep 2 12:01:02 2003 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] [PATCH] Buglet Message-ID: <3F54BEBE.1070001@irisa.fr> A colleague just hit today a bug in my previous patch to Bio.Blast.NCBIStandalone... yves -------------- next part -------------- Index: Bio/Blast/NCBIStandalone.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/Blast/NCBIStandalone.py,v retrieving revision 1.48 diff -u -p -r1.48 NCBIStandalone.py --- Bio/Blast/NCBIStandalone.py 2003/08/08 19:37:30 1.48 +++ Bio/Blast/NCBIStandalone.py 2003/09/02 15:59:11 @@ -1318,7 +1318,7 @@ class Iterator: break # If I've reached the next one, then put the line back and stop. if lines and (line.startswith('BLAST') - or line.startswith('BLAST', start = 1)): + or line.startswith('BLAST', 1)): self._uhandle.saveline(line) break lines.append(line) From piet at clondiag.com Tue Sep 2 12:45:50 2003 From: piet at clondiag.com (Peter Slickers) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] Usage of deprecated function apply() Message-ID: <3F54C93E.1090302@clondiag.com> Since python2.3 the buildin function aplly() is deprecated. Code using apply() is still running under python2.3, but the performance is reduced due to calls into python's warn() function. For example, the blast parser runs only at half speed under python2.3. Moreover, any code using apply() will NOT be executable under python2.4. I suggest to remove an usage of apply() from biopython. According to the python manual, the apply function should be replaced by the 'extended call synthax'. The extended call synthax was introduced in python2.0. Therefore, it is save to drop the apply() fucntion, since nowadays at least python2.2 is required to run biopython. Here are some examples of how to replace apply(): - obj = apply(klass, (), kwargs) + obj = klass( *(), **kwargs) - self.this = apply(_KDTreec.new_KDTree,args) + self.this = _KDTreec.new_KDTree(*args) - reader = apply(self.make_footer_reader, - (self.fileobj,) + self.footer_args, - {"lookahead": self._lookahead}) + reader = self.make_footer_reader( + *(self.fileobj,) + self.footer_args, + **{"lookahead": self._lookahead}) Today, Tue 02-sep-2003, I have scanned the cvs and found 19 file which make use of apply(). Here is a list of the affected files: Bio/EUtils/POM.py Bio/EUtils/tests/unittest.py Bio/FilteredReader.py Bio/KDTree/_KDTree.py Bio/Prosite/Pattern.py Bio/RecordFile.py Bio/SGMLExtractor.py Bio/Seq.py Bio/SeqUtils/__init__.py Bio/Std.py Bio/config/DBRegistry.py Bio/sequtils.py Martel/Iterator.py Martel/Parser.py Martel/convert_re.py Scripts/Performance/biocorba_sql_server.py Tests/test_KeyWList.py Tests/unittest.py Tests/unittestgui.py If have created a patch which will fix these 19 files. As I don't have any wright premissions to the cvs repository, I will send the patch to Jeffrey Chang. He will eventually apply the patch to the cvs (if this meets approval of the other developers). Everybody who is owning one of the affected files should give a note to Jeffrey if he/she does not like that his code is patched. With best regards, -- 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 thamelry at vub.ac.be Tue Sep 2 13:16:06 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] Usage of deprecated function apply() In-Reply-To: <3F54C93E.1090302@clondiag.com> References: <3F54C93E.1090302@clondiag.com> Message-ID: <200309021713.h82HDqPF005690@nebula.skynet.be> > - self.this = apply(_KDTreec.new_KDTree,args) > + self.this = _KDTreec.new_KDTree(*args) This is Swig-generated code, not hand-written. It's probably solved in the newest version of Swig, I'll try it out when I find the time. Tnx for the info, Regards, -Thomas --- Thomas Hamelryck ULTR/COMO Institute for molecular biology/Computer Science Department Vrije Universiteit Brussel (VUB) Brussels, Belgium http://homepages.vub.ac.be/~thamelry From jchang at jeffchang.com Tue Sep 2 13:47:04 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] [PATCH] Buglet In-Reply-To: <3F54BEBE.1070001@irisa.fr> Message-ID: <770C689F-DD6D-11D7-AD5E-000A956845CE@jeffchang.com> Thanks for the patch. I've committed it to the CVS. Jeff On Tuesday, September 2, 2003, at 09:01 AM, Yves Bastide wrote: > A colleague just hit today a bug in my previous patch to > Bio.Blast.NCBIStandalone... > > yves > Index: Bio/Blast/NCBIStandalone.py > =================================================================== > RCS file: > /home/repository/biopython/biopython/Bio/Blast/NCBIStandalone.py,v > retrieving revision 1.48 > diff -u -p -r1.48 NCBIStandalone.py > --- Bio/Blast/NCBIStandalone.py 2003/08/08 19:37:30 1.48 > +++ Bio/Blast/NCBIStandalone.py 2003/09/02 15:59:11 > @@ -1318,7 +1318,7 @@ class Iterator: > break > # If I've reached the next one, then put the line back > and stop. > if lines and (line.startswith('BLAST') > - or line.startswith('BLAST', start = 1)): > + or line.startswith('BLAST', 1)): > self._uhandle.saveline(line) > break > lines.append(line) > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From kim750 at ggbio.com Wed Sep 3 04:01:35 2003 From: kim750 at ggbio.com (kim750@ggbio.com) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] installerror Message-ID: <20030903.AAA1062575767@ggbio.com> Skipped content of type multipart/alternative From dalke at dalkescientific.com Wed Sep 3 04:14:14 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] installerror In-Reply-To: <20030903.AAA1062575767@ggbio.com> Message-ID: <9AFFEEB6-DDE6-11D7-BBDD-000393C92466@dalkescientific.com> kim750@ggbio.com wrote: > File "setup.py", line 202 > i += 1 > ^ > SyntaxError: invalid syntax > > I don't know how to handle this error. > If you have any idea, could you help me. Your version of Python is too old. The '+=' syntax wasn't added until Python 2.0 (or perhaps the "contractual obligation" 1.6 release) in October of 2000. You probably have version 1.5.2 and will need to upgrade to use Biopython. The most recent version of Python is version 2.3, and is available from python.org. Andrew dalke@dalkescientific.com From mdehoon at ims.u-tokyo.ac.jp Wed Sep 3 04:20:01 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] installerror In-Reply-To: <20030903.AAA1062575767@ggbio.com> References: <20030903.AAA1062575767@ggbio.com> Message-ID: <3F55A431.8080304@ims.u-tokyo.ac.jp> You are probably using an old version of python (see below). Try upgrading to Python 2.3. --Michiel, U Tokyo. 1 mdehoon@tulip.ims.u-tokyo.ac.jp:~ : python Python 1.5.2 (#1, Jul 5 2001, 03:02:19) [GCC 2.96 20000731 (Red Hat Linux 7.1 2 on linux-i386 Copyright 1991-1995 Stichting Mathematisch Centrum, Amsterdam >>> i = 3 >>> i += 2 File "", line 1 i += 2 ^ SyntaxError: invalid syntax >>> 2 mdehoon@tulip.ims.u-tokyo.ac.jp:~ : python2 Python 2.2.1 (#1, Apr 9 2002, 13:10:27) [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> i = 3 >>> i += 2 >>> kim750@ggbio.com wrote: > Hi! My name is Yeon-Ki Kim. I am associated with GreenGene Biotech. We are located in Yong-In, Republic of Korea. > > Thank you for your contribution for the bioinformatice through the biopython program. > Yesterday I tried to install biopython-1.21. But during the installation it gives me a SyntaxError like > > File "setup.py", line 202 > i += 1 > ^ > SyntaxError: invalid syntax > > I don't know how to handle this error. > If you have any idea, could you help me. > Thanks again. > > Yeon-Ki > > > Yeon-Ki Kim, Ph.D. > Research Scientist > > GreenGene Biotech, inc. > Myongji University > 38-2 Namdong > Yongin Kyonggido 449-728 Korea > > GreenGene BioTech Inc. > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- 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 ben.hayes at akvaforsk.nlh.no Wed Sep 3 05:06:41 2003 From: ben.hayes at akvaforsk.nlh.no (Ben Hayes) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] installerror In-Reply-To: <3F55A431.8080304@ims.u-tokyo.ac.jp> Message-ID: Hi all, I am looking for a parser for Blat (UCSC genomics website). Is any body aware of any code that would do the job? Regards, Ben. From ben.hayes at akvaforsk.nlh.no Wed Sep 3 05:49:39 2003 From: ben.hayes at akvaforsk.nlh.no (Ben Hayes) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] Parser for BLAT Message-ID: Hi all, I am looking for a parser for Blat (UCSC genomics website). Is any body aware of any code that would do the job? Regards, Ben. From kim750 at ggbio.com Wed Sep 3 06:07:45 2003 From: kim750 at ggbio.com (kim750@ggbio.com) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] streamerror_in_local_blast.py Message-ID: <20030903.AAA1062582144@ggbio.com> Skipped content of type multipart/alternative From dalke at dalkescientific.com Wed Sep 3 18:05:16 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] license web accessible? Message-ID: Hey all, I was checking my company's site's links and noticed that the one to the biopython license is no longer valid. I couldn't find it. Is there a URL to it? Andrew From kim750 at ggbio.com Thu Sep 4 00:14:54 2003 From: kim750 at ggbio.com (kim750@ggbio.com) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] streamerror Message-ID: <20030904.AAA1062648737@ggbio.com> Skipped content of type multipart/alternative From jchang at jeffchang.com Thu Sep 4 02:46:38 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:26 2005 Subject: [Biopython-dev] streamerror In-Reply-To: <20030904.AAA1062648737@ggbio.com> Message-ID: <88CB49E8-DEA3-11D7-ADA0-000A956845CE@jeffchang.com> On Wednesday, September 3, 2003, at 09:14 PM, kim750@ggbio.com wrote: > Hi! > This is Yeon-Ki. > When I run local_blast.py in the biopython package, I have an error > message like this: [... traceback cut] The "Unexpected end of stream" exception happens when the parser is looking for a line in a file, and it can't find it before the file ends. Either there's a bug in the parser, or there is an error in the file. > I modified instances for path name as abosolute one because all the > datafiles are sprayed through the directories. For ex, my_blast_db = > os.path.join(absolute path). This code doesn't look quite right. os.path.join joins bits of a path together to form a complete path for a file. Are you sure that this is generating a correct filename, and the filename it creates is the name of the BLAST format file, and not another file? If the file that it creates is not a BLAST format file, it could very well be reading the wrong file and cause the error. Jeff From jchang at jeffchang.com Thu Sep 4 15:28:52 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Usage of deprecated function apply() In-Reply-To: <3F54C93E.1090302@clondiag.com> Message-ID: <0420D1E4-DF0E-11D7-AF21-000A956845CE@jeffchang.com> I have applied this patch against the CVS. Code running python2.3 should get a speedup. Nothing appears to have been broken, but please send mail to this list if anyone sees any strange behavior. Jeff On Tuesday, September 2, 2003, at 09:45 AM, Peter Slickers wrote: > Since python2.3 the buildin function aplly() is deprecated. > Code using apply() is still running under python2.3, but the > performance is reduced due to calls into python's warn() function. > For example, the blast parser runs only at half speed under > python2.3. Moreover, any code using apply() will NOT be > executable under python2.4. > > I suggest to remove an usage of apply() from biopython. > According to the python manual, the apply function should > be replaced by the 'extended call synthax'. The extended call > synthax was introduced in python2.0. Therefore, it is save > to drop the apply() fucntion, since nowadays at least > python2.2 is required to run biopython. > > Here are some examples of how to replace apply(): > > - obj = apply(klass, (), kwargs) > + obj = klass( *(), **kwargs) > > - self.this = apply(_KDTreec.new_KDTree,args) > + self.this = _KDTreec.new_KDTree(*args) > > - reader = apply(self.make_footer_reader, > - (self.fileobj,) + self.footer_args, > - {"lookahead": self._lookahead}) > + reader = self.make_footer_reader( > + *(self.fileobj,) + self.footer_args, > + **{"lookahead": self._lookahead}) > > > Today, Tue 02-sep-2003, I have scanned the cvs and found > 19 file which make use of apply(). Here is a list of the > affected files: > > Bio/EUtils/POM.py > Bio/EUtils/tests/unittest.py > Bio/FilteredReader.py > Bio/KDTree/_KDTree.py > Bio/Prosite/Pattern.py > Bio/RecordFile.py > Bio/SGMLExtractor.py > Bio/Seq.py > Bio/SeqUtils/__init__.py > Bio/Std.py > Bio/config/DBRegistry.py > Bio/sequtils.py > Martel/Iterator.py > Martel/Parser.py > Martel/convert_re.py > Scripts/Performance/biocorba_sql_server.py > Tests/test_KeyWList.py > Tests/unittest.py > Tests/unittestgui.py > > > If have created a patch which will fix these 19 files. > As I don't have any wright premissions to the cvs repository, I will > send > the patch to Jeffrey Chang. He will eventually apply > the patch to the cvs (if this meets approval of the > other developers). > > Everybody who is owning one of the affected files > should give a note to Jeffrey if he/she does not like > that his code is patched. > > > With best regards, > -- > > > 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 > ------------------------------------------------------------------- > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From guidod-2003- at gmx.de Sat Sep 6 12:45:05 2003 From: guidod-2003- at gmx.de (Guido Draheim) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] xbbtools-fix-import-tools-01.patch Message-ID: <3F5A0F11.6080908@gmx.de> please apply. -------------- next part -------------- Index: Scripts/xbbtools/./xbb_translations.py =================================================================== RCS file: /home/repository/biopython/biopython/Scripts/xbbtools/xbb_translations.py,v retrieving revision 1.4 diff -u -r1.4 xbb_translations.py --- Scripts/xbbtools/./xbb_translations.py 2000/12/02 15:29:59 1.4 +++ Scripts/xbbtools/./xbb_translations.py 2003/09/06 16:40:03 @@ -14,7 +14,7 @@ from Bio import Seq from Bio import Alphabet from Bio.Alphabet import IUPAC -from Bio.Tools import Translate +from Bio import Translate from Bio.Data import IUPACData Index: Scripts/xbbtools/./xbb_widget.py =================================================================== RCS file: /home/repository/biopython/biopython/Scripts/xbbtools/xbb_widget.py,v retrieving revision 1.7 diff -u -r1.7 xbb_widget.py --- Scripts/xbbtools/./xbb_widget.py 2001/09/04 07:42:30 1.7 +++ Scripts/xbbtools/./xbb_widget.py 2003/09/06 16:40:04 @@ -23,7 +23,7 @@ from xbb_blast import BlastIt from xbb_search import XDNAsearch from xbb_help import xbbtools_help -from Bio.Tools import Translate +from Bio import Translate from Bio.sequtils import quick_FASTA_reader From jchang at jeffchang.com Sun Sep 7 02:03:18 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] xbbtools-fix-import-tools-01.patch In-Reply-To: <3F5A0F11.6080908@gmx.de> Message-ID: Patched. Thanks very much! Jeff On Saturday, September 6, 2003, at 09:45 AM, Guido Draheim wrote: > please apply. > Index: Scripts/xbbtools/./xbb_translations.py > =================================================================== > RCS file: > /home/repository/biopython/biopython/Scripts/xbbtools/ > xbb_translations.py,v > retrieving revision 1.4 > diff -u -r1.4 xbb_translations.py > --- Scripts/xbbtools/./xbb_translations.py 2000/12/02 15:29:59 1.4 > +++ Scripts/xbbtools/./xbb_translations.py 2003/09/06 16:40:03 > @@ -14,7 +14,7 @@ > from Bio import Seq > from Bio import Alphabet > from Bio.Alphabet import IUPAC > -from Bio.Tools import Translate > +from Bio import Translate > from Bio.Data import IUPACData > > > Index: Scripts/xbbtools/./xbb_widget.py > =================================================================== > RCS file: > /home/repository/biopython/biopython/Scripts/xbbtools/xbb_widget.py,v > retrieving revision 1.7 > diff -u -r1.7 xbb_widget.py > --- Scripts/xbbtools/./xbb_widget.py 2001/09/04 07:42:30 1.7 > +++ Scripts/xbbtools/./xbb_widget.py 2003/09/06 16:40:04 > @@ -23,7 +23,7 @@ > from xbb_blast import BlastIt > from xbb_search import XDNAsearch > from xbb_help import xbbtools_help > -from Bio.Tools import Translate > +from Bio import Translate > from Bio.sequtils import quick_FASTA_reader > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From thomas at cbs.dtu.dk Mon Sep 8 05:17:40 2003 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] cvs access Message-ID: Hej, Finally I have finished my move and got the computers up and running again. Next, I tried my CVS access ... without success :-( I guess you have changed a lot since my last active biopython sessions, how does one login in at the CVS (with write access)? the following command cvs -d :ext:thomas@biopython.org:/home/repository/biopython co biopython returns Cannot access /home/repository/biopython/CVSROOT No such file or directory any suggestions? thx -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas@biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From andreas.kuntzagk at mdc-berlin.de Mon Sep 8 07:51:55 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Genbank Format-Changes Message-ID: <1063021881.15519.19.camel@sulawesi> Hi, While trying to load Genbank entries BK000008 and BK000018 I found lines starting with PRIMARY... At the moment the GenBank parser does not understand this. I wanted to patch it but could not find any documentation on this lines. Anybody an idea where I can find this? I was looking at the Release Notes at the ftp-site. Andreas From Peter.Bienstman at ugent.be Mon Sep 8 16:03:02 2003 From: Peter.Bienstman at ugent.be (Peter Bienstman) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Genbank Format-Changes In-Reply-To: <1063021881.15519.19.camel@sulawesi> References: <1063021881.15519.19.camel@sulawesi> Message-ID: <200309082203.02955.Peter.Bienstman@ugent.be> On Monday 08 September 2003 13:51, Andreas Kuntzagk wrote: > Hi, > > While trying to load Genbank entries BK000008 and BK000018 I found lines > starting with PRIMARY... > > At the moment the GenBank parser does not understand this. I wanted to > patch it but could not find any documentation on this lines. Anybody an > idea where I can find this? I was looking at the Release Notes at the > ftp-site. It wouldn't be the first time a keyword is not documented in the Release Notes... Peter -- ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.ugent.be email: Peter.Bienstman@ugent.be ------------------------------------------------ From andreas.kuntzagk at mdc-berlin.de Tue Sep 9 10:48:37 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [Fwd: FW: genbank flat file format changes] Message-ID: <1063118882.21384.8.camel@sulawesi> Hi, Today I wrote a message to the NCBI asking about the changes and here is the answer I got. Funny that they mention the PRIMARY line in the 134th release notes but not in the current. At a first glance, the description looks not very complete, but if I have time I will incorporate it in the parser and try it for the entries that failed me. Andreas -------------- next part -------------- An embedded message was scrubbed... From: "Pham, Vyvy (NIH/NLM/NCBI)" Subject: FW: genbank flat file format changes Date: Tue, 9 Sep 2003 10:36:08 -0400 Size: 2824 Url: http://portal.open-bio.org/pipermail/biopython-dev/attachments/20030909/e0c60cbb/attachment.eml From idoerg at burnham.org Tue Sep 9 19:59:59 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Martel patch in release please? Message-ID: Hi, I'm currrently at the CRBM'03 workshop at UCSD. Thomas Hamelryck gave a great presentation of Bio.PDB, and I think I wasn't too shabby with an overview of Biopython. As a matter of fact, one participant even downloaded Biopython (we have wireless here) and tried to install it, from source Mandrake 9.1. The "cannot import Martel" problem came up. Kinda put a damp on "look how easy it is!" presentation.... Jeff, could the release version be patched please? Cheers, 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://ffas.ljcrf.edu/~iddo From jchang at jeffchang.com Tue Sep 9 20:24:58 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Martel patch in release please? In-Reply-To: Message-ID: <35BABC62-E325-11D7-9BFA-000A956845CE@jeffchang.com> Yep, maybe the thing to do is to issue another quick release. It can also incorporate Peter Slickers' patches to speed up the parsers under Python 2.3, and some other miscellaneous fixes. I'll take a look at it in the next few days. Please let me know if this is not a good time to make a release, or if your code is not ready. Jeff On Tuesday, September 9, 2003, at 04:59 PM, Iddo Friedberg wrote: > Hi, > > I'm currrently at the CRBM'03 workshop at UCSD. Thomas Hamelryck gave a > great presentation of Bio.PDB, and I think I wasn't too shabby with an > overview of Biopython. As a matter of fact, one participant even > downloaded Biopython (we have wireless here) and tried to install it, > from > source Mandrake 9.1. The > "cannot import Martel" problem came up. Kinda put a damp on "look how > easy it is!" presentation.... Jeff, could the release version be > patched > please? > > Cheers, > > 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://ffas.ljcrf.edu/~iddo > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From andreas.kuntzagk at mdc-berlin.de Wed Sep 10 08:01:09 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] need some advice regarding martel Message-ID: <1063195235.24050.23.camel@sulawesi> Hi, I've got some problem with the genbank changes a wanted to make. In genbank.format I have following lines: ----- primary_line = Martel.Group("primary_line", Martel.Str("PRIMARY") + blank_space + Martel.Str("TPA_SPAN") + blank_space + Martel.Str("PRIMARY_IDENTIFIER") + blank_space + Martel.Str("PRIMARY_SPAN") + blank_space + Martel.Str("COMP") + Martel.AnyEol()) primary_ref_line =Martel.Group("primary_ref_line", blank_space + Martel.Re(r"\d+\-\d+") + blank_space + Martel.Re("[\S]+") + blank_space + Martel.Re("\d+\-\d+")+ Martel.Opt(blank_space + Martel.Str("c"))+ Martel.AnyEol()) primary = Martel.Group("primary",primary_line + Martel.Rep(primary_ref_line)) ------ So primary_line is the line starting the whole PRIMARY-block, primary_ref_line should be _one_ line with the actual data and primary the combination of the two. BUT: In my consumer in the method primary_ref_line(self,content) content has the data for all of the lines (except the starting "PRIMARY" line) in one string without any newline. Where is my error? At least the parser doesn't choke on this lines anymore but wouldn't it be good, if it would extract this information? Andreas From Yves.Bastide at irisa.fr Wed Sep 10 12:35:14 2003 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [RFC, PATCH] Bio.Iter Message-ID: <3F5F52C2.2030300@irisa.fr> Hi all, here's a small wrapper for using Bio iterators the 'modern' way. E. g., replacing: from Bio.Blast import NCBIStandalone blast_out = open('my_file_of_blast_output', 'r') b_parser = NCBIStandalone.BlastParser() b_iterator = NCBIStandalone.Iterator(blast_out, b_parser) while 1: b_record = b_iterator.next() if b_record is None: break # ... With: from Bio.Blast import NCBIStandalone from Bio.Iter import Iter blast_out = file('my_file_of_blast_output', 'r') b_parser = NCBIStandalone.BlastParser() b_iterator = Iter(NCBIStandalone.Iterator(blast_out, b_parser)) for b_record in b_iter: # ... Regards, yves -------------- next part -------------- Index: biopython/Bio/__init__.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/__init__.py,v retrieving revision 1.21 diff -u -p -r1.21 __init__.py --- biopython/Bio/__init__.py 2003/02/20 04:35:37 1.21 +++ biopython/Bio/__init__.py 2003/09/10 16:25:44 @@ -18,6 +18,7 @@ __all__ = [ "Gobase", "Index", "InterPro", + "Iter", "KEGG", "Kabat", "Medline", --- /dev/null 2003-01-30 11:24:37.000000000 +0100 +++ biopython/Bio/Iter.py 2003-09-10 18:22:41.000000000 +0200 @@ -0,0 +1,12 @@ +# This code is part of the Biopython distribution and governed by its +# license. Please see the LICENSE file that should have been included +# as part of this package. +from __future__ import generators + +def Iter(bio_iter): + """Standard iterator wrapper for Bio iterators""" + while True: + ret = bio_iter.next() + if ret is None: + return + yield ret From jchang at jeffchang.com Wed Sep 10 14:24:47 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [RFC, PATCH] Bio.Iter In-Reply-To: <3F5F52C2.2030300@irisa.fr> Message-ID: <0F04BBBE-E3BC-11D7-BA7A-000A956845CE@jeffchang.com> Hi Yves, Does this not do the same thing? b_iterator = iter(NCBIStandalone.Iterator(blast_out, b_parser).next, None) It's a little uglier than your solution. However, the best would be to make NCBIStandalone.Iterator a true iterator. Could you also try adding, to the NCBIStandalone.Iterator class the method: def __iter__(self): return iter(self.next, None) I have not tested it. However, if it works correctly for you, please let me know and I can add it to the distribution. Jeff On Wednesday, September 10, 2003, at 09:35 AM, Yves Bastide wrote: > Hi all, > > here's a small wrapper for using Bio iterators the 'modern' way. > E. g., replacing: > > from Bio.Blast import NCBIStandalone > > blast_out = open('my_file_of_blast_output', 'r') > b_parser = NCBIStandalone.BlastParser() > b_iterator = NCBIStandalone.Iterator(blast_out, b_parser) > > while 1: > b_record = b_iterator.next() > > if b_record is None: > break > # ... > > > With: > > from Bio.Blast import NCBIStandalone > from Bio.Iter import Iter > > blast_out = file('my_file_of_blast_output', 'r') > b_parser = NCBIStandalone.BlastParser() > b_iterator = Iter(NCBIStandalone.Iterator(blast_out, b_parser)) > > for b_record in b_iter: > # ... > > > Regards, > > yves > Index: biopython/Bio/__init__.py > =================================================================== > RCS file: /home/repository/biopython/biopython/Bio/__init__.py,v > retrieving revision 1.21 > diff -u -p -r1.21 __init__.py > --- biopython/Bio/__init__.py 2003/02/20 04:35:37 1.21 > +++ biopython/Bio/__init__.py 2003/09/10 16:25:44 > @@ -18,6 +18,7 @@ __all__ = [ > "Gobase", > "Index", > "InterPro", > + "Iter", > "KEGG", > "Kabat", > "Medline", > --- /dev/null 2003-01-30 11:24:37.000000000 +0100 > +++ biopython/Bio/Iter.py 2003-09-10 18:22:41.000000000 +0200 > @@ -0,0 +1,12 @@ > +# This code is part of the Biopython distribution and governed by its > +# license. Please see the LICENSE file that should have been included > +# as part of this package. > +from __future__ import generators > + > +def Iter(bio_iter): > + """Standard iterator wrapper for Bio iterators""" > + while True: > + ret = bio_iter.next() > + if ret is None: > + return > + yield ret > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From Yves.Bastide at irisa.fr Wed Sep 10 14:42:33 2003 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [RFC, PATCH] Bio.Iter In-Reply-To: <0F04BBBE-E3BC-11D7-BA7A-000A956845CE@jeffchang.com> References: <0F04BBBE-E3BC-11D7-BA7A-000A956845CE@jeffchang.com> Message-ID: <3F5F7099.9050107@irisa.fr> Jeffrey Chang wrote: > Hi Yves, > > Does this not do the same thing? > b_iterator = iter(NCBIStandalone.Iterator(blast_out, b_parser).next, > None) Yep -- but I posted my message before thinking about it :) > > It's a little uglier than your solution. However, the best would be to > make NCBIStandalone.Iterator a true iterator. Could you also try > adding, to the NCBIStandalone.Iterator class the method: > > def __iter__(self): > return iter(self.next, None) > > I have not tested it. However, if it works correctly for you, please > let me know and I can add it to the distribution. It does. Thanks! > > Jeff > > > -------------- next part -------------- --- /local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py 2003-09-03 10:19:40.000000000 +0200 +++ Bio/Blast/NCBIStandalone.py 2003-09-10 20:34:10.000000000 +0200 @@ -33,6 +33,7 @@ blastpgp Execute blastpgp. """ +from __future__ import generators import os import re @@ -1331,6 +1332,9 @@ class Iterator: return self._parser.parse(File.StringHandle(data)) return data + def __iter__(self): + return iter(self.next, None) + def blastall(blastcmd, program, database, infile, **keywds): """blastall(blastcmd, program, database, infile, **keywds) -> read, error Undohandles From jchang at jeffchang.com Thu Sep 11 03:28:37 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [RFC, PATCH] Bio.Iter In-Reply-To: <3F5F7099.9050107@irisa.fr> Message-ID: <8F07D490-E429-11D7-9D6F-000A956845CE@jeffchang.com> CVS is patched. Thanks! jeff On Wednesday, September 10, 2003, at 11:42 AM, Yves Bastide wrote: > Jeffrey Chang wrote: >> Hi Yves, >> Does this not do the same thing? >> b_iterator = iter(NCBIStandalone.Iterator(blast_out, >> b_parser).next, None) > > Yep -- but I posted my message before thinking about it :) > > >> It's a little uglier than your solution. However, the best would be >> to make NCBIStandalone.Iterator a true iterator. Could you also try >> adding, to the NCBIStandalone.Iterator class the method: >> def __iter__(self): >> return iter(self.next, None) >> I have not tested it. However, if it works correctly for you, please >> let me know and I can add it to the distribution. > > It does. Thanks! > >> Jeff > --- > /local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py 2003- > 09-03 10:19:40.000000000 +0200 > +++ Bio/Blast/NCBIStandalone.py 2003-09-10 20:34:10.000000000 +0200 > @@ -33,6 +33,7 @@ blastpgp Execute blastpgp. > > """ > > +from __future__ import generators > import os > import re > > @@ -1331,6 +1332,9 @@ class Iterator: > return self._parser.parse(File.StringHandle(data)) > return data > > + def __iter__(self): > + return iter(self.next, None) > + > def blastall(blastcmd, program, database, infile, **keywds): > """blastall(blastcmd, program, database, infile, **keywds) -> > read, error Undohandles > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From mdehoon at ims.u-tokyo.ac.jp Fri Sep 12 08:40:57 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Installation problems -> new release Message-ID: <3F61BED9.9070401@ims.u-tokyo.ac.jp> Below I copied the installation difficulties that I ran into when I was trying to make the Windows installer for biopython. I cut out the parts that have been fixed by now. If Biopython is going to have a new release, maybe it is a good time to also fix the installation problem with the DTD files in Bio/EUtils. --Michiel. Jeff wrote: > Yep, maybe the thing to do is to issue another quick release. It can > also incorporate Peter Slickers' patches to speed up the parsers under > Python 2.3, and some other miscellaneous fixes. I'll take a look at it > in the next few days. > > Please let me know if this is not a good time to make a release, or if > your code is not ready. > > Jeff Michiel wrote a couple of weeks ago: >> I ran into some difficulties building this installer. During the >> bdist_wininst command, it cannot find the file >> build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs. This is probably a >> problem with Python's distutils for Windows; I don't run into this >> problem when compiling on Unix. So on Windows, I created that directory >> by hand and copied the files from Bio\EUtils\DTDs into it. That seems >> like the right thing to do, but I am not sure; does anybody know? >> >> >> On Unix, I get the following warning: >> >> *** Martel *** is either not installed or out of date. >> >> This package is required for many Biopython features. Please install >> it before you install Biopython. >> You can find Martel at http://www.biopython.org/~dalke/Martel/. >> >> Isn't Martel included with Biopython? Btw, the link is dead. -- 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 Yves.Bastide at irisa.fr Fri Sep 12 12:57:15 2003 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] BioSQL: patch for discussion Message-ID: <3F61FAEB.8090203@irisa.fr> Hi everybody, attached is a patch for bringing BioSQL to the current database schema, since Brad seems too busy graduating :) One of the things to discuss is that I broke the current interface: I added the sequence version to the db items ids (breaking test_BioSQL's assert item_ids == ['AF297471', 'AJ237582', 'L31939', 'M81224', 'X55053', 'X62281']). I think this is necessary, since accession numbers are not guaranteed unique... Another breakage vis-?-vis the test suite is that "no strand info" is dignified by None instead of 0. Breaking-the-testsuite-ly yr's, yves -------------- next part -------------- A non-text attachment was scrubbed... Name: biosql.diff.gz Type: application/x-gzip Size: 15305 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20030912/4496b0b4/biosql.diff.bin From jchang at jeffchang.com Sat Sep 13 17:41:25 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] maintenance release Message-ID: <06A2AC8A-E633-11D7-AB92-000A956845CE@jeffchang.com> Hello everybody, It's about time to make a release that fixes the Martel install bug. I've fixed this in the version in the CVS. Could everyone please try it out? If things go smoothly, I'll make a release later this week. The main changes in this version will be: Martel - The setup script was not detecting that Martel would be installed, and complained that it was missing. This is now fixed. EUtils DTDs - Brad fixed this in setup.py. This will go into the release. Numeric Python - If numeric is missing, Bio.Cluster does not compile. Thus, the setup script now only install Bio.Cluster if Numeric is installed. I have documented this dependency in README. There are also some other miscellaneous changes I've documented in the NEWS file. Also, test_Time.py in the Martel regression tests is failing. Can someone fix this? Jeff From mdehoon at ims.u-tokyo.ac.jp Sun Sep 14 02:54:28 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] maintenance release In-Reply-To: <06A2AC8A-E633-11D7-AB92-000A956845CE@jeffchang.com> References: <06A2AC8A-E633-11D7-AB92-000A956845CE@jeffchang.com> Message-ID: <3F6410A4.5060105@ims.u-tokyo.ac.jp> I tried to install the CVS version of Biopython with Cygwin and with Windows. On Cygwin, I don't get any errors. On Windows, I am still getting the error with EUtils\DTDs. It wasn't clear to me from CVS if the fix for this error has been committed yet, so maybe I should just try again later. --Michiel. $ /cygdrive/c/Python23/python setup.py bdist_wininst ... error: build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs: No such file or directory Jeffrey Chang wrote: > Hello everybody, > > It's about time to make a release that fixes the Martel install bug. > I've fixed this in the version in the CVS. Could everyone please try it > out? If things go smoothly, I'll make a release later this week. The > main changes in this version will be: > > Martel - The setup script was not detecting that Martel would be > installed, and complained that it was missing. This is now fixed. > > EUtils DTDs - Brad fixed this in setup.py. This will go into the release. > > Numeric Python - If numeric is missing, Bio.Cluster does not compile. > Thus, the setup script now only install Bio.Cluster if Numeric is > installed. I have documented this dependency in README. > > > There are also some other miscellaneous changes I've documented in the > NEWS file. > > Also, test_Time.py in the Martel regression tests is failing. Can > someone fix this? > > Jeff > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > -- 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 andreas.kuntzagk at mdc-berlin.de Mon Sep 15 07:06:39 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] incomplete patch to parse Genbank-TPA record BK000008 Message-ID: <1063624001.31579.13.camel@sulawesi> Since I'm stuck with this, I'm giving you the incomplete patch in hope, somebody will have time to look at it. At the moment it parses the BK000008 and BK000018 entries in GenBank and hopefully others as well. BUT: the information is put into the Record only in form of one long string with newlines deleted. If anybody really neads this info, it should be stored in a better way. -------------- next part -------------- Index: Bio/GenBank/Record.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/GenBank/Record.py,v retrieving revision 1.8 diff -r1.8 Record.py 9,11d8 < # standard modules < import string < 175a173 > self.primary=[] Index: Bio/GenBank/__init__.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/GenBank/__init__.py,v retrieving revision 1.42 diff -r1.42 __init__.py 988c988 < --- > 1068c1068 < --- > 1074c1074 < --- > 1077a1078,1084 > def primary_ref_line(self,content): > """Data for the PRIMARY line""" > self.data.primary.append(content) > > def primary(self,content): > pass > 1217c1224 < "sequence", "contig_location", "record_end"] --- > "sequence", "contig_location", "record_end","primary_ref_line"] Index: Bio/GenBank/genbank_format.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/GenBank/genbank_format.py,v retrieving revision 1.28 diff -r1.28 genbank_format.py 22,24c22 < # standard library < import string < --- > 303a302,313 > # PRIMARY > primary_line = Martel.Group("primary_line", > Martel.Str("PRIMARY") + > blank_space + > Martel.Str("TPA_SPAN") + > blank_space + > Martel.Str("PRIMARY_IDENTIFIER") + > blank_space + > Martel.Str("PRIMARY_SPAN") + > blank_space + > Martel.Str("COMP") + > Martel.ToEol()) 304a315,327 > primary_ref_line =Martel.Group("primary_ref_line", > blank_space + > Martel.Re(r"\d+\-\d+") + > blank_space + > Martel.Re("[\S]+") + > blank_space + > Martel.Re("\d+\-\d+")+ > Martel.Opt(blank_space + Martel.Str("c"))+ > Martel.ToEol()) > > primary = Martel.Group("primary",primary_line + > Martel.Rep1(primary_ref_line)) > 735a759 > Martel.Opt(primary) +\ From Peter.Bienstman at ugent.be Mon Sep 15 08:49:21 2003 From: Peter.Bienstman at ugent.be (Peter Bienstman) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] incomplete patch to parse Genbank-TPA record BK000008 In-Reply-To: <1063624001.31579.13.camel@sulawesi> References: <1063624001.31579.13.camel@sulawesi> Message-ID: <200309151449.21720.Peter.Bienstman@ugent.be> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Monday 15 September 2003 13:06, Andreas Kuntzagk wrote: > Since I'm stuck with this, I'm giving you the incomplete patch in hope, > somebody will have time to look at it. At the moment it parses the > BK000008 and BK000018 entries in GenBank and hopefully others as well. > > BUT: the information is put into the Record only in form of one long > string with newlines deleted. If anybody really neads this info, it > should be stored in a better way. Thanks for looking into this! My personal view is that it's better to have a patch that parses the records (even though it lumps the info), rather than no patch at all. Jeff, what do you think, can we commit this? Peter - ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.ugent.be email: Peter.Bienstman@ugent.be - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.2 (GNU/Linux) iD8DBQE/ZbVR4dgPAIjyquoRAidWAJ41ljrhVqRGY9ea90Yqv00RD3GUHgCfVliC HCQqa4qyFmhfiR0waHrfV3Y= =aiqq -----END PGP SIGNATURE----- From jchang at jeffchang.com Mon Sep 15 18:33:03 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] maintenance release In-Reply-To: <3F6410A4.5060105@ims.u-tokyo.ac.jp> Message-ID: <9178A5A5-E7CC-11D7-A581-000A956845CE@jeffchang.com> Yuck, this was broken. Previously, the dtd installation was hacked in by modifying the Distutils "install" command. This only gets called from unix, so nothing was happening for bdist_wininst. The dtds were not getting installed. I've gone back and reworked the dtd installation so that the dtd filenames are passed into the Distutils.setup function as a data file. However, the directory layout for python packages in windows and unix are different. I took a best guess at how to do this for windows based on what I've seen documented on the web. Michiel, do you mind checking this again and seeing whether it works on windows? Specifically, I need to know 1) whether the ".dtd" files are getting installed, 2) whether they are installed in the right place, and 3) where they are installed if they are in the wrong place. Thanks, Jeff On Saturday, September 13, 2003, at 11:54 PM, Michiel Jan Laurens de Hoon wrote: > I tried to install the CVS version of Biopython with Cygwin and with > Windows. On Cygwin, I don't get any errors. On Windows, I am still > getting the error with EUtils\DTDs. It wasn't clear to me from CVS if > the fix for this error has been committed yet, so maybe I should just > try again later. > > --Michiel. > > $ /cygdrive/c/Python23/python setup.py bdist_wininst > ... > error: build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs: No such file > or directory > > > Jeffrey Chang wrote: > >> Hello everybody, >> It's about time to make a release that fixes the Martel install bug. >> I've fixed this in the version in the CVS. Could everyone please try >> it out? If things go smoothly, I'll make a release later this week. >> The main changes in this version will be: >> Martel - The setup script was not detecting that Martel would be >> installed, and complained that it was missing. This is now fixed. >> EUtils DTDs - Brad fixed this in setup.py. This will go into the >> release. >> Numeric Python - If numeric is missing, Bio.Cluster does not compile. >> Thus, the setup script now only install Bio.Cluster if Numeric is >> installed. I have documented this dependency in README. >> There are also some other miscellaneous changes I've documented in >> the NEWS file. >> Also, test_Time.py in the Martel regression tests is failing. Can >> someone fix this? >> Jeff >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev > > -- > 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 > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From mdehoon at ims.u-tokyo.ac.jp Mon Sep 15 21:41:38 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] maintenance release In-Reply-To: <9178A5A5-E7CC-11D7-A581-000A956845CE@jeffchang.com> References: <9178A5A5-E7CC-11D7-A581-000A956845CE@jeffchang.com> Message-ID: <3F666A52.9060206@ims.u-tokyo.ac.jp> I tried this on Windows. I don't get any error messages when compiling and building the installer. The *.dtd files get installed in C:\Python23\Bio\EUtils\DTDs, while C:\Python23\Lib\site-packages\Bio\EUtils\DTDs contains the .py, .pyc, and .pyo files. However, on Cygwin the *.dtd and *.py, *.pyc files both get installed into /usr/local/lib/python2.3/site-packages/Bio/EUtils/DTDs. Are these the correct locations? Is there a way to check if EUtils is working correctly? --Michiel Jeffrey Chang wrote: > Yuck, this was broken. > > Previously, the dtd installation was hacked in by modifying the > Distutils "install" command. This only gets called from unix, so > nothing was happening for bdist_wininst. The dtds were not getting > installed. > > I've gone back and reworked the dtd installation so that the dtd > filenames are passed into the Distutils.setup function as a data file. > However, the directory layout for python packages in windows and unix > are different. I took a best guess at how to do this for windows based > on what I've seen documented on the web. > > Michiel, do you mind checking this again and seeing whether it works on > windows? Specifically, I need to know 1) whether the ".dtd" files are > getting installed, 2) whether they are installed in the right place, and > 3) where they are installed if they are in the wrong place. > > Thanks, > Jeff > > > > On Saturday, September 13, 2003, at 11:54 PM, Michiel Jan Laurens de > Hoon wrote: > >> I tried to install the CVS version of Biopython with Cygwin and with >> Windows. On Cygwin, I don't get any errors. On Windows, I am still >> getting the error with EUtils\DTDs. It wasn't clear to me from CVS if >> the fix for this error has been committed yet, so maybe I should just >> try again later. >> >> --Michiel. >> >> $ /cygdrive/c/Python23/python setup.py bdist_wininst >> ... >> error: build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs: No such file >> or directory >> >> >> Jeffrey Chang wrote: >> >>> Hello everybody, >>> It's about time to make a release that fixes the Martel install bug. >>> I've fixed this in the version in the CVS. Could everyone please try >>> it out? If things go smoothly, I'll make a release later this week. >>> The main changes in this version will be: >>> Martel - The setup script was not detecting that Martel would be >>> installed, and complained that it was missing. This is now fixed. >>> EUtils DTDs - Brad fixed this in setup.py. This will go into the >>> release. >>> Numeric Python - If numeric is missing, Bio.Cluster does not compile. >>> Thus, the setup script now only install Bio.Cluster if Numeric is >>> installed. I have documented this dependency in README. >>> There are also some other miscellaneous changes I've documented in >>> the NEWS file. >>> Also, test_Time.py in the Martel regression tests is failing. Can >>> someone fix this? >>> Jeff >>> _______________________________________________ >>> Biopython-dev mailing list >>> Biopython-dev@biopython.org >>> http://biopython.org/mailman/listinfo/biopython-dev >> >> >> -- >> 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 >> >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev > > > > -- 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 jchang at jeffchang.com Mon Sep 15 23:26:42 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] maintenance release In-Reply-To: <3F666A52.9060206@ims.u-tokyo.ac.jp> Message-ID: <979298FE-E7F5-11D7-B873-000A956845CE@jeffchang.com> > I tried this on Windows. I don't get any error messages when compiling > and building the installer. > > The *.dtd files get installed in C:\Python23\Bio\EUtils\DTDs, while > C:\Python23\Lib\site-packages\Bio\EUtils\DTDs contains the .py, .pyc, > and .pyo files. Hmm, I want the .dtd files to be in the same place as the .py files. Can you try making a slight change to the setup.py file and see if it does that? Please replace the line: if sys.platform == 'win32': with: if 0 and sys.platform == 'win32': > However, on Cygwin the *.dtd and *.py, *.pyc files both get installed > into /usr/local/lib/python2.3/site-packages/Bio/EUtils/DTDs. Yep, that's what I want. > Are these the correct locations? Is there a way to check if EUtils is > working correctly? Not sure how to check, because I haven't used EUtils. However, this is how Brad (who has used EUtils) had set up the installer for Unix. Andrew, can you confirm? Jeff From mdehoon at ims.u-tokyo.ac.jp Tue Sep 16 00:02:12 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] maintenance release In-Reply-To: <979298FE-E7F5-11D7-B873-000A956845CE@jeffchang.com> References: <979298FE-E7F5-11D7-B873-000A956845CE@jeffchang.com> Message-ID: <3F668B44.2000502@ims.u-tokyo.ac.jp> > Please replace the line: > if sys.platform == 'win32': > with: > if 0 and sys.platform == 'win32': This puts the .dtd files in C:\Python23\Python23\lib\site-packages\Bio\EUtils\DTDs\. (Note the double Python23). However, the following does seem to work: dtd_path = os.path.join("Bio", "EUtils", "DTDs") if sys.platform == 'win32': path = os.path.join("Lib\\site-packages", dtd_path) else: path = os.path.join( os.path.split(os.__file__)[0], "site-packages", dtd_path) x = os.listdir(os.path.join(os.getcwd(), dtd_path)) x = [os.path.join(dtd_path, x) for x in x if x.endswith(".dtd")] DATA_FILES.append((path, x)) del dtd_path, path, x This puts the .dtd files in C:\Python23\lib\site-packages\Bio\EUtils\DTDs\. --Michiel. Jeffrey Chang wrote: >> I tried this on Windows. I don't get any error messages when compiling >> and building the installer. >> >> The *.dtd files get installed in C:\Python23\Bio\EUtils\DTDs, while >> C:\Python23\Lib\site-packages\Bio\EUtils\DTDs contains the .py, .pyc, >> and .pyo files. > > > Hmm, I want the .dtd files to be in the same place as the .py files. > Can you try making a slight change to the setup.py file and see if it > does that? > > Please replace the line: > if sys.platform == 'win32': > with: > if 0 and sys.platform == 'win32': > > >> However, on Cygwin the *.dtd and *.py, *.pyc files both get installed >> into /usr/local/lib/python2.3/site-packages/Bio/EUtils/DTDs. > > > Yep, that's what I want. > >> Are these the correct locations? Is there a way to check if EUtils is >> working correctly? > > > Not sure how to check, because I haven't used EUtils. However, this is > how Brad (who has used EUtils) had set up the installer for Unix. > Andrew, can you confirm? > > Jeff > > > -- 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 ngkc at starhub.net.sg Tue Sep 16 02:22:46 2003 From: ngkc at starhub.net.sg (Justin Ng) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Request for Copyright information for BioPython Message-ID: <1063693366.3f66ac36d78a0@cms2.starhub.net.sg> Dear Sir/Ms I need to find out the Copyright Regulation for the usage of BioPython program, will you be able to send me the detail information for this. Thanks Best Regards, Justin Ng "What you do in life, Echoes in eternity" Powered by Gee! - Wireless Access Anywhere From jchang at jeffchang.com Tue Sep 16 12:58:00 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] maintenance release In-Reply-To: <3F668B44.2000502@ims.u-tokyo.ac.jp> Message-ID: Cool, I've committed this. jeff On Monday, September 15, 2003, at 09:02 PM, Michiel Jan Laurens de Hoon wrote: > > Please replace the line: > > if sys.platform == 'win32': > > with: > > if 0 and sys.platform == 'win32': > > This puts the .dtd files in > C:\Python23\Python23\lib\site-packages\Bio\EUtils\DTDs\. > (Note the double Python23). > > However, the following does seem to work: > > dtd_path = os.path.join("Bio", "EUtils", "DTDs") > if sys.platform == 'win32': > path = os.path.join("Lib\\site-packages", dtd_path) > else: > path = os.path.join( > os.path.split(os.__file__)[0], "site-packages", dtd_path) > x = os.listdir(os.path.join(os.getcwd(), dtd_path)) > x = [os.path.join(dtd_path, x) for x in x if x.endswith(".dtd")] > DATA_FILES.append((path, x)) > del dtd_path, path, x > > This puts the .dtd files in > C:\Python23\lib\site-packages\Bio\EUtils\DTDs\. > > --Michiel. > > Jeffrey Chang wrote: > >>> I tried this on Windows. I don't get any error messages when >>> compiling and building the installer. >>> >>> The *.dtd files get installed in C:\Python23\Bio\EUtils\DTDs, while >>> C:\Python23\Lib\site-packages\Bio\EUtils\DTDs contains the .py, >>> .pyc, and .pyo files. >> Hmm, I want the .dtd files to be in the same place as the .py files. >> Can you try making a slight change to the setup.py file and see if it >> does that? >> Please replace the line: >> if sys.platform == 'win32': >> with: >> if 0 and sys.platform == 'win32': >>> However, on Cygwin the *.dtd and *.py, *.pyc files both get >>> installed into >>> /usr/local/lib/python2.3/site-packages/Bio/EUtils/DTDs. >> Yep, that's what I want. >>> Are these the correct locations? Is there a way to check if EUtils >>> is working correctly? >> Not sure how to check, because I haven't used EUtils. However, this >> is how Brad (who has used EUtils) had set up the installer for Unix. >> Andrew, can you confirm? >> Jeff > > -- > 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 chapmanb at uga.edu Fri Sep 19 03:30:59 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] BioSQL: patch for discussion In-Reply-To: <3F61FAEB.8090203@irisa.fr> References: <3F61FAEB.8090203@irisa.fr> Message-ID: <20030919073059.GA380@evostick.agtec.uga.edu> Hi Yves; > attached is a patch for bringing BioSQL to the current database schema, > since Brad seems too busy graduating :) Heh. Graduating. That would be a nice thing. I have heard that sometimes they let folks do that :-). Thanks much for these patches. I'm sorry I haven't had a chance to look at them earlier -- I have been fighting with this cluster for so many days and hours it's overall an ugly glazed over look that fills my eyes. I checked in your changes but couldn't fix the Test suite and new SQL because for some unknown reason I suddenly can't make the test suite load any SQL without complaining on the comments. I'm sure it is something foolish, but after a million straight hours on the computer I can't get it figured. Oh well, that'll get updated soon enough. > One of the things to discuss is that I broke the current interface: I > added the sequence version to the db items ids (breaking test_BioSQL's > assert item_ids == ['AF297471', 'AJ237582', 'L31939', 'M81224', > 'X55053', 'X62281']). I think this is necessary, since accession > numbers are not guaranteed unique... > > Another breakage vis-?-vis the test suite is that "no strand info" is > dignified by None instead of 0. Both of these changes make good sense. The test suite should really be updated to deal with them. I will do that real soon like when I regain my sanity (or if someone beats me to it :-). Checking-in-patches-and-making-no-sense-and-heading-to-sleep-ly yr's, Brad From andreas.kuntzagk at mdc-berlin.de Mon Sep 22 09:18:45 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] GenBank.NCBIDictionary Message-ID: <1064236733.12566.18.camel@sulawesi> Hi, i noticed that loading GenBank-record D32129 actually gives two records and the parser complains on this. This can be fixed by adding a retmax=y parameter to the efetch call. Greetings, Andreas From bugzilla-daemon at portal.open-bio.org Tue Sep 23 11:34:59 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [Bug 1523] New: Iterator broken in Bio.Blast.NCBIStandalone.Iterator Message-ID: <200309231534.h8NFYxVi025282@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1523 Summary: Iterator broken in Bio.Blast.NCBIStandalone.Iterator Product: Biopython Version: 1.10 Platform: All OS/Version: Linux Status: NEW Severity: minor Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: j.a.casbon@qmul.ac.uk The standard python iterator interface not implemented. Add: def __iter__(self): return self to class to fix, and raise StopIteration at end of file instead of: return None ------- 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 Sep 24 05:30:15 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [Bug 1523] Iterator broken in Bio.Blast.NCBIStandalone.Iterator Message-ID: <200309240930.h8O9UFNT026492@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1523 j.a.casbon@qmul.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From j.a.casbon@qmul.ac.uk 2003-09-24 05:30 ------- Changelog suggests this is fixed in 1.22 ------- 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 Sep 24 06:33:16 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [Bug 1524] New: Bio.Blast.Record.multiple_alignment should be in multiple alignment format Message-ID: <200309241033.h8OAXGJo030325@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1524 Summary: Bio.Blast.Record.multiple_alignment should be in multiple alignment format Product: Biopython Version: 1.10 Platform: All OS/Version: Linux Status: NEW Severity: enhancement Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: j.a.casbon@qmul.ac.uk I think Bio.Blast.Record.multiple_alignment should return an instance of Bio.Align.Generic rather than a list of tuples. Maybe this is a matter of taste, but it perhaps warrants another method implementing this feature. This method will convert, if this helps: def blast_alignment_to_generic(b_record): seq = {} for frag in b_record.multiple_alignment.alignment: if frag[0] in seq: seq[frag[0]] = seq[frag[0]] + frag[2] else: seq[frag[0]] = frag[2] generic = Alignment(IUPAC.IUPACProtein) for prot in seq: generic.add_sequence(prot, seq[prot]) return generic ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From andreas.kuntzagk at mdc-berlin.de Wed Sep 24 09:18:18 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] OT:Strange behaviour of traceback Message-ID: <1064409508.26107.8.camel@sulawesi> Maybe anybody has an explanation for the following: My Python-Programm is ----------------------- from Bio import GenBank def main(): p=GenBank.RecordParser() n=GenBank.NCBIDictionary(parser=p) n["Y07610"] if __name__ == "__main__": main() ----------------------- Test1: ----------------------- murple/swissprot_new> setenv PYTHONPATH /home/murple/cvs3/biopython/ murple/swissprot_new> python find_problematic_entries2.py Traceback (most recent call last): File "find_problematic_entries2.py", line 10, in ? main() File "find_problematic_entries2.py", line 7, in main n["Y07610"] File "/usr/lib/python2.2/site-packages/PIL/__init__.py", line 1563, in __getitem__ # ;-) KeyError: Empty information returned. ----------------------- Test2: ---------------------- murple/swissprot_new> unsetenv PYTHONPATH murple/swissprot_new> python find_problematic_entries2.py Traceback (most recent call last): File "find_problematic_entries2.py", line 10, in ? main() File "find_problematic_entries2.py", line 7, in main n["Y07610"] File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1565, in __getitem__ raise KeyError, "Empty information returned." KeyError: Empty information returned. --------------------- where home/murple/cvs3/biopython/ is my directory with a slightly modified biopython. But _NO_WAY_ im using PIL anywhere! And there is no line 1563 in /usr/lib/python2.2/site-packages/PIL/__init__.py (this is a short file with only comments). So it seems, traceback is broken. Did anybody see something like that ever before? I skimmed the Python bug database on sourceforge but where unable to find anything like this. I would file a bug, but for this I have to strip this down to a non-biopython bug. At the moment I don't have the time, maybe in october. Andreas From mdehoon at ims.u-tokyo.ac.jp Wed Sep 24 23:16:42 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] Documentation Message-ID: <3F725E1A.1030407@ims.u-tokyo.ac.jp> Dear biopythoneers, Currently, the documentation for Bio.Cluster is available from my website only. Would it be possible to make a link to it from the Biopython documentation page? On a related note, the Biopython documentation seems to be lagging behind. Is there some way to add or submit documentation, and is there some format to adhere to? If users are looking at the code to understand how to use it, it would be nice if they could submit documentation based on what they just learned to make things easier for the next user. --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 jchang at jeffchang.com Mon Sep 22 14:01:18 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] incomplete patch to parse Genbank-TPA record BK000008 In-Reply-To: <200309151449.21720.Peter.Bienstman@ugent.be> Message-ID: On Monday, September 15, 2003, at 05:49 AM, Peter Bienstman wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > On Monday 15 September 2003 13:06, Andreas Kuntzagk wrote: >> Since I'm stuck with this, I'm giving you the incomplete patch in >> hope, >> somebody will have time to look at it. At the moment it parses the >> BK000008 and BK000018 entries in GenBank and hopefully others as well. >> >> BUT: the information is put into the Record only in form of one long >> string with newlines deleted. If anybody really neads this info, it >> should be stored in a better way. > > Thanks for looking into this! > > My personal view is that it's better to have a patch that parses the > records > (even though it lumps the info), rather than no patch at all. > > Jeff, what do you think, can we commit this? Yes, I agree. I've patched it, and will commit it to CVS shortly. Thanks for the patch, Andreas, and Peter for checking it over. Jeff From jchang at jeffchang.com Thu Sep 25 03:55:37 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] GenBank.NCBIDictionary In-Reply-To: <1064236733.12566.18.camel@sulawesi> Message-ID: Hi Andreas, Do you mean retmax=1? If I do retmax=y, I get an error, "Empty information returned." What does retmax do? Does it just drop everything after the first match? Are you sure this is what you want it to do? Jeff On Monday, September 22, 2003, at 06:18 AM, Andreas Kuntzagk wrote: > Hi, > > i noticed that loading GenBank-record D32129 actually gives two records > and the parser complains on this. This can be fixed by adding a > retmax=y > parameter to the efetch call. > > Greetings, Andreas > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From the_murple at gmx.de Sat Sep 27 09:05:09 2003 From: the_murple at gmx.de (Andreas Kuntzagk) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] NCBIDictionary and staff ... Message-ID: <10663.1064667909@www68.gmx.net> Hi Jeffrey and others, I`m sending this from my privat account because I`m in Paris for ECCB and haven`t figured out how to access my work smtp-server, but can read email. Regarding the retmax value on efetch, yeah should be retmax=1, i _think_ it gives the maximum number of returned entries. I`ve to recheck later on the etools manual. If I remember right, for my example of two entries with same accession, the most recent came back if I used retmax = 1. So this was maybe more of a workaround for my problem then a general fix. by from Paris, Andreas -- Andreas "Murple" Kuntzagk mailto:the_murple@gmx.de snail_mail: Andreas Kuntzagk, Glatzer Stra?e 5, 10247 Berlin NEU F?R ALLE - GMX MediaCenter - f?r Fotos, Musik, Dateien... Fotoalbum, File Sharing, MMS, Multimedia-Gru?, GMX FotoService Jetzt kostenlos anmelden unter http://www.gmx.net +++ GMX - die erste Adresse f?r Mail, Message, More! +++ From bugzilla-daemon at portal.open-bio.org Mon Sep 29 12:53:43 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:27 2005 Subject: [Biopython-dev] [Bug 1531] New: Bio.Fasta.RecordParser, SequenceParser Message-ID: <200309291653.h8TGrhDY014417@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1531 Summary: Bio.Fasta.RecordParser, SequenceParser Product: Biopython Version: Not Applicable Platform: Sun OS/Version: SunOS Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: ktdiedrich@yahoo.com The Bio.Fasta RecordParser and SequenceParser can only handle FASTA sequence files with spaces between the records ie > name 1 aggcgcgatcgatg cgagcatcagcgag acgata > name 2 aaggcttagcatcg cacgcatcaa But many FASTA sequence files are statcked together > name 1 aggcgcgatcgatg cgagcatcagcgag acgata > name 2 aaggcttagcatcg cacgcatcaa They also can't hangle empty lines at the beginning of the FastaSequence file. The error occurs in line 300 Bio/ParserSupport.py The RecordParser.parse() definition also doesn't advance the file handle position when it gets to the end of the file handle. It keeps returning the last record so a loop reading records never ends. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.