From ulask at bu.edu Tue Jul 1 18:10:25 2003 From: ulask at bu.edu (ulas karaoz) Date: Tue Jul 1 17:10:41 2003 Subject: [BioPython] Installation problem:triemodules.c Message-ID: Hi, I have downloaded version 1.10 and tried to installed it on Mac OSX. This gave a warning in trie.h and lots of errors in triemodules.c I think triemodules.c is not updated: static char trie__doc__[] = " Should be static char trie__doc__[] = "\ Am I right? Thanks. Ulas. From jchang at jeffchang.com Tue Jul 1 15:50:40 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Tue Jul 1 17:50:16 2003 Subject: [BioPython] Installation problem:triemodules.c In-Reply-To: Message-ID: <0E8853BC-AC0E-11D7-A19B-000A956845CE@jeffchang.com> Yes. It's been fixed in the latest version. Thanks, Jeff On Tuesday, July 1, 2003, at 02:10 PM, ulas karaoz wrote: > Hi, > I have downloaded version 1.10 and tried to installed it on Mac OSX. > This gave a warning in trie.h and lots of errors in triemodules.c > I think triemodules.c is not updated: > > static char trie__doc__[] = > " > > Should be > > static char trie__doc__[] = > "\ > > Am I right? > Thanks. > Ulas. > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From idoerg at burnham.org Tue Jul 1 15:55:19 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue Jul 1 17:55:48 2003 Subject: [BioPython] logo vote results In-Reply-To: <0E8853BC-AC0E-11D7-A19B-000A956845CE@jeffchang.com> References: <0E8853BC-AC0E-11D7-A19B-000A956845CE@jeffchang.com> Message-ID: <3F020347.7010609@burnham.org> Jeff, who's the winner? ./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://ffas.ljcrf.edu/~iddo From ulask at bu.edu Tue Jul 1 19:00:28 2003 From: ulask at bu.edu (ulas karaoz) Date: Tue Jul 1 18:00:41 2003 Subject: [BioPython] BLOCKS parser and BLIMPS driver in biopython Message-ID: Hi again, I am a new user of biopython, is there a Blocks parser in it, and also things related to Blimps. Would it be useful to contribute those? Thanks. From idoerg at burnham.org Tue Jul 1 16:08:50 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue Jul 1 18:09:20 2003 Subject: [BioPython] BLOCKS parser and BLIMPS driver in biopython In-Reply-To: References: Message-ID: <3F020672.4030404@burnham.org> Nope, no BLOCKS or BLIMPS parsers, and yes, it would be great to have those! Iddo ulas karaoz wrote: > Hi again, > I am a new user of biopython, is there a Blocks parser in it, and also > things related to Blimps. > Would it be useful to contribute those? > Thanks. > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- 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 jefftc at stanford.edu Wed Jul 2 00:07:07 2003 From: jefftc at stanford.edu (Jeffrey Chang) Date: Wed Jul 2 02:06:42 2003 Subject: [BioPython] logo vote results In-Reply-To: <3F020347.7010609@burnham.org> Message-ID: <691FA47F-AC53-11D7-941A-000A956845CE@stanford.edu> On Tuesday, July 1, 2003, at 02:55 PM, Iddo Friedberg wrote: > Jeff, who's the winner? > > ./I Hello Everyone (and Iddo :), First of all, thank you very much for everyone that submitted logos, contributed to their design, and to everyone that voted! In the end, we received 20 votes for 9 proposed logos. (Curiously, I did not receive votes from some people who had submitted logos!) I tallied the votes according to instant run-off voting. At every round, I eliminated the logo that had received the least 1st place picks. In the end, by a slim margin of 3 votes, the last logo standing was by the team of Henrik Vestergaard and Thomas Hamelryck. Congratulations, Henrik and Thomas! Now the work part. We will need versions of the logo appropriate for: - slides - webpage - icon Should Henrik and Thomas be unable to fulfill their duties, the runner up Gyro Funch will be called upon to become Logo King. Thus concludes the Biopython logo contest. I hope everyone had fun! Jeff From andreas.kuntzagk at mdc-berlin.de Wed Jul 2 09:54:01 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Wed Jul 2 04:54:02 2003 Subject: [BioPython] locations Message-ID: <1057136027.17645.46.camel@sulawesi> Hi, I want to do the following: Starting whith a GB entry, i search for a feature. Then I look into the location of the feature. (easy) Now, e.g. the location is join(SEQ1:1..5,SEQ2:4..7) (or more complex) I want to get the sequence for this location (assuming SEQ1 and SEQ2 are stored somewhere local), also I want the get for a position inside the location the position in the corresponding entry. Looking through the code, I assume GFF.easy would be a good starting point. Do you agree? Btw. what GFF stands for? It's not an acronym I know. Also GFF.easy defines a ambiguous_rna_complement starting from Bio.Data.IUPACData.ambiguous_dna_complement. Wouldn't this fit better into Bio.Data.IUPACData as well? Ciao, Andreas From Yves.Bastide at irisa.fr Wed Jul 2 15:35:40 2003 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Wed Jul 2 10:04:31 2003 Subject: [BioPython] Some proposed code-cleanup In-Reply-To: <1FD473A0-A593-11D7-9E09-000A956845CE@jeffchang.com> References: <1FD473A0-A593-11D7-9E09-000A956845CE@jeffchang.com> Message-ID: <3F02D19C.6080800@irisa.fr> Jeffrey Chang wrote: > > On Monday, June 23, 2003, at 01:58 AM, Andreas Kuntzagk wrote: >> [...] >> >> I'm sorry. I tried the regression tests and all seemed fine. What I >> didn't notice was, the tests used my already installed biopython and not >> the code from the build-directory. Grr, why do I keep tripping over this >> errors? Shouldn't the "python setup.py test" use the directory it is >> positioned in? If it is required to set PYTHONPATH before test, it >> should be mentioned in the README. I will look into the problems now to >> see if I could find out. > > > Yes, we should do something about this. It has caused us problems many > times. Probably the best thing to do is to modify run_tests.py to: > - identify its directory > - insert the build path (../build/lib.XXX/Bio, etc) to the front of > sys.path, if it exists > - insert the source path (../Bio) to the front of sys.path, if it exists > Here's a patch to run_tests.py. Should do the right thing... > Jeff yves -------------- next part -------------- Index: Tests/run_tests.py =================================================================== RCS file: /home/repository/biopython/biopython/Tests/run_tests.py,v retrieving revision 1.6 diff -u -p -r1.6 run_tests.py --- Tests/run_tests.py 2001/12/17 21:24:51 1.6 +++ Tests/run_tests.py 2003/07/02 12:31:17 @@ -25,7 +25,24 @@ import getopt # PyUnit import unittest +import distutils.util + def main(argv): + # insert our pathes in sys.path: + # ../build/lib.* + # .. + # Q. Why this order? + # A. To find the C modules (which are in ../build/lib.*/Bio) + # Q. Then, why ".."? + # A. Because Martel may not be in ../build/lib.* + test_path = sys.path[0] or "." + source_path = os.path.abspath("%s/.." % test_path) + sys.path.insert(1, source_path) + build_path = os.path.abspath("%s/../build/lib.%s-%s" % ( + test_path, distutils.util.get_platform(), sys.version[:3])) + if os.access(build_path, os.F_OK): + sys.path.insert(1, build_path) + # start off using the GUI use_gui = 1 From jchang at jeffchang.com Wed Jul 2 09:01:34 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Wed Jul 2 11:01:12 2003 Subject: [BioPython] Some proposed code-cleanup In-Reply-To: <3F02D19C.6080800@irisa.fr> Message-ID: <122E0645-AC9E-11D7-A9D7-000A956845CE@jeffchang.com> Great patch! I've committed it to the source tree. Thanks, Jeff On Wednesday, July 2, 2003, at 05:35 AM, Yves Bastide wrote: > Jeffrey Chang wrote: >> On Monday, June 23, 2003, at 01:58 AM, Andreas Kuntzagk wrote: >>> [...] >>> >>> I'm sorry. I tried the regression tests and all seemed fine. What I >>> didn't notice was, the tests used my already installed biopython and >>> not >>> the code from the build-directory. Grr, why do I keep tripping over >>> this >>> errors? Shouldn't the "python setup.py test" use the directory it is >>> positioned in? If it is required to set PYTHONPATH before test, it >>> should be mentioned in the README. I will look into the problems now >>> to >>> see if I could find out. >> Yes, we should do something about this. It has caused us problems >> many times. Probably the best thing to do is to modify run_tests.py >> to: >> - identify its directory >> - insert the build path (../build/lib.XXX/Bio, etc) to the front of >> sys.path, if it exists >> - insert the source path (../Bio) to the front of sys.path, if it >> exists > > Here's a patch to run_tests.py. Should do the right thing... > >> Jeff > > yves > Index: Tests/run_tests.py > =================================================================== > RCS file: /home/repository/biopython/biopython/Tests/run_tests.py,v > retrieving revision 1.6 > diff -u -p -r1.6 run_tests.py > --- Tests/run_tests.py 2001/12/17 21:24:51 1.6 > +++ Tests/run_tests.py 2003/07/02 12:31:17 > @@ -25,7 +25,24 @@ import getopt > # PyUnit > import unittest > > +import distutils.util > + > def main(argv): > + # insert our pathes in sys.path: > + # ../build/lib.* > + # .. > + # Q. Why this order? > + # A. To find the C modules (which are in ../build/lib.*/Bio) > + # Q. Then, why ".."? > + # A. Because Martel may not be in ../build/lib.* > + test_path = sys.path[0] or "." > + source_path = os.path.abspath("%s/.." % test_path) > + sys.path.insert(1, source_path) > + build_path = os.path.abspath("%s/../build/lib.%s-%s" % ( > + test_path, distutils.util.get_platform(), sys.version[:3])) > + if os.access(build_path, os.F_OK): > + sys.path.insert(1, build_path) > + > # start off using the GUI > use_gui = 1 > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From bartek at rezolwenta.eu.org Thu Jul 3 03:16:44 2003 From: bartek at rezolwenta.eu.org (Bartek Wilczynski) Date: Wed Jul 2 20:15:11 2003 Subject: [BioPython] Gene Ontology interface Message-ID: <1057191404.3f0375eccef0e@imp.rezolwenta.eu.org> Hi All, I was wondering if there is any kind of support for Gene Ontology (http://www.geneontology.org) in BioPython. I'm about to write somrthing myself just thought it might be a good idea to ask if someone has done it before. thanks -- regards Bartek Wilczy?ski From jchang at jeffchang.com Wed Jul 2 18:51:00 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Wed Jul 2 20:50:48 2003 Subject: [BioPython] Gene Ontology interface In-Reply-To: <1057191404.3f0375eccef0e@imp.rezolwenta.eu.org> Message-ID: <6A44A80E-ACF0-11D7-96A1-000A956845CE@jeffchang.com> Yes, Biopython is missing support for Gene Ontology. There is support for it in bioperl, so you can either directly use that, or "borrow" their API's or ideas for a python interface. Jeff On Wednesday, July 2, 2003, at 05:16 PM, Bartek Wilczynski wrote: > Hi All, > > I was wondering if there is any kind of support for Gene Ontology > (http://www.geneontology.org) in BioPython. I'm about to write > somrthing myself > just thought it might be a good idea to ask if someone has done it > before. > > thanks > > -- > regards > Bartek Wilczy?ski > > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From cheung_auyeung at yahoo.com Fri Jul 4 14:26:29 2003 From: cheung_auyeung at yahoo.com (Cheung Auyeung) Date: Fri Jul 4 16:26:03 2003 Subject: [BioPython] New User problem with GenBank Message-ID: <3F05E2F5.6050804@yahoo.com> Hi I try to follow the GenBank tortorila from the Biopython Tutorial and Cookbook and I get the following error messages: auyeung@sunday auyeung]$ python Python 2.2.2 (#1, Feb 24 2003, 19:13:11) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from Bio import GenBank >>> gi_list = GenBank.search_for("Opuntia AND rpl16") >>> record_parser = GenBank.FeatureParser() >>> ncbi_dict = GenBank.NCBIDictionary(parser = record_parser) >>> gb_seqrecord = ncbi_dict[gi_list[0]] Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1563, in __getitem__ return self.parser.parse(handle) File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 268, in parse self._scanner.feed(handle, self._consumer) File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1255, in feed self._parser.parseFile(handle) File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 338, in parseFile self.parseString(fileobj.read()) File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 366, in parseString self._err_handler.fatalError(result) File "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserPositionException: error parsing at or beyond character 1108 Any suggestion to fix the problem? Thanks Cheung From Peter.Bienstman at ugent.be Sun Jul 6 22:01:25 2003 From: Peter.Bienstman at ugent.be (Peter Bienstman) Date: Sun Jul 6 15:00:51 2003 Subject: [BioPython] New User problem with GenBank In-Reply-To: <3F05E2F5.6050804@yahoo.com> References: <3F05E2F5.6050804@yahoo.com> Message-ID: <200307062101.25391.Peter.Bienstman@ugent.be> On Friday 04 July 2003 22:26, Cheung Auyeung wrote: > Hi > > I try to follow the GenBank tortorila from the Biopython Tutorial and > Cookbook and I get the following error messages: > > auyeung@sunday auyeung]$ python > Python 2.2.2 (#1, Feb 24 2003, 19:13:11) > [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > > >>> from Bio import GenBank > >>> gi_list = GenBank.search_for("Opuntia AND rpl16") > >>> record_parser = GenBank.FeatureParser() > >>> ncbi_dict = GenBank.NCBIDictionary(parser = record_parser) > >>> gb_seqrecord = ncbi_dict[gi_list[0]] Hi Cheung, GenBank searches currently time out for me, so I cannot reproduce the problem at the moment. Have you tried upgrading to the latest CVS version of BioPython? It's possible that after the tutorial was written, additional new GenBank records now satisfy the search criterion, and that these new records need the fixes in CVS. Hope this helps, 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 nandan at ibioinformatics.org Mon Jul 7 13:39:27 2003 From: nandan at ibioinformatics.org (nandan) Date: Mon Jul 7 02:43:41 2003 Subject: [BioPython] Blast local implementation : Query abt graphical overview module Message-ID: <20030707123927.12504.qmail@ns1.irisitech.com> Hello Sir, My name is Nandan Deshpande and I work as a Research Scientist in "Institute of Bioinformatics", Bangalore, India. Ours is a "Not-for-profit" research organization and we work in the area of genetics and Bioinformatics in particular. I have implemented "BLAST" locally on my server. The problem is the local implementation does not come with the "graphical overview". I have confirmed with "BLAST" guys that they do not provide graphical overview for local implementation. Does BioPython have any such module? I would appreciate if you can assist me in this. Thanks and regards, Nandan Deshpande. IOB From fababasa at yahoo.fr Mon Jul 7 10:01:59 2003 From: fababasa at yahoo.fr (=?iso-8859-1?q?fababasa?=) Date: Mon Jul 7 03:01:20 2003 Subject: [BioPython] Blast local implementation : Query abt graphical overview module In-Reply-To: <20030707123927.12504.qmail@ns1.irisitech.com> Message-ID: <20030707070159.18611.qmail@web41411.mail.yahoo.com> Hi, To get the "graphical overview", you only need to install the standalone server version of BLAST (WWWBlast) from the following link : ftp://ftp.ncbi.nih.gov/blast/server/ good luck ! --- nandan a ?crit?: > Hello Sir, > > My name is Nandan Deshpande and I work as a > Research Scientist in > "Institute of Bioinformatics", Bangalore, India. > Ours is a "Not-for-profit" > research organization and we work in the area of > genetics and Bioinformatics > in particular. > > I have implemented "BLAST" locally on my server. > The problem is the local > implementation does not come with the "graphical > overview". I have confirmed > with "BLAST" guys that they do not provide graphical > overview for local > implementation. > > Does BioPython have any such module? I would > appreciate if you can assist > me in this. > > Thanks and regards, > > > Nandan Deshpande. > IOB > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython ___________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Yahoo! Mail : http://fr.mail.yahoo.com From sbassi at asalup.org Mon Jul 7 10:05:04 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Mon Jul 7 08:06:44 2003 Subject: [BioPython] Blast local implementation : Query abt graphical overview module In-Reply-To: <20030707123927.12504.qmail@ns1.irisitech.com> References: <20030707123927.12504.qmail@ns1.irisitech.com> Message-ID: <3F0961F0.8000707@asalup.org> nandan wrote: > My name is Nandan Deshpande and I work as a Research Scientist in > "Institute of Bioinformatics", Bangalore, India. Ours is a > "Not-for-profit" research organization and we work in the area of > genetics and Bioinformatics in particular. > I have implemented "BLAST" locally on my server. The problem is the > local implementation does not come with the "graphical overview". I have > confirmed with "BLAST" guys that they do not provide graphical overview > for local implementation. > Does BioPython have any such module? I would appreciate if you can > assist me in this. I'm working on that. Take a look here: http://genes.unq.edu.ar/guiblast/ It is still ALPHA stage software, not for general consumer. But it works. -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From cmcgruder at mcn.net Mon Jul 7 15:50:51 2003 From: cmcgruder at mcn.net (cmcgruder@mcn.net) Date: Mon Jul 7 17:50:14 2003 Subject: [BioPython] mod_python Message-ID: <5935146.1057614651818.JavaMail.nobody@dewey.psp.pas.earthlink.net> Hello, Do you know if anyone has tried using BioPython with Apache's mod_python? Thanks, Casey From andreas.kuntzagk at mdc-berlin.de Tue Jul 8 09:25:55 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Tue Jul 8 04:25:57 2003 Subject: [BioPython] mod_python In-Reply-To: <5935146.1057614651818.JavaMail.nobody@dewey.psp.pas.earthlink.net> References: <5935146.1057614651818.JavaMail.nobody@dewey.psp.pas.earthlink.net> Message-ID: <1057652755.1082.12.camel@sulawesi> Hi Casey, hi all, > Do you know if anyone has tried using BioPython with Apache's mod_python? I don't, but I used BioPython for CGIs. What do you plan to do whith mod_python? As I understand, mod_python only gives control over the apache-server. (right?) I don't see where there could be a possible use for mod_python whith BioPython. If you just want write simple CGIs, stick whith the cgi module of the python library. For more complex webapps, there are other options out there (Zope etc.) Never needed to use one of them. See http://www.python.org/cgi-bin/moinmoin/WebProgramming for an overview. HTH, Andreas From cmcgruder at mcn.net Tue Jul 8 09:39:16 2003 From: cmcgruder at mcn.net (cmcgruder@mcn.net) Date: Tue Jul 8 11:38:40 2003 Subject: [BioPython] mod_python Message-ID: <2281415.1057678756584.JavaMail.nobody@beaker.psp.pas.earthlink.net> Hi Andreas, Hi All, If you are developing with the Apache web server, the mod_python module embeds the Python interpreter directly into Apache, resulting in application execution speeds that supposedly rival Perl. If you're using Apache, using mod_python is not absolutely necessary but is recommended for most applications. It doesn't affect anything in your program other than the (perceived) execution speed because it eliminates the start up time for the interpreter with each connection. I am mainly interested in developing a web application that incorporates BioPython with mod_python to eliminate start up time for the interpreter for each connection. Does anyone know if BioPython is compatible with mod_python? TIA, Casey -------Original Message------- From: Andreas Kuntzagk Sent: 07/08/03 02:25 AM To: cmcgruder@mcn.net, BioPython Mailing List Subject: Re: [BioPython] mod_python > > Hi Casey, hi all, > Do you know if anyone has tried using BioPython with Apache's mod_python? I don't, but I used BioPython for CGIs. What do you plan to do whith mod_python? As I understand, mod_python only gives control over the apache-server. (right?) I don't see where there could be a possible use for mod_python whith BioPython. If you just want write simple CGIs, stick whith the cgi module of the python library. For more complex webapps, there are other options out there (Zope etc.) Never needed to use one of them. See http://www.python.org/cgi-bin/moinmoin/WebProgramming for an overview. HTH, Andreas > From andreas.kuntzagk at mdc-berlin.de Tue Jul 8 16:41:15 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Tue Jul 8 11:41:16 2003 Subject: [BioPython] mod_python In-Reply-To: <1057677943.24297.5.camel@charlie> References: <5935146.1057614651818.JavaMail.nobody@dewey.psp.pas.earthlink.net> <1057652755.1082.12.camel@sulawesi> <1057677943.24297.5.camel@charlie> Message-ID: <1057678875.1082.25.camel@sulawesi> Hi, > If you are developing with the Apache web server, the mod_python module > embeds the Python interpreter directly into Apache, resulting in > application execution speeds that supposedly rival Perl. Ahh, thanx. So I should turn on mod_python on my apache (it's installed but not configured.) > Does anyone know if BioPython is compatible with mod_python? What makes you think it's not? From your description I don't see, why it should break biopython aslong as apache can find it and the needed modules. Or are there any special hacks inside mod_python, which make it run only with some python-modules? Why don't you just try it? If it breaks your script, you can easily go back to normal cgi and tell us about it. ;-) I think, installing mod_python is not much work (from what i read, i just installed a rpm), so it should be worth the time. I'm looking forward to hear about your experiences. Andreas From krocea at yahoo.com.cn Wed Jul 9 11:54:45 2003 From: krocea at yahoo.com.cn (=?gb2312?q?yu=20huang?=) Date: Tue Jul 8 22:54:04 2003 Subject: [BioPython] BioSQL without commit Message-ID: <20030709025445.99671.qmail@web15311.mail.bjs.yahoo.com> Hello everybody, I write a program to load genbank files into the biodatabase following instructions in the tutorial given by Brad. When the program is running, everything is right and Records are all deposited in the biodatabases. However, When the program exits, there is no record physically residing in the biodatabase. SQL without commit may be the cause. Anyone give a clue? Yu Huang _________________________________________________________ Do You Yahoo!? 网恋的诠释：真情还是放纵？ http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/netlove From chapmanb at uga.edu Thu Jul 10 13:45:44 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Jul 10 12:48:17 2003 Subject: [BioPython] BioSQL without commit In-Reply-To: <20030709025445.99671.qmail@web15311.mail.bjs.yahoo.com> References: <20030709025445.99671.qmail@web15311.mail.bjs.yahoo.com> Message-ID: <20030710164544.GB89442@evostick.agtec.uga.edu> Hello; > I write a program to load genbank files into the > biodatabase following instructions in the tutorial > given by Brad. When the program is running, everything > is right and Records are all deposited in the > biodatabases. However, When the program exits, there > is no record physically residing in the biodatabase. > > SQL without commit may be the cause. > > Anyone give a clue? Right now you need to commit the changes and close the database after doing a load. This is not covered in the documentation because, uh, I forgot it. Thanks for pointing out my oversight. It is also an ugly way to do things so I should clean it up when I update BioSQL (hopefully soon, still way behind over here) in addition to documenting it. Any ideas about how to make it cleaner are gratefully accepted. Right now the thing to do after the load is: server.adaptor.conn.commit() server.adaptor.conn.close() and this should get everything committed. Probably the right thing to do is to have a database function so that you can do: db.load(iterator) db.commit_and_close() or something of that sort. Thanks for the question. Hope this helps! Brad From MCariaso at Endogenybio.com Thu Jul 10 14:18:20 2003 From: MCariaso at Endogenybio.com (Mike Cariaso) Date: Thu Jul 10 13:17:34 2003 Subject: [BioPython] mod_python (cmcgruder@mcn.net) Message-ID: I've used mod_perl, back in my perl days, and would like to raise one extra issue with mod_python & biopython. Since the interpreter is embedded into the webserver, it remains running for a very long time. Which is great for speed, but means that as the cgi is executed, it is not starting with a fresh clean memory space. Variables that are not explicitly reset to default values, will retain values from the previous cgi. Python will probably have less of this, since it seems to generate warning if a variable is used without being initialized, unlike perl's autovivication, which developers too often rely on. If there are any issues with mod_python & biopython this is likely to be the source. It's probably quite safe to use these two together, but if you notice any strange behavior this is a probable cause. Please report it back to the list if you find any such concerns. Michael Cariaso Director Bioinformatics Endogeny Bio Corp 9700 Great Seneca Highway Rockville, MD 20850 Tel: 240-453-8461 Fax: 301-424-4828 mcariaso@endogenybio.com From dalke at dalkescientific.com Fri Jul 11 00:52:54 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Fri Jul 11 01:51:07 2003 Subject: [BioPython] mod_python (cmcgruder@mcn.net) In-Reply-To: Message-ID: Mike Cariaso wrote: > Python will probably have less of this, since it seems to generate > warning if a variable is used without being initialized, unlike perl's > autovivication, which developers too often rely on. Actually, Python will raise an exception, so this is unlikely to be a problem. But I have no experience in this topic. Andrew dalke@dalkescientific.com From mohatafiq at o2.pl Fri Jul 11 17:35:53 2003 From: mohatafiq at o2.pl (TAFIQ MOHAMMED,) Date: Fri Jul 11 11:38:54 2003 Subject: [BioPython] NICE TO MEET YOU Message-ID: <200307111538.h6BFcVmG000484@localhost.localdomain> FROM: TAFIQ MOHAMMED. AMMAN JORDAN DEAR:Sir My Name is TAFIQ MOHAMMED, an Iraqis National from the Kurds an Accountant in Oil refinery in Durra. I am presently in Amman, Jordan Capital since U.S.strike Iraqi, few days to the expiration of the 48 hours Ultimatum before the strike. I moved $45.5M dollars call-deposit to Security Company in Iran for safe-keeping.In my capacity as the accountant to the oil refinery in durra, I was the only person aware of this financial transaction call-deposit with the security company in Iran to be released to whom I will introduce to the security company as the beneficiary of the call- deposit of $45.5M, whom the oil installation company is been owed since I can not be able to go to Iran because of the war. Now that the situation is not condusive for me to go to Iran, I am appealing to you if i can present you as the beneficiary of the call- deposit to the security company for the release of the deposit to your Account or any of your destination as part of the money being owed to you by Durra oil Refinery Company Iraq. As soon as this deposit is released to your Account by the security company in Iran or any of your destination,I will come over to meet you for disbursement 30%-70%. On your acceptance on this transaction I will send to you the deposit slip Certificate for the call deposit to you as the beneficiary to be release to you as part of the refunds owed to you by Durra Oil Refinery company Iraq.Or contact me through my alternative E-mailaddress:mohatafiq@o2.pl Awaiting your quick response, Best Regards, TAFIQ MOHAMMED, From service-south at epaper.com.tw Tue Jul 15 19:39:27 2003 From: service-south at epaper.com.tw (service-south) Date: Tue Jul 15 06:34:11 2003 Subject: [BioPython] (no subject) Message-ID: <200307151034.h6FAY5qs015548@localhost.localdomain> From MCariaso at Endogenybio.com Tue Jul 15 10:14:17 2003 From: MCariaso at Endogenybio.com (Mike Cariaso) Date: Tue Jul 15 09:13:22 2003 Subject: [BioPython] python equiv of perl's null operator <> Message-ID: Michael Cariaso Director Bioinformatics Endogeny Bio Corp 9700 Great Seneca Highway Rockville, MD 20850 Tel: 240-453-8461 Fax: 301-424-4828 mcariaso@endogenybio.com This is nothing specific to BIOpython about this, but I imagine many folks on this list may be able to help. After moving from perl to python I find I miss the ability to do a while (<>) { } which reads from either stdin or from files listed on the command line. Any other perl to python converts who've written a subroutine to emulate this, or perhaps a more pythonic idiom? Michael Cariaso Endogeny Bio Corp From dalke at dalkescientific.com Tue Jul 15 10:04:24 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue Jul 15 11:02:24 2003 Subject: [BioPython] python equiv of perl's null operator <> In-Reply-To: Message-ID: <9F06BE76-B6D5-11D7-B4E7-000393C92466@dalkescientific.com> Mike Cariaso: > After moving from perl to python I find I miss the ability to do a > > while (<>) { } Look at 'fileinput' in the standard library. However, using it will be slower than using, say try: args, filenames = getopt.getopt ... except getopt.error: ... if not filenames: filenames = ["-"] for filename in filenames: if filename == "-": infile = sys.stdin else: infile = file(filename) for line in infile: ... because 'fileinput' also preserves the line number, in-place filtering, and a few other perl-isms, implemented in Python, and not C as Perl does it. Andrew dalke@dalkescientific.com From sunnysheng55 at hotmail.com Thu Jul 17 22:13:52 2003 From: sunnysheng55 at hotmail.com (sheng ying) Date: Fri Jul 18 09:55:52 2003 Subject: [BioPython] some question about use biopython to blast Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biopython/attachments/20030717/4b1c3fbd/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: blast_question.doc Type: application/msword Size: 19456 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20030717/4b1c3fbd/blast_question-0001.doc -------------- next part -------------- A non-text attachment was scrubbed... Name: structure.doc Type: application/msword Size: 19456 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20030717/4b1c3fbd/structure-0001.doc From Peter.Bienstman at ugent.be Tue Jul 22 19:08:56 2003 From: Peter.Bienstman at ugent.be (Peter Bienstman) Date: Tue Jul 22 12:07:52 2003 Subject: [BioPython] New User problem with GenBank In-Reply-To: <3F05E2F5.6050804@yahoo.com> References: <3F05E2F5.6050804@yahoo.com> Message-ID: <200307221808.56253.Peter.Bienstman@ugent.be> FYI, I've confirmed that the parsing errors don't occur with the current CVS version, so the fix should be in the upcoming new release. Cheers, Peter On Friday 04 July 2003 22:26, Cheung Auyeung wrote: > Hi > > I try to follow the GenBank tortorila from the Biopython Tutorial and > Cookbook and I get the following error messages: > > auyeung@sunday auyeung]$ python > Python 2.2.2 (#1, Feb 24 2003, 19:13:11) > [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > > >>> from Bio import GenBank > >>> gi_list = GenBank.search_for("Opuntia AND rpl16") > >>> record_parser = GenBank.FeatureParser() > >>> ncbi_dict = GenBank.NCBIDictionary(parser = record_parser) > >>> gb_seqrecord = ncbi_dict[gi_list[0]] > > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line > 1563, in __getitem__ > return self.parser.parse(handle) > File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line > 268, in parse > self._scanner.feed(handle, self._consumer) > File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line > 1255, in feed > self._parser.parseFile(handle) > File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 338, > in parseFile > self.parseString(fileobj.read()) > File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 366, > in parseString > self._err_handler.fatalError(result) > File "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line > 38, in fatalError > raise exception > Martel.Parser.ParserPositionException: error parsing at or beyond > character 1108 > > Any suggestion to fix the problem? > > Thanks > > Cheung > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- ------------------------------------------------ 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 djaeggi at imim.es Wed Jul 23 19:29:29 2003 From: djaeggi at imim.es (Daniel Jaeggi) Date: Wed Jul 23 12:51:38 2003 Subject: [BioPython] BIND XML parser Message-ID: <200307231829.29551.djaeggi@imim.es> Hello! We're trying to parse BIND XML files. I know that a biopython version doesn't exist, but does anyone have one (written in any language) before we write our own. It would save a lot of time - the BIND specification looks really dense! Thanks, Daniel From f.crozet at free.fr Thu Jul 24 10:29:36 2003 From: f.crozet at free.fr (Fabien Crozet) Date: Thu Jul 24 03:28:26 2003 Subject: [BioPython] LocusLink Parser Message-ID: <200307240728.h6O7SLqr022426@localhost.localdomain> Hello everyone, I'm looking for a LocusLink parser. I wonder if there is one in Biopython... Anybody knows ? Thanks a lot for advices, Fabien From jchang at jeffchang.com Thu Jul 24 10:22:34 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Thu Jul 24 12:21:24 2003 Subject: [BioPython] LocusLink Parser In-Reply-To: <200307240728.h6O7SLqr022426@localhost.localdomain> Message-ID: <083B7EF5-BDF3-11D7-99F2-000A956845CE@jeffchang.com> Yes, Kayte Lindner was working on one at Bio.LocusLink. I do not know how well tested it is, though. Jeff On Thursday, July 24, 2003, at 01:29 AM, Fabien Crozet wrote: > Hello everyone, > I'm looking for a LocusLink parser. I wonder if there is one in > Biopython... > Anybody knows ? > Thanks a lot for advices, > Fabien > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From peterjung at quickemail.de Fri Jul 25 14:13:55 2003 From: peterjung at quickemail.de (peterjung@quickemail.de) Date: Fri Jul 25 07:14:13 2003 Subject: [BioPython] Falsche Adresse? Message-ID: <200307251113.h6PBDtgW025246@ns1.smart-weblications.de> Guten Tag. Wir hatten Sie bereits vor einigen Wochen angeschrieben und wollten Kontakt mit Ihrem Marketing- oder EDV Leiter aufnehmen. M鰃licherweise ist das Mail bei Ihnen oder bei uns verloren gegangen. Kurze Frage: Wer ist bei Ihnen der richtige Ansprechpartner f黵 Marketing/Internet/Werbung. Wir w黵den Ihnen gerne Unterlagen bez黦lich Suchmaschinenmarketing* zusenden und Ihnen eine kostenlose Analyse Ihre Seite anbieten. Eine kurze Info w鋜e nett. Mit freundlichen Gren Peter Jung Lyngbyhus Parallelvej 10 Copenhagen, 2800 Lyngby DENMARK *Suchmaschinenmarketing bringt Ihre Webseite sehr schnell bei Google oder yahoo auf die erste Seite. From andreas.kuntzagk at mdc-berlin.de Fri Jul 25 12:46:03 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Fri Jul 25 07:46:04 2003 Subject: [BioPython] Falsche Adresse? In-Reply-To: <200307251113.h6PBDtgW025246@ns1.smart-weblications.de> References: <200307251113.h6PBDtgW025246@ns1.smart-weblications.de> Message-ID: <1059133500.15989.58.camel@sulawesi> FYI, this is SPAM in German (despite address in Denmark). I just wrote a complain to abuse@quickemal.de because I think the email-adress is real (he is asking for a contact for marketing) I hope the will kick him out. Am Fre, 2003-07-25 um 13.13 schrieb peterjung@quickemail.de: > > Guten Tag. > > Wir hatten Sie bereits vor einigen Wochen angeschrieben und wollten Kontakt mit Ihrem Marketing- oder EDV Leiter aufnehmen. M?glicherweise ist das Mail bei Ihnen oder bei uns verloren gegangen. > > Kurze Frage: Wer ist bei Ihnen der richtige Ansprechpartner f?r Marketing/Internet/Werbung. Wir w?rden Ihnen gerne Unterlagen bez?glich Suchmaschinenmarketing* zusenden und Ihnen eine kostenlose Analyse Ihre Seite anbieten. > Eine kurze Info w?re nett. > > > Mit freundlichen Gr??en > > Peter Jung > > Lyngbyhus > Parallelvej 10 > Copenhagen, 2800 Lyngby DENMARK > > *Suchmaschinenmarketing bringt Ihre Webseite sehr schnell bei Google oder yahoo auf die erste Seite. > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From news4 at hot777.com Sat Jul 26 05:46:42 2003 From: news4 at hot777.com (=?ISO-2022-JP?B?GyRCJCIkLSRKGyhC?=) Date: Fri Jul 25 15:38:49 2003 Subject: [BioPython] =?iso-2022-jp?b?GyRCTCQ+NUJ6OS05cCIoJF4kQDRWJEsbKEI=?= =?iso-2022-jp?b?GyRCOWckJiEqGyhC?= Message-ID: <20030726.0446420291.babaq@news4-hot777.com> ???? ???????news1@hot777.com????????? ????????? ????????????? ????????????? [???????]?????? ?????????????? http://7855.tv/?epc ????(@?@? ???????1-3-9-803 045-313-0280 From nzanzaluzy at spinfinder.com Sun Jul 27 02:16:15 2003 From: nzanzaluzy at spinfinder.com (MR.LUZIZILA NZANZA) Date: Sat Jul 26 20:22:02 2003 Subject: [BioPython] PLEASE GET BACK TO ME Message-ID: <200307270021.h6R0Ln4T003761@localhost.localdomain> ATTN.SIR/MADAM GOOD DAY, MY NAME IS LUZIZILA NZANZA FROM CONGO NATIONAL FROM THE KURDS. I AM THE SON IN-LAW TO WILLIAMS NGUESSO, A SENIOR GOVERNMENT OFFICIAL OF CONGO WHO WAS RECENTLY IMPLICATED IN AN OIL DEAL IN THE COUNTRY AND WHO IS CURRENTLY UNDER DETENTION AND TRIAL. I CAME TO KNOW ABOUT YOU AFTER MAKING SEVERAL RESEARCH ABOUT VERY HONEST, TRUSTWORTHY AND GOD FEARING PERSON, I DISCOVERED THAT THIS FUND CAN BE PROPERLY INVESTED IN YOUR COUNTRY, MY FATHER AND HIS TOP GOVERNMENT OFFICIAL WHO WAS INVOLVED IN THE GROSS EMBEZZLEMENT, FINANCIAL MISAPPROPRIATION, AND OIL THEFT THAT OCCURED AT THE CONGOLESE OIL COMPANY (HYDRO-CONGO) SOMETIME IN THE YEAR 2002, AND WHICH WAS VASTLY PUBLICISED BY ONE OF THE WORLDS LEADING NEWS CHANNELS, BBC NEWS. FOR MORE INFORMATION ON THE MATTER, CLICK ON THIS WEBPAGE: http://news.bbc.co.uk/1/hi/world/africa/1100852.stm MY FATHER IN-LAW WAS ABLE TO SYPHONE THE SUM OF US$42.8 MILLION. THIS MONEY WAS TAKEN ABROAD WITH HIS CONTACTS IN GOVERNMENT AND HAS BEEN DEPOSITED IN MY NAME WITH A SECURITY COMPANY AS FAMILY VAULABLE OLD ART WORKS,THROUGH A DIPLOMATIC MEANS,WHICH ALL THE VALUABLE DOCUMENT WAS HANDED OVER TO ME, ALL I NEED FROM YOU NOW IS FOR YOU TO HELP ME CLEAR IT OUT, THE NAME I AM NOT GOING TO DISCLOSE NOW FOR SECURITY REASONS,AND ALL DOCUMENTS REGARDS THE DEPOSIT ARE WITH ME,SINCE MY FAMILY HAVE BEEN FACING PRESSURE FROM THE PRESENT GOVERNMET AND PEOPLE OF MY COUNTRY,WE HAVE TO RUN AWAY SINCE OUR HOUSE WAS SET ON FIRE BY ANGRY MOBS,HIS WIFE AND TWO HIS SISTER AND ARE LIVING NOW IN A REFUGEE CAMP IN ONE OF THE AFRICAN-CONTRY. UNTIL I HEAR FROM YOU. I WILL GREATLY APPRECIATE YOUR KIND AND VERY HONEST ASSISTANCE IN INVESTING THIS MONEY IN YOUR COUNTRY, I will then inform you on how you will safeguard my share{68%}for investment in your country as l have decided to offer you {32%}. On your acceptance on this transaction I will send to you the deposit slip Certificate for the call deposit.I WILL GIVE YOU A COMPREHENSIVE BREAKDOWN ON HOW THIS TRANSACTION WILL WORK OUT IMMEDIATELY I HEAR FROM YOU. I WANT TO GIVE YOU MY UTMOST ASSURANCE THAT THIS TRANSACTION WILL NOT TAKE US MORE THAN TEN DAYS TO FINISH EVERYTHING. URGENTLY AWAITING YOUR RESPONSE. BEST REGARDS LUZIZILA NZANZA From jefftc at stanford.edu Sun Jul 27 20:45:06 2003 From: jefftc at stanford.edu (Jeffrey Chang) Date: Sun Jul 27 20:45:11 2003 Subject: [BioPython] Biopython 1.20 released Message-ID: Hello Everybody, After months of work, Biopython 1.20 has been released! This release includes substantial new features including: - Andrew Dalke EUtils library for accessing databases at NCBI - Michiel de Hoon's gene expression analysis package - Thomas Hamelryck's PDB package. It also contains a bunch of the usual bug fixes and incremental updates. All users are encouraged to upgrade to this version. The change notes are appended to the end of this file. The sources are now available at: http://www.biopython.org/download/ As usual, please report any bugs, problems, or comments to biopython-dev@biopython.org . Many thanks to the people who have contributed to this release! Jeff The Biopython Consortium added Andrew Dalke's EUtils library added Michiel de Hoon's gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman's fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi submitted code to calculate LCC complexity Greg Kettler's NCBIStandalone fix for long query lengths slew of miscellaneous fixes from George Paci miscellaneous cleanups and updates from Andreas Kuntzagk Peter Bienstman's fixes to Genbank code -- now parses whole database Kayte Lindner's LocusLink package miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman miscellaneous BLAST fixes and updates Iddo added new code to parse BLAST table output format Karl Diedrich's patch to read T_Coffee files Larry Heisler's fix for primer3 output Bio.Medline now uses proper iterator objects copen now handles SIGTERM correctly small bugfixes and updates in Thomas Hamelryck's PDB package bugfixes and updates to SeqIO.FASTA reader updates to Registry system, conforms to 2003 hackathon OBDA spec Yu Huang patch to support tblastn in wublast expression From piet at clondiag.com Mon Jul 28 09:56:23 2003 From: piet at clondiag.com (Peter Slickers) Date: Mon Jul 28 09:52:37 2003 Subject: [BioPython] Biopython 1.20 released In-Reply-To: <20030707070159.18611.qmail@web41411.mail.yahoo.com> References: <20030707070159.18611.qmail@web41411.mail.yahoo.com> Message-ID: <3F252B87.4000001@clondiag.com> The newly released archive I have obtained from http://www.biopython.org/download/ in incomplete. The whole './Martel' subdirectory is missing. As a result of this, it is impossible to run python setup.py successfully in the main directory. But this problem ONLY occurs when no Martel is installed at all. If you already have a Martel from a previous biopython installation, that code is used and no errors occur. Is it intended to distribute Martel as a standalone package? ---------------------------------------------------------------- To reproduce the error, you have to remove any old Martel before starting the new installation: cd $somewhere/lib/python2.2/site-packages/ mv Martel Martel_old cd $elsewhere tar zxf biopython-1.20.tar.gz cd biopython-1.20 python setup.py build running build running build_py Traceback (most recent call last): File "setup.py", line 382, in ? ext_modules=EXTENSIONS, File "/data/bioexe/lib/python2.2/distutils/core.py", line 138, in setup dist.run_commands() File "/data/bioexe/lib/python2.2/distutils/dist.py", line 902, in run_commands self.run_command(cmd) File "/data/bioexe/lib/python2.2/distutils/dist.py", line 922, in run_command cmd_obj.run() File "/data/bioexe/lib/python2.2/distutils/command/build.py", line 107, in run self.run_command(cmd_name) File "/data/bioexe/lib/python2.2/distutils/cmd.py", line 330, in run_command self.distribution.run_command(command) File "/data/bioexe/lib/python2.2/distutils/dist.py", line 922, in run_command cmd_obj.run() File "setup.py", line 140, in run if not is_Martel_installed(): File "setup.py", line 192, in is_Martel_installed del sys.modules["Martel"] # Delete the old version of Martel. KeyError: Martel -- 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 absmythe at ucdavis.edu Mon Jul 28 15:15:10 2003 From: absmythe at ucdavis.edu (ashleigh smythe) Date: Mon Jul 28 15:15:11 2003 Subject: [BioPython] biopython clustalw command line question Message-ID: <1059419714.765.16.camel@nate.ucdavis.edu> Hello. I'm trying to use clustalw through biopython for the first time. I'm following the tutorial but it doesn't show the syntax for setting the multiple alignment parameters. From the __init__ I figured out that it is something like gap_open_pen=desired value so I tried cline.gap_open_pen=20 but when I try to show that command line string I get an error: >>> cline=MultipleAlignCL(os.path.join(os.curdir, 'aligntest')) >>> cline.set_output('alignout.aln') >>> cline.gap_open_pen=20 >>> cline.gap_ext_pen=10 >>> str(cline) Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line 420, in __str__ cline = cline + " -GAPOPEN=" + self.gap_open_pen TypeError: cannot concatenate 'str' and 'int' objects How do I set those values properly? Thanks very much for any suggestions. Ashleigh -- **************************** Ashleigh B. Smythe Graduate Research Assistant Department of Nematology University of California, Davis, CA 95616 email:absmythe@ucdavis.edu phone:530-754-4321 From jchang at smi.stanford.edu Mon Jul 28 19:21:41 2003 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Mon Jul 28 19:21:41 2003 Subject: [BioPython] Biopython 1.21 released Message-ID: <3EDD04F8-C152-11D7-989F-000A956845CE@smi.stanford.edu> Hello everybody, I've made Biopython 1.21 available on the website at: http://www.biopython.org/download/ Martel was inadvertently left out of the Biopython 1.20 distribution. This release corrects that problem. Also incorporated in this release is: Martel added back into the released package new AlignACE module by Bartek Wilczynski Andreas Kuntzagk fix for GenBank Iterator on empty files Many thanks to everyone who noticed the Martel problem and reported it! Jeff From L.Pritchard at scri.sari.ac.uk Tue Jul 29 11:07:31 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Tue Jul 29 11:08:08 2003 Subject: [BioPython] 1.21 installation difficulty Message-ID: <5.2.1.1.0.20030729160329.00ba26d8@caird> Hi guys, I'm coming across problems building BIopython 1.21 on my XP machine at my new job. Unfortunately, copies of Visual Studio are harder to come by here than at the university, so I don't have a copy of cl.exe - the build fails at Bio.cSVM with "command 'cl.exe' failed: No such file or directory" :( Are there plans for a Windows installer version? From chapmanb at uga.edu Tue Jul 29 13:52:36 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Tue Jul 29 13:56:54 2003 Subject: [BioPython] 1.21 installation difficulty In-Reply-To: <5.2.1.1.0.20030729160329.00ba26d8@caird> References: <5.2.1.1.0.20030729160329.00ba26d8@caird> Message-ID: <20030729175236.GC68723@evostick.agtec.uga.edu> Hi Leighton; > I'm coming across problems building BIopython 1.21 on my XP machine at my > new job. Unfortunately, copies of Visual Studio are harder to come by here > than at the university, so I don't have a copy of cl.exe - the build fails > at Bio.cSVM with "command 'cl.exe' failed: No such file or directory" :( You should be able to build everything with the free Borland compiler. I put directions, as far as I know them (as I'm no Windows expert) in the install documentation: http://www.biopython.org/docs/install/Installation.html#htoc27 > Are there plans for a Windows installer version? I am definitely planning on making one. My access to Windows computers that I have admin permissions on sucks right now, but I hope to have one made over the next couple of days. If you beat me to making it, the instructions for making Windows installers are here: http://www.biopython.org/docs/tutorial/Tutorial006.html#toc26 Someone who uses Windows regularly who wants to make and maintain the windows installer would be great (hint, hint :-). Brad From mdehoon at ims.u-tokyo.ac.jp Wed Jul 30 01:38:56 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Wed Jul 30 01:37:15 2003 Subject: [BioPython] 1.21 installation difficulty In-Reply-To: <20030729175236.GC68723@evostick.agtec.uga.edu> References: <5.2.1.1.0.20030729160329.00ba26d8@caird> <20030729175236.GC68723@evostick.agtec.uga.edu> Message-ID: <3F2759F0.4010202@ims.u-tokyo.ac.jp> I made a Biopython installer for python 2.2 on windows; it is available at http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/biopython-1.21.win32-py2.2.exe. 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? The "python setup.py install" command works fine with Python 2.2.3 on Windows, so you can also install Biopython yourself using Cygwin. I put some explanation of how to do that on http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/index.html 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. One more issue: with Python 2.3, mxTextTools (and therefore Biopython) cannot be compiled. The gcc compiler on Cygwin gets farther than Microsoft's cl.exe. With cl.exe, it fails at C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe /c /nologo /Ox /MD /W3 /GX /DNDEBUG /O2 /Gf /GB /GD -DBAD_STATIC_FORWARD=1 -UHAVE_STRPTIME -UHAVE_TIMEGM -Imx/DateTime/mxDateTime -Ic:\Python23\include -Ic:\Python23\PC /Tcmx/DateTime /mxDateTime/mxDateTime.c /Fobuild\temp.win32-2.3\Release\mx\DateTime\mxDateTime\ mxDateTime\mx/DateTime/mxDateTime/mxDateTime.obj mxDateTime.c mx/DateTime/mxDateTime/mxDateTime.c(163) : error C2133: 'mxDateTime_Methods' : ? ????????? mx/DateTime/mxDateTime/mxDateTime.c(166) : error C2133: 'mxDateTimeDelta_Methods ' : ?????????? (My Microsoft Visual Studio is in Japanese, I can't read the compiler messages either). With gcc, the problem occurs in the final linking stage: C:\cygwin\usr\local\bin\gcc.exe -mno-cygwin -shared -s build\temp.win32-2.3\Rele ase\mx\TextTools\mxTextTools\mxTextTools\mx\texttools\mxtexttools\mxtexttools.o build\temp.win32-2.3\Release\mx\TextTools\mxTextTools\mxTextTools\mx\texttools\m xtexttools\mxte.o build\temp.win32-2.3\Release\mx\TextTools\mxTextTools\mxTextTo ols\mx\texttools\mxtexttools\mxbmse.o build\temp.win32-2.3\Release\mx\TextTools\ mxTextTools\mxTextTools\mx\texttools\mxtexttools\mxTextTools.def -Lc:\Python23\libs -Lc:\Python23\PCBuild -lpython23 -o build\lib.win32-2.3\mx\TextTools\mxTextTools\mxTextTools.pyd build\temp.win32-2.3\Release\mx\TextTools\mxTextTools\mxTextTools\mx\texttools\m xtexttools\mxte.o(.text+0x1200):mxte.c: undefined reference to `__imp__mxBMS_Type' collect2: ld returned 1 exit status The same error occurs with Python 2.2, but then I can compile it with Microsoft's cl.exe. --Michiel, U Tokyo. Brad Chapman wrote: >>Are there plans for a Windows installer version? > I am definitely planning on making one. My access to Windows > computers that I have admin permissions on sucks right now, but I > hope to have one made over the next couple of days. If you beat me > to making it, the instructions for making Windows installers are > here: > > http://www.biopython.org/docs/tutorial/Tutorial006.html#toc26 > > Someone who uses Windows regularly who wants to make and maintain > the windows installer would be great (hint, hint :-). > -- 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 L.Pritchard at scri.sari.ac.uk Wed Jul 30 05:20:14 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Wed Jul 30 05:20:30 2003 Subject: [BioPython] 1.21 installation difficulty In-Reply-To: <3F26ACBC.2050401@ims.u-tokyo.ac.jp> References: <5.2.1.1.0.20030729174038.00bcfb88@caird> <5.2.1.1.0.20030729160329.00ba26d8@caird> <5.2.1.1.0.20030729160329.00ba26d8@caird> <5.2.1.1.0.20030729174038.00bcfb88@caird> Message-ID: <5.2.1.1.0.20030730090900.02aed968@caird> Thanks, Michiel and Brad, That worked brilliantly. I had to get the CVS version of 1.21 due to the absent Martel, but under Python2.2 the mingw32 and a test Borland install both went pretty well (one failure and two errors in the test suite... Error: test_GenBank Traceback (most recent call last): File "test_GenBank.py", line 121, in ? cur_seqrecord = gb_dict[key] File "e:\Applications\Python2_2\Lib\site-packages\Bio\GenBank\__init__.py", line 88, in __getitem__ return self._parser.parse(File.StringHandle(data)) File "e:\Applications\Python2_2\Lib\site-packages\Bio\GenBank\__init__.py", line 229, in parse self._scanner.feed(handle, self._consumer) File "e:\Applications\Python2_2\Lib\site-packages\Bio\GenBank\__init__.py", line 1244, in feed self._parser.parseFile(handle) File "E:\APPLIC~1\PYTHON~1\lib\site-packages\Martel\Parser.py", line 328, in parseFile self.parseString(fileobj.read()) File "E:\APPLIC~1\PYTHON~1\lib\site-packages\Martel\Parser.py", line 356, in parseString self._err_handler.fatalError(result) File ".\xml\sax\handler.py", line 38, in fatalError Martel.Parser.ParserPositionException: error parsing at or beyond character 0 [The test_GenBank error only seems to come up in the CVS installation, by the way. The test build with the Borland compiler from the published source .zip file didn't throw the this error.] Failure: test_SVDSuperimposer - AssertionError, line 285 of run_tests.py, in compare_output Output: '[[5.16518888e+001 .... Expected: '[[5.16518888e+01 .... Could this be a typo in the assertion? There are zeros missing in the exponents of the other expected array values, too... Error: test_copen Traceback (most recent call last): File "test_copen.py", line 14, in ? handle = copen.copen_fn(print_args, *(range(2) + ['a', 'b', 'c'])) File "E:\APPLIC~1\PYTHON~1\lib\site-packages\Bio\MultiProc\copen.py", line 67, in copen_fn pid = os.fork() AttributeError: 'module' object has no attribute 'fork') I found the same problems as Michiel with Python2.3c - the Borland compiler gets about as far as the MS compiler with the egenix source: building 'mx.TextTools.mxTextTools.mxTextTools' extension mx\TextTools\mxTextTools\mxTextTools.c: Error E2209 E:\APPLIC~1\PYTHON~1\include\pyconfig.h 37: Unable to open include file 'io.h' Error E2209 E:\APPLIC~1\PYTHON~1\include\pyconfig.h 163: Unable to open include file 'stdio.h' Error E2209 E:\APPLIC~1\PYTHON~1\include\Python.h 27: Unable to open include file 'limits.h' Error E2209 E:\APPLIC~1\PYTHON~1\include\Python.h 42: Unable to open include file 'stdio.h' Fatal F1003 E:\APPLIC~1\PYTHON~1\include\Python.h 44: Error directive: "Python.h requires that stdio.h define NULL." *** 5 errors in Compile *** creating build\temp.win32-2.2 creating build\temp.win32-2.2\Release creating build\temp.win32-2.2\Release\mx creating build\temp.win32-2.2\Release\mx\TextTools creating build\temp.win32-2.2\Release\mx\TextTools\mxTextTools creating build\temp.win32-2.2\Release\mx\TextTools\mxTextTools\mxTextTools e:\Applications\bcc55\bin\bcc32.exe -c /tWM /O2 /q /g0 -UHAVE_STRPTIME -UHAVE_TIMEGM -Imx/TextTools/mxTextTools -IE:\APPLIC~1\PYTHON~1\include -obuild\temp.win32-2.2\Release\mx\TextTools\mxTextTools\mxTextTools\mxtexttools.obj mx\TextTools\mxTextTools\mxTextTools.c error: command 'bcc32.exe' failed with exit status 1 Attempting to build a Windows distribution from the mingw32-compiled code throws up the same problems as Michiel encountered, which I got round the same way. When I attempted to install the package on my machine (over the existing installation), I also came across some file permission problems with writing the EUtils/DTD files, which I corrected by changing read-only permissions (are these default on XP or something?) to read-write on the Bio sub-tree. Many thanks for all your help, From kim at inb.uni-luebeck.de Wed Jul 30 05:47:58 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Wed Jul 30 05:47:51 2003 Subject: [BioPython] 1.21 installation difficulty In-Reply-To: <3F2759F0.4010202@ims.u-tokyo.ac.jp>; from mdehoon@ims.u-tokyo.ac.jp on Wed, Jul 30, 2003 at 02:38:56PM +0900 References: <5.2.1.1.0.20030729160329.00ba26d8@caird> <20030729175236.GC68723@evostick.agtec.uga.edu> <3F2759F0.4010202@ims.u-tokyo.ac.jp> Message-ID: <20030730114757.A1354@pc10.inb.mu-luebeck.de> On Wed, Jul 30, 2003 at 02:38:56PM +0900, Michiel Jan Laurens de Hoon wrote: > 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. Incidentally, I saw the same message yesterday night, when I installed Biopython 1.21 on my Linux box at home on which no previous Biopython installation existed. I just went ahead, by answering "y" to the question that appeared, just to see what's going to happen, and everything worked out fine. Upon installing a second time, the message did not appear anymore. Recently, there were messages on this list indicating that Martel was not included in Biopython 1.20, and that this has been repaired in 1.21. I've looked around in the setup.py script a bit, and it seems to me that the tuple ("Martel", is_Martel_installed, 1, "http://www.biopython.org/~dalke/Martel/") (line 81) is probably not needed anymore in the dependencies list -- there is no need to complain about outdated or missing Martel installations as the bundled one can be installed anyway: if not is_Martel_installed(): self.packages.append("Martel") (line 140). Greetinx, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim@inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From absmythe at ucdavis.edu Wed Jul 30 12:38:54 2003 From: absmythe at ucdavis.edu (ashleigh smythe) Date: Wed Jul 30 12:38:55 2003 Subject: [BioPython] biopython clustalw command line take 2 Message-ID: <1059583139.2699.38.camel@nate.ucdavis.edu> Hello biopython experts. At the risk of seeming like a pest, I'm reposting a question I asked a couple of days ago to see if I can get a bite this time. I'm trying to use clustalw through biopython for the first time. I'm following the tutorial but it doesn't show the syntax for setting the multiple alignment parameters. From the __init__ I figured out that it is something like gap_open_pen=desired value so I tried cline.gap_open_pen=20 but when I try to show that command line string I get an error: >>> cline=MultipleAlignCL(os.path.join(os.curdir, 'aligntest')) >>> cline.set_output('alignout.aln') >>> cline.gap_open_pen=20 >>> cline.gap_ext_pen=10 >>> str(cline) Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line 420, in __str__ cline = cline + " -GAPOPEN=" + self.gap_open_pen TypeError: cannot concatenate 'str' and 'int' objects How do I set those values properly? Thanks very much for any suggestions. Ashleigh -- **************************** Ashleigh B. Smythe Graduate Research Assistant Department of Nematology University of California, Davis, CA 95616 email:absmythe@ucdavis.edu phone:530-754-4321 _______________________________________________ From mdehoon at ims.u-tokyo.ac.jp Wed Jul 30 13:02:19 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Wed Jul 30 13:03:25 2003 Subject: [BioPython] biopython clustalw command line take 2 In-Reply-To: <1059583139.2699.38.camel@nate.ucdavis.edu> References: <1059583139.2699.38.camel@nate.ucdavis.edu> Message-ID: <3F27FA1B.9040007@ims.u-tokyo.ac.jp> ashleigh smythe wrote: > I'm trying to use clustalw through biopython for the first > time. I'm following the tutorial but it doesn't show the syntax for > setting the multiple alignment parameters. Did you try >>> help(MultipleAlignCL) > ... when I try to show that command line string I get an error: >>>>cline=MultipleAlignCL(os.path.join(os.curdir, 'aligntest')) >>>>cline.set_output('alignout.aln') >>>>cline.gap_open_pen=20 >>>>cline.gap_ext_pen=10 >>>>str(cline) > > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line > 420, in __str__ > cline = cline + " -GAPOPEN=" + self.gap_open_pen > TypeError: cannot concatenate 'str' and 'int' objects > It looks like that should be str(self.gap_open_pen) instead of just self.gap_open_pen. If you change that line and similar lines in the __init__.py file, it will work. --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 l.heisler at utoronto.ca Wed Jul 30 13:11:21 2003 From: l.heisler at utoronto.ca (Larry) Date: Wed Jul 30 13:05:02 2003 Subject: [BioPython] biopython clustalw command line take 2 References: <1059583139.2699.38.camel@nate.ucdavis.edu> Message-ID: <004801c356bd$99c2e440$1651968e@Larry> Hi Ashleighe, not a biopython expert, but tried your code and was able to proceed by making sure the variables were defined as strings ie cline.gap_open_pen="20" cline.gap_ext_pen="10" then i am able to run the str command, returning a command string ...not really having used this module, I'm not sure where to go from there, but hopefully this will get you past that point in the problem Larry Lawrence Heisler, PhD Department of Laboratory Medicine and Pathobiology Faculty of Medicine University of Toronto Phone: 416-946-7921 email: l.heisler@utoronto.ca ----- Original Message ----- From: "ashleigh smythe" To: Sent: Wednesday, July 30, 2003 12:38 PM Subject: [BioPython] biopython clustalw command line take 2 > Hello biopython experts. At the risk of seeming like a pest, I'm > reposting a question I asked a couple of days ago to see if I can get a > bite this time. > > I'm trying to use clustalw through biopython for the first > time. I'm following the tutorial but it doesn't show the syntax for > setting the multiple alignment parameters. From the __init__ I figured > out that it is something like gap_open_pen=desired value so I tried > cline.gap_open_pen=20 but when I try to show that command line string I > get an error: > > >>> cline=MultipleAlignCL(os.path.join(os.curdir, 'aligntest')) > >>> cline.set_output('alignout.aln') > >>> cline.gap_open_pen=20 > >>> cline.gap_ext_pen=10 > >>> str(cline) > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line > 420, in __str__ > cline = cline + " -GAPOPEN=" + self.gap_open_pen > TypeError: cannot concatenate 'str' and 'int' objects > > How do I set those values properly? > > Thanks very much for any suggestions. > > Ashleigh > -- > **************************** > Ashleigh B. Smythe > Graduate Research Assistant > Department of Nematology > University of California, > Davis, CA 95616 > email:absmythe@ucdavis.edu > phone:530-754-4321 > > _______________________________________________ > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > From chapmanb at uga.edu Wed Jul 30 13:10:50 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Jul 30 13:55:31 2003 Subject: [BioPython] biopython clustalw command line take 2 In-Reply-To: <1059583139.2699.38.camel@nate.ucdavis.edu> References: <1059583139.2699.38.camel@nate.ucdavis.edu> Message-ID: <20030730171050.GB6961@evostick.agtec.uga.edu> Hi Ashleigh; > Hello biopython experts. At the risk of seeming like a pest, I'm > reposting a question I asked a couple of days ago to see if I can get a > bite this time. Sorry to be so slow in responding. I've been beyond swamped recently. Grad school is very evil. > I'm trying to use clustalw through biopython for the first > time. I'm following the tutorial but it doesn't show the syntax for > setting the multiple alignment parameters. From the __init__ I figured > out that it is something like gap_open_pen=desired value so I tried > cline.gap_open_pen=20 but when I try to show that command line string I > get an error: [...] > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line > 420, in __str__ > cline = cline + " -GAPOPEN=" + self.gap_open_pen > TypeError: cannot concatenate 'str' and 'int' objects As Michiel pointed out, this isn't an error in how you are using it, but rather an error in my ugly code. I've attached a patch which fixes all of these types of potential problems (the patch is also checked into CVS). This should be applied to Bio/Clustalw/__init__.py if you (or anyone else) wants to use it. As Larry pointed out, you can work around my bug and save yourself from having to patch the Biopython code by passing in strings instead of integers. Sorry about the bug. Thanks much for reporting it! Brad -------------- next part -------------- Index: __init__.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/Clustalw/__init__.py,v retrieving revision 1.6 diff -c -r1.6 __init__.py *** __init__.py 13 Jun 2003 03:25:17 -0000 1.6 --- __init__.py 30 Jul 2003 17:16:11 -0000 *************** *** 388,394 **** # general options if self.type: ! cline = cline + " -TYPE=" + self.type if self.is_quick == 1: cline = cline + " -INTERACTIVE" if self.allow_negative == 1: --- 388,394 ---- # general options if self.type: ! cline = cline + " -TYPE=%s" % self.type if self.is_quick == 1: cline = cline + " -INTERACTIVE" if self.allow_negative == 1: *************** *** 396,429 **** # output options if self.output_file: ! cline = cline + " -OUTFILE=" + self.output_file if self.output_type: ! cline = cline + " -OUTPUT=" + self.output_type if self.output_order: ! cline = cline + " -OUTORDER=" + self.output_order if self.change_case: ! cline = cline + " -CASE=" + self.change_case if self.add_seqnos: ! cline = cline + " -SEQNOS=" + self.add_seqnos if self.new_tree: # clustal does not work if -align is written -ALIGN ! cline = cline + " -NEWTREE=" + self.new_tree + " -align" # multiple alignment options if self.guide_tree: ! cline = cline + " -USETREE=" + self.guide_tree if self.protein_matrix: ! cline = cline + " -MATRIX=" + self.protein_matrix if self.dna_matrix: ! cline = cline + " -DNAMATRIX=" + self.dna_matrix if self.gap_open_pen: ! cline = cline + " -GAPOPEN=" + self.gap_open_pen if self.gap_ext_pen: ! cline = cline + " -GAPEXT=" + self.gap_ext_pen if self.is_no_end_pen == 1: cline = cline + " -ENDGAPS" if self.gap_sep_range: ! cline = cline + " -GAPDIST=" + self.gap_sep_range if self.is_no_pgap == 1: cline = cline + " -NOPGAP" if self.is_no_hgap == 1: --- 396,429 ---- # output options if self.output_file: ! cline = cline + " -OUTFILE=%s" % self.output_file if self.output_type: ! cline = cline + " -OUTPUT=%s" % self.output_type if self.output_order: ! cline = cline + " -OUTORDER=%s" % self.output_order if self.change_case: ! cline = cline + " -CASE=%s" % self.change_case if self.add_seqnos: ! cline = cline + " -SEQNOS=%s" % self.add_seqnos if self.new_tree: # clustal does not work if -align is written -ALIGN ! cline = cline + " -NEWTREE=%s -align" % self.new_tree # multiple alignment options if self.guide_tree: ! cline = cline + " -USETREE=%s" % self.guide_tree if self.protein_matrix: ! cline = cline + " -MATRIX=%s" % self.protein_matrix if self.dna_matrix: ! cline = cline + " -DNAMATRIX=%s" % self.dna_matrix if self.gap_open_pen: ! cline = cline + " -GAPOPEN=%s" % self.gap_open_pen if self.gap_ext_pen: ! cline = cline + " -GAPEXT=%s" % self.gap_ext_pen if self.is_no_end_pen == 1: cline = cline + " -ENDGAPS" if self.gap_sep_range: ! cline = cline + " -GAPDIST=%s" % self.gap_sep_range if self.is_no_pgap == 1: cline = cline + " -NOPGAP" if self.is_no_hgap == 1: *************** *** 433,443 **** residue_list = '' for residue in self.h_gap_residues: residue_list = residue_list + residue ! cline = cline + " -HGAPRESIDUES=" + residue_list if self.max_div: ! cline = cline + " -MAXDIV=" + self.max_div if self.trans_weight: ! cline = cline + " -TRANSWEIGHT=" + self.trans_weight return cline --- 433,443 ---- residue_list = '' for residue in self.h_gap_residues: residue_list = residue_list + residue ! cline = cline + " -HGAPRESIDUES=%s" % residue_list if self.max_div: ! cline = cline + " -MAXDIV=%s" % self.max_div if self.trans_weight: ! cline = cline + " -TRANSWEIGHT=%s" % self.trans_weight return cline From chapmanb at uga.edu Wed Jul 30 14:33:04 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Jul 30 14:37:18 2003 Subject: [BioPython] 1.21 installation difficulty In-Reply-To: <3F2759F0.4010202@ims.u-tokyo.ac.jp> References: <5.2.1.1.0.20030729160329.00ba26d8@caird> <20030729175236.GC68723@evostick.agtec.uga.edu> <3F2759F0.4010202@ims.u-tokyo.ac.jp> Message-ID: <20030730183304.GE6961@evostick.agtec.uga.edu> Hi Michiel, Jan, Leighton; > I made a Biopython installer for python 2.2 on windows; it is available at > http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/biopython-1.21.win32-py2.2.exe. Sweet. Thanks. It's on the website now. You rule. > 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? Yeah, this is partially Andrew's fault and partly my fault. It's Andrew's fault because EUtils requires DTDs to be installed in the EUtils python directory, so you have non-python files in the python directories. It's my fault because I wrote the hack in setup.py to install these DTDs (see install_eutils_dtds in the setup.py file) and didn't think about building the windows installers. I'm not sure what exactly to do about this, but what you did is the right "hack" way to fix it. We can figure something better later 'cause if this works -- well, that is good. > 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/. Yeah, I think you get this if you are installing a fresh Biopython. It seems like a bad thing, but this is Jeff's invention so he probably knows better than I how to fix it. > One more issue: with Python 2.3, mxTextTools (and therefore Biopython) > cannot be compiled. The gcc compiler on Cygwin gets farther than > Microsoft's cl.exe. With cl.exe, it fails at I wouldn't sweat this. mxTextTools is very well maintained and I'm pretty positive that a compilable version along with Windows installers will come along fairly quickly. Since 2.3 was just released yesterday I'll bet if we just sit for a bit the TextTools problem will take care of itself. So I think this hits on the major problems you all talked about: => Installer -- on the web pages. Sweet. => EUtils DTDs -- bad hack in the setup.py file. We need to make it Windows compliant. I'm open to suggestions on how to do this. => bad Martel messages -- deferring to Jeff. He's the man. => mxTextTools -- I think we should just wait a bit and save ourselves work. I'm really happy you all are looking at this on Windows. It's a huge help as I never use it myself and so know next to nothing about it. Thanks! But-I-wanna-use-Python-2.3-today-ly yr's, Brad From dalke at dalkescientific.com Wed Jul 30 14:44:32 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed Jul 30 14:44:22 2003 Subject: [BioPython] 1.21 installation difficulty In-Reply-To: <20030730183304.GE6961@evostick.agtec.uga.edu> Message-ID: Brad: > Yeah, this is partially Andrew's fault and partly my fault. It's > Andrew's fault because EUtils requires DTDs to be installed in the > EUtils python directory, so you have non-python files in the python > directories. Yup. And it's something that should be fixed. Along with replacing the DTD->Python data structure converter. There are better ways that I didn't know about when I started, including ways which are included in PyXML. Andrew dalke@dalkescientific.com From absmythe at ucdavis.edu Thu Jul 31 00:26:02 2003 From: absmythe at ucdavis.edu (ashleigh smythe) Date: Thu Jul 31 00:26:03 2003 Subject: [BioPython] biopython clustalw command line take 2 In-Reply-To: <20030730171050.GB6961@evostick.agtec.uga.edu> References: <1059583139.2699.38.camel@nate.ucdavis.edu> <20030730171050.GB6961@evostick.agtec.uga.edu> Message-ID: <1059625567.4811.19.camel@nate.ucdavis.edu> On Wed, 2003-07-30 at 10:10, Brad Chapman wrote: > Hi Ashleigh; > > > Hello biopython experts. At the risk of seeming like a pest, I'm > > reposting a question I asked a couple of days ago to see if I can get a > > bite this time. > > Sorry to be so slow in responding. I've been beyond swamped > recently. Grad school is very evil. > > > I'm trying to use clustalw through biopython for the first > > time. I'm following the tutorial but it doesn't show the syntax for > > setting the multiple alignment parameters. From the __init__ I figured > > out that it is something like gap_open_pen=desired value so I tried > > cline.gap_open_pen=20 but when I try to show that command line string I > > get an error: > [...] > > Traceback (most recent call last): > > File "", line 1, in ? > > File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line > > 420, in __str__ > > cline = cline + " -GAPOPEN=" + self.gap_open_pen > > TypeError: cannot concatenate 'str' and 'int' objects > > As Michiel pointed out, this isn't an error in how you are using it, > but rather an error in my ugly code. I've attached a patch which > fixes all of these types of potential problems (the patch is also > checked into CVS). This should be applied to > Bio/Clustalw/__init__.py if you (or anyone else) wants to use it. > > As Larry pointed out, you can work around my bug and save yourself > from having to patch the Biopython code by passing in strings > instead of integers. > > Sorry about the bug. Thanks much for reporting it! > Brad Thanks to Michiel and Larry for the suggestions, and Brad for coming up with the patch so quickly. Sorry to repost and pester like that, I just thought I might have fallen through the cracks. I actually didn't know how to patch it so I just got your new __init__.py from CVS and replaced my old one. The setting of the parameters works now, but now I can't specify an outfile: >>> cline=MultipleAlignCL(os.path.join(os.curdir, 'aligntest2')) >>> cline.set_output('aligntest2out.aln') >>> cline.gap_open_pen=20 >>> cline.gap_ext_pen=10 >>> str(cline) 'clustalw ./aligntest2 -OUTFILE=aligntest2out.aln -GAPOPEN=20 -GAPEXT=10' >>> from Bio import Clustalw >>> alignment=Clustalw.do_alignment(cline) Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line 118, in do_alignment raise IOError("Output .aln file %s not produced, commandline: %s" IOError: Output .aln file aligntest2out.aln not produced, commandline: clustalw ./aligntest2 -OUTFILE=aligntest2out.aln - GAPOPEN=20 -GAPEXT=10 If I don't specify an outfile it works fine. I just a few moments ago figured out that there is an actual program called patch that does the patching (newbie, can you tell?). Should I have patched instead of replacing, or does that have anything to do with it? Of course it won't let me do patch it now. Anyway, any suggestions from anyone would be appreciated. I know Brad is busy with the evils of grad school (me too :( ) - anybody else have any clues? Thanks! Ashleigh ________________________________________________________________________ From kim at inb.uni-luebeck.de Thu Jul 31 05:53:12 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Thu Jul 31 05:53:04 2003 Subject: [BioPython] KDTreec missing in biopython 1.21 Message-ID: <20030731115312.M1354@pc10.inb.mu-luebeck.de> Hi all, while playing around with a newly installed biopython 1.21, I noticed that the KDTree module requires a KDTreec module which does not seem to be included in the archive. This is what I get: >>> import Bio >>> import Bio.KDTree Traceback (most recent call last): File "", line 1, in ? File "/opt/local/biosoft/lib/python2.2/site-packages/PIL/__init__.py", line 8, in ? # File "/sdb1/local/biosoft/src/python-extensions/biopython-1.21/build/lib.linux-i686-2.2/Bio/KDTree/_KDTree.py", line 2, in ? ImportError: No module named _KDTreec Greetinx, Jan P.S.: No, I don't use the KDTree module, in fact I don't have much of an idea what it is / does. I just tried to find out by running pydoc on it, and that failed. -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim@inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From jchang at jeffchang.com Thu Jul 31 11:58:14 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Thu Jul 31 11:58:06 2003 Subject: [BioPython] KDTreec missing in biopython 1.21 In-Reply-To: <20030731115312.M1354@pc10.inb.mu-luebeck.de> Message-ID: Hi Jan, The KDTree module is disabled by default. It is C++ code, and does not compile correctly on many platforms due to a shortcoming in the distutils with Python 2.2. If you need the code, you can enable it by following the instructions in the README file. Thank you for your report. Jeff On Thursday, July 31, 2003, at 02:53 AM, Jan T. Kim wrote: > Hi all, > > while playing around with a newly installed biopython 1.21, I noticed > that the KDTree module requires a KDTreec module which does not seem to > be included in the archive. This is what I get: > >>>> import Bio >>>> import Bio.KDTree > Traceback (most recent call last): > File "", line 1, in ? > File > "/opt/local/biosoft/lib/python2.2/site-packages/PIL/__init__.py", line > 8, in ? > # > File > "/sdb1/local/biosoft/src/python-extensions/biopython-1.21/build/ > lib.linux-i686-2.2/Bio/KDTree/_KDTree.py", line 2, in ? > ImportError: No module named _KDTreec > > Greetinx, Jan > > P.S.: No, I don't use the KDTree module, in fact I don't have much of > an idea what it is / does. I just tried to find out by running pydoc on > it, and that failed. > -- > +- Jan T. Kim -------------------------------------------------------+ > | *NEW* email: kim@inb.uni-luebeck.de | > | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | > *-----=< hierarchical systems are for files, not for humans >=-----* > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From idoerg at burnham.org Thu Jul 31 17:34:32 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu Jul 31 18:14:17 2003 Subject: [BioPython] GRAVY index program anyone? Message-ID: <3F298B68.4060200@burnham.org> Hi, Does anybody have a program which calculates a sequence's Grand average of hydropathicity (GRAVY)? TIA, ./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://ffas.ljcrf.edu/~iddo