From bugzilla-daemon at portal.open-bio.org Thu Aug 5 18:36:54 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:35 2005 Subject: [Biopython-dev] [Bug 1675] New: complement() returns string instead of Seq object Message-ID: <200408052236.i75Masvq021084@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1675 Summary: complement() returns string instead of Seq object Product: Biopython Version: Not Applicable Platform: Macintosh OS/Version: MacOS X Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: martin.ligr@rockefeller.edu complement in SeqUtils (and therefore also antiparallel) return string, but a Seq object would be more logical, IMHO. The way it is now one has to type additional code to get a Seq obj. back. (Ideal would be complement, reverse, and reverse_complement as MutableSeq methods, though.) ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From syl_schupp at yahoo.fr Thu Aug 12 10:49:41 2004 From: syl_schupp at yahoo.fr (=?iso-8859-1?q?Sylvain=20Sch=FCpp?=) Date: Sat Mar 5 14:43:52 2005 Subject: [Biopython-dev] Blast invent his own sequence Message-ID: <20040812144941.33288.qmail@web21126.mail.yahoo.com> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: ig_Bacillus_subtilis_subsp._subtilis_str._168.fasta Type: application/octet-stream Size: 5641476 bytes Desc: ig_Bacillus_subtilis_subsp._subtilis_str._168.fasta Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20040812/f8edceb7/ig_Bacillus_subtilis_subsp._subtilis_str._168.obj From bugzilla-daemon at portal.open-bio.org Fri Aug 13 08:41:25 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:52 2005 Subject: [Biopython-dev] [Bug 1678] New: NCBIXML error in 1.30 Message-ID: <200408131241.i7DCfP8L002970@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1678 Summary: NCBIXML error in 1.30 Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: blocker Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: d.lapointe@comcast.net Running Betrtands script generates an error at line 111 of NCBIXML.py that filename is not defined globally. 'filename' should be changed to 'handler' ... def parse(self, handler): """Parses the XML data handler -- file handler or StringIO ''' self._parser.parse(filename) <=== line 111 return self._blast should read self._parser.parse(handler) I changed this in my source and it worked fine. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From chapmanb at 50mail.com Fri Aug 13 14:19:16 2004 From: chapmanb at 50mail.com (Brad Chapman) Date: Sat Mar 5 14:43:52 2005 Subject: [Biopython-dev] Restriction analysis package. In-Reply-To: <411CA3DF.5040001@users.sourceforge.net> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> <411CA3DF.5040001@users.sourceforge.net> Message-ID: <20040813181916.GC727@lebowski.bos.east.verizon.net> Hi Fred; > I would like to know where do we stand for the Restriction analysis package. > I posted a message on the biopython-dev list but got no response. > As previously said, I am ready to maintain the package in Biopython. > Just tell me if you still are interested. Sorry for the delay in getting back with you. We are definitely still interested in the code, and I've went and integrated into Biopython CVS. Please let me know if I didn't get anything into CVS correctly. For those who are interested in checking it out, here is what is included: Bio/Restriction -- very nice set of modules for dealing with Restriction Enzymes, including searching for enzymes within sequences and performing cuts with them Doc/cookbook/Restriction -- documentation on using the modules (also included on the website) Scripts/Restriction -- scripts for updating the enzyme classes from Rebase The only modification I made was to add a catalyze function (which just calls the catalyse function). I was having a bit of trouble getting used to the British spelling :-). I also added some basic tests in Tests/test_Restriction.py -- please do feel free to add to these, they are pretty basic right now. Thanks much for this contribution -- everything looks very well designed and useful. And with documentation. Woo. Brad From mdehoon at ims.u-tokyo.ac.jp Sat Aug 14 04:10:34 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:52 2005 Subject: [Biopython-dev] complement, reverse_complement in Bio.Seq Message-ID: <411DC8FA.6070004@ims.u-tokyo.ac.jp> Dear Biopythoneers (especially Dr. Chapman), I have added the functions 'complement' and 'reverse_complement' to Bio.Seq's Seq and MutableSeq objects, which we discussed some weeks ago. Similar functions previously existed in various locations in BioPython: - forward_complement, reverse_complement in Bio.GFF.easy - complement, antiparallel in Bio.SeqUtils These functions have now been deprecated, and will generate a DeprecationWarning when used. The functions complement and reverse_complement, when applied to a Seq object, will return a new Seq object. The same function applied to a MutableSeq object will modify the MutableSeq object itself, and don't return anything. By the way, do we still need separate Seq and MutableSeq classes? As far as I understand, Seq is needed so that we can use strings, but since strings are immutable in Python we also need a MutableSeq. Wouldn't it be possible to implement this class in C, so that we can have mutable sequences that are still fast? --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 f.sohm at whsmithnet.co.uk Tue Aug 17 05:35:37 2004 From: f.sohm at whsmithnet.co.uk (f.sohm@whsmithnet.co.uk) Date: Sat Mar 5 14:43:52 2005 Subject: [Biopython-dev] Re: Restriction analysis package. In-Reply-To: <20040813181916.GC727@lebowski.bos.east.verizon.net> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> <411CA3DF.5040001@users.sourceforge.net> <20040813181916.GC727@lebowski.bos.east.verizon.net> Message-ID: Hi Brad Felicitation for your PhD and thank you for uploading the code into the CVS. For the catalyse method, you are right and I should have made the change earlier. There is a simpler way to add a catalyze method though : in the classes : Unknown, Blunt, Ov5 and Ov3 at the end of the definition of the catalyse method, you need to replace : catalyse = classmethod(catalyse) by catalyze = catalyse = classmethod(catalyse) This suppress the need for a new class and avoid to add a function call. I have made the modif but how do you want me to send them ? a bug report against Restriction and the module as an attachement ? Bye Fred From j.a.casbon at qmul.ac.uk Tue Aug 17 09:02:34 2004 From: j.a.casbon at qmul.ac.uk (James Casbon) Date: Sat Mar 5 14:43:52 2005 Subject: [Biopython-dev] interface/SQL development policies Message-ID: <200408171402.34694.j.a.casbon@qmul.ac.uk> Hi, Say I have a module X, which depends heavily on flat file databases. I wish to decompose into two classes XFile and XDatabase, where XFile uses the files and XDatabase use and SQL backend. This raises a number of questions: * the two classes imply a common interface X, what is the best way of handling this in python? An abstract base class? * How are regression tests managed for SQL based classes (ie how do you provide a dummy database, given there might not be an sql server on a particular client)? These questions might be best answered with an example, so if there are any examples covering this kind of stuff already in biopython, please point them out. Thanks, James -- James Casbon PhD Student Centre for Infectious Disease Institute of Cell and Molecular Science Barts and The London http://compbio.mds.qmw.ac.uk From j.a.casbon at qmul.ac.uk Tue Aug 17 09:45:42 2004 From: j.a.casbon at qmul.ac.uk (James Casbon) Date: Sat Mar 5 14:43:52 2005 Subject: [Biopython-dev] outstanding bug Message-ID: <200408171445.42261.j.a.casbon@qmul.ac.uk> I submitted this patch: http://portal.open-bio.org/pipermail/biopython-dev/2004-June/002082.html a while back, but it seems to have gone unnoticed. James -- James Casbon PhD Student Centre for Infectious Disease Institute of Cell and Molecular Science Barts and The London http://compbio.mds.qmw.ac.uk From bugzilla-daemon at portal.open-bio.org Tue Aug 17 12:22:37 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1680] New: Problems with the GenBank indexing Message-ID: <200408171622.i7HGMb7o029515@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1680 Summary: Problems with the GenBank indexing Product: Biopython Version: Not Applicable Platform: PC OS/Version: Windows XP Status: NEW Severity: major Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: sameet@nccs.res.in I am using the latest Biopython(1.3) and latest Python (2.3.4). I want to make an index file using a genbank file. I am doing the following: >>> from Bio import GenBank >>> dict_file = r'C:\Sameet\correspondence\genbank.gb' >>> index_file = r'C:\Sameet\correspondence\genbank.idx' >>> GenBank.index_file(dict_file, index_file) I get the following trace: Traceback (most recent call last): File "", line 1, in -toplevel- GenBank.index_file(dict_file, index_file) File "C:\Python23\Lib\site-packages\Bio\GenBank\__init__.py", line 1283, in index_file SimpleSeqRecord.create_flatdb([filename], indexname, indexer) File "C:\Python23\Lib\site-packages\Bio\Mindy\SimpleSeqRecord.py", line 152, in create_flatdb creator.load(filename, builder = builder, fileid_info = {}) File "C:\Python23\Lib\site-packages\Bio\Mindy\BaseDB.py", line 52, in load for record in iterator.iterate(source, cont_handler = builder): File "C:\Python23\Lib\site-packages\Martel\IterParser.py", line 76, in iterateFile self.record_parser.parseString(rec) File "C:\Python23\Lib\site-packages\Martel\Parser.py", line 356, in parseString self._err_handler.fatalError(result) File "C:\Python23\lib\xml\sax\handler.py", line 38, in fatalError raise exception ParserPositionException: error parsing at or beyond character 1843 I am also attaching the file that i used in this experiment, it is the text that follows after this ------------GenBank File------------------ LOCUS AY517242 312 bp DNA linear PRI 29-FEB-2004 DEFINITION Homo sapiens clone HIV1-H9-362 HIV-1 integration site. ACCESSION AY517242 VERSION AY517242.1 GI:42767637 KEYWORDS . SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 312) AUTHORS Wu,X., Li,Y., Crise,B. and Burgess,S.M. TITLE Transcription start regions in the human genome are favored targets for MLV integration JOURNAL Unpublished REFERENCE 2 (bases 1 to 312) AUTHORS Wu,X., Li,Y., Crise,B. and Burgess,S.M. TITLE Direct Submission JOURNAL Submitted (02-JAN-2004) Genome Technology Branch, National Human Genome Research Institute, NIH, 50 South Drive, Rm 5537, Bethesda, MD 20892, USA FEATURES Location/Qualifiers source 70..312 /organism="Homo sapiens" /mol_type="genomic DNA" /db_xref="taxon:9606" /clone="HIV1-H9-362" /focus source 1..69 /organism="Human immunodeficiency virus 1" /mol_type="genomic DNA" /db_xref="taxon:11676" LTR <1..69 ORIGIN 1 gtctgttgtg tgactctggt aactagagat ccctcagacc cttttagtca gtgtggaaaa 61 tctctagcac aagccaaagt gataatcaaa actcaggaac agtaagtcgg atgcgtcaca 121 ttttttactc aatttatcaa acagtagcta catataggac atttgccagt tatataagga 181 tgtacaaagt tcttgcacac tcaaatagca tatccagcca attgtctcaa tccagactgt 241 tttagtgatg tgaaagaatg tggcaggtct ggaagtatca gaagctcagg aaagggcgga 301 gatttttgtt aa // LOCUS AY517241 310 bp DNA linear PRI 29-FEB-2004 DEFINITION Homo sapiens clone HIV1-H9-361 HIV-1 integration site. ACCESSION AY517241 VERSION AY517241.1 GI:42767636 KEYWORDS . SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 310) AUTHORS Wu,X., Li,Y., Crise,B. and Burgess,S.M. TITLE Transcription start regions in the human genome are favored targets for MLV integration JOURNAL Unpublished REFERENCE 2 (bases 1 to 310) AUTHORS Wu,X., Li,Y., Crise,B. and Burgess,S.M. TITLE Direct Submission JOURNAL Submitted (02-JAN-2004) Genome Technology Branch, National Human Genome Research Institute, NIH, 50 South Drive, Rm 5537, Bethesda, MD 20892, USA FEATURES Location/Qualifiers source 70..310 /organism="Homo sapiens" /mol_type="genomic DNA" /db_xref="taxon:9606" /clone="HIV1-H9-361" /focus source 1..69 /organism="Human immunodeficiency virus 1" /mol_type="genomic DNA" /db_xref="taxon:11676" LTR <1..69 ORIGIN 1 gtctgttgtg tgactctggt aactagagat ccctcagacc cttttagtca gtgtggaaaa 61 tctctagcag tccttgagtt cgctcagtaa gtccagcacc tgcacatttt cttccgaatc 121 accaacatca agttctccca ggaggcgctg agtggtcacc agttcatgct gcaccacttt 181 tcataaaagc ccaaagatgg aaacagccaa atgtctatca gatgatggat aaacaaaatg 241 tggtacaggc acacctcata tttattgcag ttcactttat cgtgctttac aaatattgct 301 ttttttttaa // LOCUS AY517240 310 bp DNA linear PRI 29-FEB-2004 DEFINITION Homo sapiens clone HIV1-H9-360 HIV-1 integration site. ACCESSION AY517240 VERSION AY517240.1 GI:42767635 KEYWORDS . SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 310) AUTHORS Wu,X., Li,Y., Crise,B. and Burgess,S.M. TITLE Transcription start regions in the human genome are favored targets for MLV integration JOURNAL Unpublished REFERENCE 2 (bases 1 to 310) AUTHORS Wu,X., Li,Y., Crise,B. and Burgess,S.M. TITLE Direct Submission JOURNAL Submitted (02-JAN-2004) Genome Technology Branch, National Human Genome Research Institute, NIH, 50 South Drive, Rm 5537, Bethesda, MD 20892, USA FEATURES Location/Qualifiers source 70..310 /organism="Homo sapiens" /mol_type="genomic DNA" /db_xref="taxon:9606" /clone="HIV1-H9-360" /focus source 1..69 /organism="Human immunodeficiency virus 1" /mol_type="genomic DNA" /db_xref="taxon:11676" LTR <1..69 ORIGIN 1 gtctgttgtg tgactctggt aactagagat ccctcagacc cttttagtca gtgtggaaaa 61 tctctagcag attcctcaac aaattaaaaa agtaaaagta ctctgtgata agtgctatag 121 taagggtagg caaaaggtgc tatggagccc agagaagaag accagagggt aagaggaggg 181 gagggaaatg ttgacagggt gctgggacag gctgcctgga ctgtcacaaa acctcccatg 241 gtcacaccag ggcctgcaag cagaagtctt cctcttgatt acatgatcca tggatggtca 301 gcatttttaa // -------------GenBank File------------------------- This problem has occured recurrently, irrespective of the operating system. I think this is a problem regards Sameet ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From Yves.Bastide at irisa.fr Wed Aug 18 04:57:34 2004 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] interface/SQL development policies In-Reply-To: <200408171402.34694.j.a.casbon@qmul.ac.uk> References: <200408171402.34694.j.a.casbon@qmul.ac.uk> Message-ID: <412319FE.6030304@irisa.fr> James Casbon wrote: > Hi, > > Say I have a module X, which depends heavily on flat file databases. I wish > to decompose into two classes XFile and XDatabase, where XFile uses the files > and XDatabase use and SQL backend. This raises a number of questions: > > * the two classes imply a common interface X, what is the best way of handling > this in python? An abstract base class? Separate classes, the interface being checked via unit tests > > * How are regression tests managed for SQL based classes (ie how do you > provide a dummy database, given there might not be an sql server on a > particular client)? No good answer. 1. Skip the tests if there's no db available 2. Use Gadfly? > > These questions might be best answered with an example, so if there are any > examples covering this kind of stuff already in biopython, please point them > out. > > Thanks, > James > yves From j.a.casbon at qmul.ac.uk Wed Aug 18 12:14:21 2004 From: j.a.casbon at qmul.ac.uk (James Casbon) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] interface/SQL development policies In-Reply-To: <412319FE.6030304@irisa.fr> References: <200408171402.34694.j.a.casbon@qmul.ac.uk> <412319FE.6030304@irisa.fr> Message-ID: <200408181714.21038.j.a.casbon@qmul.ac.uk> > > * the two classes imply a common interface X, what is the best way of > > handling this in python? An abstract base class? > > Separate classes, the interface being checked via unit tests As the classes have developed, it has become apparent there is identical code in both classes which is independent of the implementation of the backend. In the light of this, an abstract class with some defined methods becomes more appealing, or should the common functionality be moved out of the class? james -- James Casbon PhD Student Centre for Infectious Disease Institute of Cell and Molecular Science Barts and The London http://compbio.mds.qmw.ac.uk From Yves.Bastide at irisa.fr Wed Aug 18 12:36:24 2004 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] interface/SQL development policies In-Reply-To: <200408181714.21038.j.a.casbon@qmul.ac.uk> References: <200408171402.34694.j.a.casbon@qmul.ac.uk> <412319FE.6030304@irisa.fr> <200408181714.21038.j.a.casbon@qmul.ac.uk> Message-ID: <41238588.7070500@irisa.fr> James Casbon wrote: >>>* the two classes imply a common interface X, what is the best way of >>>handling this in python? An abstract base class? >> >>Separate classes, the interface being checked via unit tests > > > As the classes have developed, it has become apparent there is identical code > in both classes which is independent of the implementation of the backend. > > In the light of this, an abstract class with some defined methods becomes more > appealing, or should the common functionality be moved out of the class? Nonono. Think XP: develop two separate classes with slightly differing internals, then refactor. :-) Seriously, using a common base class looks like the best solution. (Course, don't call it abstract, since its main appeal will be to implement the commonalities.) However there are two distinct roles mixed-up here: common functions, interface, and default behavior. Pythoners are less interested in explicit interface (i.e. writing a bunch of methods raising NotImplemented) > > james > yves From bugzilla-daemon at portal.open-bio.org Mon Aug 23 11:17:25 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1684] New: Error in Compiling DNAUtils Message-ID: <200408231517.i7NFHP5G027167@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1684 Summary: Error in Compiling DNAUtils Product: Biopython Version: Not Applicable Platform: HP OS/Version: Linux Status: NEW Severity: blocker Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: mcolosimo@mitre.org Compile errors in DNAUtils is blocking building and installing. Full output below. gcc -DNDEBUG -O2 -g -pipe -march=i386 -mcpu=i686 -D_GNU_SOURCE -fPIC -fPIC -I/us r/include/python2.2 -c Bio/Restriction/DNAUtils.c -o build/temp.linux-i686-2.2/D NAUtils.o Bio/Restriction/DNAUtils.c:99: syntax error before string constant Bio/Restriction/DNAUtils.c:99: warning: data definition has no type or storage c lass Bio/Restriction/DNAUtils.c:105: syntax error before string constant Bio/Restriction/DNAUtils.c:105: warning: data definition has no type or storage class Bio/Restriction/DNAUtils.c:112: syntax error before string constant Bio/Restriction/DNAUtils.c:112: warning: data definition has no type or storage class Bio/Restriction/DNAUtils.c:118: `DNA_checkbases_doc' undeclared here (not in a f unction) Bio/Restriction/DNAUtils.c:118: initializer element is not constant Bio/Restriction/DNAUtils.c:118: (near initialization for `DNAUtils_functions[0]. ml_doc') Bio/Restriction/DNAUtils.c:118: initializer element is not constant Bio/Restriction/DNAUtils.c:118: (near initialization for `DNAUtils_functions[0]' ) Bio/Restriction/DNAUtils.c:119: `DNA_complement_doc' undeclared here (not in a f unction) Bio/Restriction/DNAUtils.c:119: initializer element is not constant Bio/Restriction/DNAUtils.c:119: (near initialization for `DNAUtils_functions[1]. ml_doc') Bio/Restriction/DNAUtils.c:119: initializer element is not constant Bio/Restriction/DNAUtils.c:119: (near initialization for `DNAUtils_functions[1]' ) Bio/Restriction/DNAUtils.c:120: `DNA_rev_compl_doc' undeclared here (not in a fu nction) Bio/Restriction/DNAUtils.c:120: initializer element is not constant Bio/Restriction/DNAUtils.c:120: (near initialization for `DNAUtils_functions[2]. ml_doc') Bio/Restriction/DNAUtils.c:120: initializer element is not constant Bio/Restriction/DNAUtils.c:120: (near initialization for `DNAUtils_functions[2]' ) Bio/Restriction/DNAUtils.c:121: initializer element is not constant Bio/Restriction/DNAUtils.c:121: (near initialization for `DNAUtils_functions[3]' ) Bio/Restriction/DNAUtils.c:125: syntax error before "initDNAUtils" error: command 'gcc' failed with exit status 1 ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From f.sohm at whsmithnet.co.uk Wed Aug 25 07:43:10 2004 From: f.sohm at whsmithnet.co.uk (f.sohm@whsmithnet.co.uk) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] Re: New: Error in Compiling DNAUtils In-Reply-To: <200408231517.i7NFHP5G027167@portal.open-bio.org> References: <200408231517.i7NFHP5G027167@portal.open-bio.org> Message-ID: Hi Sorry for the bug. I have never seen this one on linux before, but I have never tried it with Python 2.2 either. The Restriction package (which DNAUtils is part of) will not work with Python2.2 A fix might be to try to update your Python to version 2.3 If you update and still get the problem let me know. If you don't want or can't update your python, it will need a bit more work. You will need to comment out the following lines in the biopython setup.py script : lines 437-439 : Extension('Bio.Restriction.DNAUtils', ['Bio/Restriction/DNAUtils.c'] ), To comment, put a # in front of them. This will break the Restriction package but it would not have worked on Python2.2 anyway. Hope this is of some help Fred From bugzilla-daemon at portal.open-bio.org Wed Aug 25 10:38:57 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1684] Error in Compiling DNAUtils Message-ID: <200408251438.i7PEcvwr004345@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1684 f.sohm@whsmithnet.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- 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 Aug 25 11:10:32 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1684] Error in Compiling DNAUtils Message-ID: <200408251510.i7PFAWtp004785@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1684 ------- Additional Comments From f.sohm@whsmithnet.co.uk 2004-08-25 11:10 ------- The problem come from the Python version used. I installed 2.2 back and tested the install with 2.2 and it break as described. Upgrading python is certainly the best thing to do. If you can't update comment the lines 437 to 439 of setup.py this will allow the install to proceed. This will break Restriction, but it would not have worked under Python2.2 anyway. The lines to comment are : Extension('Bio.Restriction.DNAUtils', ['Bio/Restriction/DNAUtils.c'] ), ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mcolosimo at mitre.org Wed Aug 25 11:38:46 2004 From: mcolosimo at mitre.org (Marc Colosimo) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] Re: New: Error in Compiling DNAUtils In-Reply-To: References: <200408231517.i7NFHP5G027167@portal.open-bio.org> Message-ID: I think a similar problem came up for KDTree package in the setup.py file. Does anyone remember how the whole Python2.2 ver Python2.3 release issue ended? I just checked and 1.30 does build with Python2.2 and the web site lists python 2.2. It really is a shame that my newly installed version of Red Hat Linux WS comes with python2.2.3 only, whereas my G5 Mac comes with python2.3 (and Java installed). Marc On Aug 25, 2004, at 7:43 AM, f.sohm@whsmithnet.co.uk wrote: > Hi > Sorry for the bug. I have never seen this one on linux before, but I > have never > tried it with Python 2.2 either. > The Restriction package (which DNAUtils is part of) will not work with > Python2.2 > > A fix might be to try to update your Python to version 2.3 > If you update and still get the problem let me know. > If you don't want or can't update your python, it will need a bit more > work. > You will need to comment out the following lines in the biopython > setup.py > script : > lines 437-439 : > > Extension('Bio.Restriction.DNAUtils', > ['Bio/Restriction/DNAUtils.c'] > ), > > To comment, put a # in front of them. This will break the Restriction > package but it would not have worked on Python2.2 anyway. > Hope this is of some help > Fred From bugzilla-daemon at portal.open-bio.org Wed Aug 25 11:27:30 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1684] Error in Compiling DNAUtils Message-ID: <200408251527.i7PFRUA3005011@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1684 ------- Additional Comments From f.sohm@whsmithnet.co.uk 2004-08-25 11:27 ------- Created an attachment (id=166) --> (http://bugzilla.open-bio.org/attachment.cgi?id=166&action=view) modified biopython setup.py to fix bug #1684 Added conditional compilation of DNAUtils.c if Python version is less than 2.3 DNAUtils.c will not be compiled. This break Restriction but it would not have worked under Python2.2 anyway ------- 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 Aug 25 11:30:33 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1684] Error in Compiling DNAUtils Message-ID: <200408251530.i7PFUXfJ005068@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1684 f.sohm@whsmithnet.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Additional Comments From f.sohm@whsmithnet.co.uk 2004-08-25 11:30 ------- The new setup.py should fix any problem on Python2.2 No need to fix DNAUtils.c in order to get it to compile under 2.2 as Restriction needs the facilities provided by Python2.3 ------- 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 Aug 25 12:14:37 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1689] New: Seq is broken in CVS Message-ID: <200408251614.i7PGEbBE005483@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1689 Summary: Seq is broken in CVS Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: f.sohm@whsmithnet.co.uk CC: biopython-dev@biopython.org Hi, The last modification in Bio.Seq to integrate the complement() and reverse_complement() break the module. Notably a seq.alphabet in place of self.alphabet block complement to work While I was at it I have made some modification to support lower case DNA. See in the attachement take what you like and discard the rest. Bye Fred ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are on the CC list for the bug, or are watching someone who is. From bugzilla-daemon at portal.open-bio.org Wed Aug 25 11:56:29 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1687] New: triemodule.c broken under Python2.4 Message-ID: <200408251556.i7PFuTvv005303@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1687 Summary: triemodule.c broken under Python2.4 Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: blocker Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: f.sohm@whsmithnet.co.uk CC: biopython-dev@biopython.org Biopython (CVS version) does not compile under Python2.4 This is due to a change in the marshall.c in python 2.4. The change break triemodule.c the call : if(!(py_marshalled = PyMarshal_WriteObjectToString(py_value))) break the compilation because the new PyMarshal_WriteObjectToString take 2 arguments in Python2.4. The second argument being an integer corresponding to the version of Marshal used. Here is a fix : in the function line 472 of triemodule.c: _write_value_to_handle(const void *value, void *handle) The fix is to replace the following lines : if(!(py_marshalled = PyMarshal_WriteObjectToString(py_value))) goto _write_value_to_handle_cleanup; by : #ifdef Py_MARSHAL_VERSION if(!(py_marshalled = PyMarshal_WriteObjectToString(py_value, Py_MARSHAL_VERSION))) goto _write_value_to_handle_cleanup; #else if(!(py_marshalled = PyMarshal_WriteObjectToString(py_value))) goto _write_value_to_handle_cleanup; #endif Py_MARSHAL_VERSION is a new macro defined in marshal.h It correspond to the version of marshal.c (1 at the moment). If Py_MARSHAL_VERSION is not defined we can assume that the Python version is less than 2.4 and carry on as normal, otherwise we provide the integer. I have not verified that triemodule.c still perform as expected but the compilation can carry on. Hope this is helpful Fred ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are on the CC list for the bug, or are watching someone who is. From bugzilla-daemon at portal.open-bio.org Wed Aug 25 12:09:22 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1688] Restriction.py problem with catalyze method Message-ID: <200408251609.i7PG9MbI005457@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1688 ------- Additional Comments From f.sohm@whsmithnet.co.uk 2004-08-25 12:09 ------- Created an attachment (id=167) --> (http://bugzilla.open-bio.org/attachment.cgi?id=167&action=view) Modified Restriction.py module Modified the catalyze method. Now support circular sequences. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are on the CC list for the bug, or are watching someone who is. From bugzilla-daemon at portal.open-bio.org Wed Aug 25 12:07:43 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1688] New: Restriction.py problem with catalyze method Message-ID: <200408251607.i7PG7hxB005437@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1688 Summary: Restriction.py problem with catalyze method Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: f.sohm@whsmithnet.co.uk CC: biopython-dev@biopython.org Hi Brad, You wont get ride of the British so easily. Your modification to allow an americanized catalyze method forbid the use of circular sequences. It is partly my fault because it was a mistake in one of the class. I have made remodified the module will attach it to the bug report. Bye Fred ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are on the CC list for the bug, or are watching someone who is. From bugzilla-daemon at portal.open-bio.org Wed Aug 25 12:22:37 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1689] Seq is broken in CVS Message-ID: <200408251622.i7PGMb7Y005640@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1689 ------- Additional Comments From f.sohm@whsmithnet.co.uk 2004-08-25 12:22 ------- Created an attachment (id=168) --> (http://bugzilla.open-bio.org/attachment.cgi?id=168&action=view) Seq.py with some fix in complement and reverse_complement() Added a method __maketrans in Seq in Seq.complement() and Seq.reverse_complement() replaced seq.alphabet by self.alphabet. Added support for lower case DNA in Seq.complement() and Seq.reverse_complement. Same thing in MutableSeq.complement() I wonder if returning a Seq from a complement is a good idea as well if your original sequence is a DNA(going 5'->3') the complement will not be a DNA (it goes 3'->5'). Bye Fred Fred ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are on the CC list for the bug, or are watching someone who is. From mdehoon at ims.u-tokyo.ac.jp Thu Aug 26 09:15:06 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1689] Seq is broken in CVS Message-ID: <412DE25A.5000907@ims.u-tokyo.ac.jp> bugzilla-daemon@portal.open-bio.org wrote: > http://bugzilla.open-bio.org/show_bug.cgi?id=1689 > in Seq.complement() and Seq.reverse_complement() replaced seq.alphabet by > self.alphabet. Oops. That was a typo. Thanks for catching that. > Added a method __maketrans in Seq > > Added support for lower case DNA in Seq.complement() and > Seq.reverse_complement. Same thing in MutableSeq.complement() Looks good to me. I'll add that to CVS. Thanks. >> I wonder if returning a Seq from a complement is a good idea as well >> if your original sequence is a DNA(going 5'->3') the complement will not be a >> DNA (it goes 3'->5'). The complement and reverse_complement were added to Seq.py because previously several implementations of similar functions existed in different parts of Biopython. The function forward_complement in Bio.GFF.easy takes a Seq object and returns a Seq object. The function complement in Bio.SeqUtils takes a string and returns a string. I have a slight preference for returning a Seq object for consistency with MutableSeq, and also because a user might expect to receive an object of the same type. Anybody else have an opinion on this? >>> from Bio.Seq import * >>> from Bio.GFF.easy import * >>> s = Seq('ATCGCT') >>> forward_complement(s) Seq('TAGCGA', Alphabet()) >>> >>> from Bio.SeqUtils import complement >>> s = 'ATCGCT' >>> complement(s) 'TAGCGA' >>> Thanks, Fred. --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 hoffman at ebi.ac.uk Thu Aug 26 09:17:38 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1689] Seq is broken in CVS In-Reply-To: <412DE25A.5000907@ims.u-tokyo.ac.jp> References: <412DE25A.5000907@ims.u-tokyo.ac.jp> Message-ID: On Thu, 26 Aug 2004, Michiel Jan Laurens de Hoon wrote: > The complement and reverse_complement were added to Seq.py because previously > several implementations of similar functions existed in different parts of > Biopython. The function forward_complement in Bio.GFF.easy takes a Seq object > and returns a Seq object. The function complement in Bio.SeqUtils takes a string > and returns a string. I have a slight preference for returning a Seq object for > consistency with MutableSeq, and also because a user might expect to receive an > object of the same type. I understand what Fred was saying but I agree with Michiel's logic here. If I started with a Seq I would expect to get one back from a reverse function. -- Michael Hoffman European Bioinformatics Institute From bugzilla-daemon at portal.open-bio.org Thu Aug 26 10:00:30 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1687] triemodule.c broken under Python2.4 Message-ID: <200408261400.i7QE0UZM024844@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1687 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From jchang@biopython.org 2004-08-26 10:00 ------- I've committed this to the CVS. Behavior is still unverified, though, but unlikely to cause problems. Thanks for the patch! ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are on the CC list for the bug, or are watching someone who is. From f.sohm at whsmithnet.co.uk Thu Aug 26 11:32:15 2004 From: f.sohm at whsmithnet.co.uk (f.sohm@whsmithnet.co.uk) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] Re: Seq is broken in CVS In-Reply-To: References: <412DE25A.5000907@ims.u-tokyo.ac.jp> Message-ID: Michael Hoffman writes: > On Thu, 26 Aug 2004, Michiel Jan Laurens de Hoon wrote: > >> The complement and reverse_complement were added to Seq.py because previously >> several implementations of similar functions existed in different parts of >> Biopython. The function forward_complement in Bio.GFF.easy takes a Seq object >> and returns a Seq object. The function complement in Bio.SeqUtils takes a string >> and returns a string. I have a slight preference for returning a Seq object for >> consistency with MutableSeq, and also because a user might expect to receive an >> object of the same type. > > I understand what Fred was saying but I agree with Michiel's logic > here. If I started with a Seq I would expect to get one back from a > reverse function. > -- > Michael Hoffman > European Bioinformatics Institute > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev Hi, I see your point there. But I still think that for some applications the chance to do a silly mistake outweight the benefit. In fact, thinking about it : would not be a good time to add another set of class to take care of sequences. DNA, RNA and protein respectively? I mean Seq and MutableSeq do their job and do it well, but it is mainly database oriented. A translation in plain English of what Seq and MutableSeq do, is more or less : 'containing the boring lines of repetitive letters that people keep adding at the end of their genbank/EMBL records.' ;-) Seq and MutableSeq do not 'care' about what the sequence they hold really is. Hence the lake of consistency between the Alphabet and the data (see the mail of Michiel some time ago). You get as well a problem with the representation of biological forms of DNA for example. Seq do not make the difference between a circular sequence and a linear sequence. You can add without problem two DNAs cut with incompatible restriction enzymes. etc ... I would like to know if people think it is worth to go this way and implement these three types of class (may be more double stranded and single stranded nucleic acids are to be considered). I can throw in a set of class to implement the DNA. But it will only be interesting if somebody else help to tackle the Protein. Anyway if people are interested I think it would be better to think about it carefully before hand. bye Fred From hoffman at ebi.ac.uk Thu Aug 26 11:38:29 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] Re: Seq is broken in CVS In-Reply-To: References: <412DE25A.5000907@ims.u-tokyo.ac.jp> Message-ID: On Thu, 26 Aug 2004 f.sohm@whsmithnet.co.uk wrote: > Seq do not make the difference between a circular sequence and > a linear sequence. You can add without problem two DNAs cut with > incompatible restriction enzymes. etc ... > > I would like to know if people think it is worth to go this way and > implement these three types of class (may be more double stranded and single > stranded nucleic acids are to be considered). YAGNI. http://c2.com/cgi/wiki?YouArentGonnaNeedIt -- Michael Hoffman European Bioinformatics Institute From bugzilla-daemon at portal.open-bio.org Sun Aug 29 02:40:47 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1689] Seq is broken in CVS Message-ID: <200408290640.i7T6elVu025908@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1689 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2004-08-29 02:40 ------- Accepted the changes as described in the attachment. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are on the CC list for the bug, or are watching someone who is.