From bugzilla-daemon at portal.open-bio.org Wed Jun 8 14:11:38 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Jun 8 14:34:27 2005 Subject: [Biopython-dev] [Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so... Message-ID: <200506081811.j58IBX7C001528@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1812 misiek@genesilico.pl changed: What |Removed |Added ---------------------------------------------------------------------------- Severity|normal |enhancement ------- 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 Jun 8 14:14:28 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Jun 8 14:34:33 2005 Subject: [Biopython-dev] [Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so... Message-ID: <200506081814.j58IESSc001577@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1812 misiek@genesilico.pl changed: What |Removed |Added ---------------------------------------------------------------------------- BugsThisDependsOn| |1813 ------- 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 Jun 8 14:04:03 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Jun 8 14:34:35 2005 Subject: [Biopython-dev] [Bug 1812] New: Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so... Message-ID: <200506081804.j58I43L1001373@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1812 Summary: Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so... 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: misiek@genesilico.pl Writing a structure with Bio.PDB.PDBIO means a loss of all header information (essentially all anything that's not ATOM,HETATM,TER,END,MODEL,CONECT). ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 13 16:24:19 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Jun 13 16:31:51 2005 Subject: [Biopython-dev] [Bug 1816] New: Error when importing GenBank file into BioSQL database Message-ID: <200506132024.j5DKOJjJ029593@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1816 Summary: Error when importing GenBank file into BioSQL database Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: BioSQL AssignedTo: biopython-dev@biopython.org ReportedBy: scresawn@ufl.edu When importing a GenBank file with accession number AY243312 into a BioSQL database, I get an error. (See below.) Importing the file was done according to the documentation at http://biopython.org/docs/biosql/python_biosql_basic.html I'm using python-2.3.4 and biopython-1.40b. The biosql-schema was checked out today (6/13/05) from cvs. The error follows: >>> db.load(iterator) Traceback (most recent call last): File "", line 1, in ? File "BioSQL/BioSeqDatabase.py", line 414, in load db_loader.load_seqrecord(cur_record) File "BioSQL/Loader.py", line 43, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "BioSQL/Loader.py", line 324, in _load_reference (reference.pubmed_id,)) File "BioSQL/BioSeqDatabase.py", line 287, in execute_and_fetch_col0 self.cursor.execute(sql, args or ()) File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 95, in execute return self._execute(query, args) File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 114, in _execute self.errorhandler(self, exc, value) File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler raise errorclass, errorvalue _mysql_exceptions.ProgrammingError: (1064, "You have an error in your SQL syntax near 'USING (dbxref_id) WHERE dbname = 'PUBMED' AND accession = '7060133'' at line 1") ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at c2b2.columbia.edu Fri Jun 17 15:42:22 2005 From: mdehoon at c2b2.columbia.edu (Michiel De Hoon) Date: Fri Jun 17 15:37:17 2005 Subject: [Biopython-dev] Re; Rethinking Seq objects Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AE7AC199@cgcmail.cgc.cpmc.columbia.edu> Dear biopythoneers, A couple of weeks ago there was a discussion on the Biopython mailing lists about the Seq and MutableSeq classes in Bio.Seq. Whereas opinions were divided on most of my proposals (which I therefore did not implement), most people agreed that there was a need for a more user-friendly way to transcribe and translate sequences. So I added a transcribe, back_transcribe, and translate function to Bio.Seq. I wrote these as functions rather than a method so that it can take both Seq objects and Python string objects as input. These functions work approximately the same as the corresponding methods in Bio.Transcribe and Bio.Translate. The example in the Biopython tutorial would look like this: Using strings: >>> my_seq = 'GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA' >>> transcribe(my_seq) 'GCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGA' >>> back_transcribe(_) 'GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA' >>> translate(my_seq) 'AIVMGR*KGAR' >>> translate(my_seq,table="Vertebrate Mitochondrial") 'AIVMGRWKGAR' >>> translate(my_seq,table=1) 'AIVMGR*KGAR' >>> translate(my_seq,table=2) 'AIVMGRWKGAR' Using Seq objects: >>> from Bio.Alphabet import IUPAC >>> my_alpha = IUPAC.unambiguous_dna >>> from Bio.Seq import * >>> my_seq = Seq('GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA', IUPAC.unambiguous_dna) >>> transcribe(my_seq) Seq('GCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGA', IUPACUnambiguousRNA()) >>> back_transcribe(_) Seq('GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA', IUPACUnambiguousDNA()) >>> translate(my_seq) Seq('AIVMGR*KGAR', HasStopCodon(IUPACProtein(), '*')) >>> translate(my_seq,table="Vertebrate Mitochondrial") Seq('AIVMGRWKGAR', HasStopCodon(IUPACProtein(), '*')) >>> translate(my_seq,table=1) Seq('AIVMGR*KGAR', HasStopCodon(IUPACProtein(), '*')) >>> translate(my_seq,table=2) Seq('AIVMGRWKGAR', HasStopCodon(IUPACProtein(), '*')) >>> The original methods in Bio.Transcribe and Bio.Translate of course still work (for Seq objects). Thanks, everybody, for contributing to this discussion. I hope these functions will prove to be useful. --Michiel. Michiel de Hoon Center for Computational Biology and Bioinformatics Columbia University 1150 St Nicholas Avenue New York, NY 10032 From bugzilla-daemon at portal.open-bio.org Wed Jun 22 08:24:08 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Jun 22 09:07:05 2005 Subject: [Biopython-dev] [Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so... Message-ID: <200506221224.j5MCO8I2022591@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1812 thamelry@binf.ku.dk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |WONTFIX ------- Additional Comments From thamelry@binf.ku.dk 2005-06-22 08:24 ------- This is not a bug but a feature request. ------- 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 Jun 22 08:26:22 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Jun 22 09:07:07 2005 Subject: [Biopython-dev] [Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so... Message-ID: <200506221226.j5MCQMDn022682@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1812 Bug 1812 depends on bug 1813, which changed state. Bug 1813 Summary: Bio.PDB doesn't understand SEQRES... http://bugzilla.open-bio.org/show_bug.cgi?id=1813 What |Old Value |New Value ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |WONTFIX ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.