From bugzilla-daemon at portal.open-bio.org Thu Jan 5 12:47:08 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Jan 5 12:59:00 2006 Subject: [Biopython-dev] [Bug 1920] Bio.Geo does not support recent GEO files Message-ID: <200601051747.k05Hl8FT019768@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1920 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from biopython-bugzilla@maubp.freeserve.co.uk 2006-01-05 12:47 ------- Changes checked into CVS to tackle the issues raised in comment 1 and comment 3 I have also confirmed the existing test cases still pass. Barring any objections, I plan to include the five NCBI test cases soon - see comment 2 Their total size is 55kb, and this would also increase the size of the Bio/Tests/output/test_geo file from 16kb to 74kb - so an extra 113kb or thereabouts. By my reading of the NCBI's Data Disclaimer there is no problem with copyright: http://www.ncbi.nlm.nih.gov/projects/geo/info/disclaimer.html ------- 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 Fri Jan 6 13:07:38 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Jan 6 13:58:52 2006 Subject: [Biopython-dev] [Bug 1758] genbank parser chokes on /transl_except Message-ID: <200601061807.k06I7coe012490@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1758 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #3 from biopython-bugzilla@maubp.freeserve.co.uk 2006-01-06 13:07 ------- This example also failed to parse in the replacement non-martel GenBank parser. A fix has been checking into CVS which will accept such files, but will print a warning message. Confirmed that test_GenBank.py and test_GenBankFormat.py both still pass. ------- 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 Tue Jan 17 06:19:10 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Jan 17 06:58:59 2006 Subject: [Biopython-dev] [Bug 1929] Extra reference in BLASTPGP plain text output Message-ID: <200601171119.k0HBJA2k004805@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1929 ------- Comment #1 from biopython-bugzilla@maubp.freeserve.co.uk 2006-01-17 06:19 ------- Created an attachment (id=263) --> (http://bugzilla.open-bio.org/attachment.cgi?id=263&action=view) Example BLASTAPGP output, plain text Script from the bug reporter: #!/usr/bin/python import os from Bio.Blast import NCBIStandalone blast_out = open('blast.output2', 'r') b_parser = NCBIStandalone.BlastParser() b_iterator = NCBIStandalone.Iterator(blast_out, b_parser) while 1: b_record = b_iterator.next() if b_record is None: break for alignment in b_record.alignments: for hsp in alignment.hsps: if hsp.expect < 0.04: print 'sequence:' , alignment.title ------- 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 Tue Jan 17 06:17:17 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Tue Jan 17 06:59:00 2006 Subject: [Biopython-dev] [Bug 1929] New: Extra reference in BLASTPGP plain text output Message-ID: <200601171117.k0HBHHnV004696@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1929 Summary: Extra reference in BLASTPGP plain text output Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: biopython-bugzilla@maubp.freeserve.co.uk Reported on the mailing list by Alessandro Nascimento, http://portal.open-bio.org/pipermail/biopython/2006-January/002883.html BLASTP 2.2.12 [Aug-07-2005] and possibly other versions include a second reference which breaks the plain text blast parser: Reference for composition-based statistics: Schaffer, Alejandro A., L. Aravaind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005. Removing these lines from the blast output allows the file to be parsed. I tested this on BioPython 1.41, Python 2.4 under linux ------- 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 Thu Jan 19 11:37:29 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Jan 19 11:58:59 2006 Subject: [Biopython-dev] [Bug 1933] Iterator support for Standalone XML blast output with multiple querys Message-ID: <200601191637.k0JGbTxT014023@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1933 ------- Comment #1 from biopython-bugzilla@maubp.freeserve.co.uk 2006-01-19 11:37 ------- Created an attachment (id=266) --> (http://bugzilla.open-bio.org/attachment.cgi?id=266&action=view) Updates the NCBI BLAST iterator Suggested fixed from Michael Anthony Maibaum http://www.biopython.org/pipermail/biopython/2006-January/002889.html This makes the NCBI Blast iterator aware of breaking lines at the declation. ------- 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 Thu Jan 19 11:42:42 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Jan 19 11:59:00 2006 Subject: [Biopython-dev] [Bug 1933] Iterator support for Standalone XML blast output with multiple querys Message-ID: <200601191642.k0JGggO7014209@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1933 ------- Comment #2 from biopython-bugzilla@maubp.freeserve.co.uk 2006-01-19 11:42 ------- I'm wondering if it would be better to create a separate "XML Blast Iterator" to live in the NCBIXML.py file, rather than enhance the existing iterator in NCBIStandalone.py Comments? ------- 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 Thu Jan 19 11:36:29 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Thu Jan 19 11:59:01 2006 Subject: [Biopython-dev] [Bug 1933] New: Iterator support for Standalone XML blast output with multiple querys Message-ID: <200601191636.k0JGaTHt013970@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1933 Summary: Iterator support for Standalone XML blast output with multiple querys Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: biopython-bugzilla@maubp.freeserve.co.uk Reported on the mailing lists by David Weisman: http://www.biopython.org/pipermail/biopython/2006-January/002881.html > I tried using NCBIXML parsing on a local blast run, > in which the input had multiple query sequences. > Blastall writes multiple xml documents to the output file, > and the SAX parser threw a SAXParseException on the second > declaration, complaining of junk after the > document element. i.e. The output is a series of valid XML documents concatenated together. ------- 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 Sun Jan 22 12:09:50 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sun Jan 22 12:59:18 2006 Subject: [Biopython-dev] [Bug 1936] New: Bio.PDB.PDBParser throws PDBException, 'No parent' in error Message-ID: <200601221709.k0MH9obd019728@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1936 Summary: Bio.PDB.PDBParser throws PDBException, 'No parent' in error Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: biopython-bugzilla@maubp.freeserve.co.uk Tested on Linux with Python 2.4, BioPython 1.41 I have also updated the Bio/PDB/ directory to CVS, and the problem is the same. Test script using file 5NUL.pdb which was downloaded from the the PDB (one of several files which will trigger this error): from Bio.PDB.PDBParser import PDBParser parser=PDBParser(PERMISSIVE=True) pdb = "5NUL" filename = pdb + ".pdb" structure=parser.get_structure(pdb, filename) print structure.id for model in structure : for chain in model : print "%s:%i:%s" % (structure.id,model.id,chain.id) Traceback (most recent call last): File "/home/maubp/ramachandran/test_bio.py", line 5, in -toplevel- structure=parser.get_structure(pdb, filename) File "/usr/lib/python2.4/site-packages/Bio/PDB/PDBParser.py", line 66, in get_structure self._parse(file.readlines()) File "/usr/lib/python2.4/site-packages/Bio/PDB/PDBParser.py", line 87, in _parse self.trailer=self._parse_coordinates(coords_trailer) File "/usr/lib/python2.4/site-packages/Bio/PDB/PDBParser.py", line 179, in _parse_coordinates structure_builder.init_residue(resname, hetero_flag, resseq, icode) File "/usr/lib/python2.4/site-packages/Bio/PDB/StructureBuilder.py", line 155, in init_residue self.chain.add(residue) File "/usr/lib/python2.4/site-packages/Bio/PDB/Entity.py", line 80, in add raise PDBConstructionException, "%s defined twice" % entity.get_full_id() File "/usr/lib/python2.4/site-packages/Bio/PDB/Entity.py", line 132, in get_full_id parent=self.get_parent() File "/usr/lib/python2.4/site-packages/Bio/PDB/Entity.py", line 102, in get_parent raise PDBException, 'No parent' PDBException: No parent It looks like it tries to raise a PDBConstructionException for some entity being defined twice, but getting the full ID for the exception message fails. Possible fix in Bio/PDB/Entity.py class Entity add method: def add(self, entity): "Add a child to the Entity." entity_id=entity.get_id() if self.has_id(entity_id): #PJC change #raise PDBConstructionException, \ #"%s defined twice" % entity.get_full_id() try : full_id = entity.get_full_id() except: full_id = "%s/%s/%s" % entity_id raise PDBConstructionException, "%s defined twice" % full_id entity.set_parent(self) self.child_list.append(entity) #self.child_list.sort(self._sort) self.child_dict[entity_id]=entity Results in this output from my example: PDBConstructionException: W/285/ defined twice at line 1684. Exception ignored. Some atoms or residues will be missing in the data structure. PDBConstructionException: Atom O defined twice in residue at line 1684. Exception ignored. Some atoms or residues will be missing in the data structure. 5NUL 5NUL:0: ------- 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 Jan 25 14:35:50 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Wed Jan 25 15:35:22 2006 Subject: [Biopython-dev] [Bug 1933] Iterator support for Standalone XML blast output with multiple querys Message-ID: <200601251935.k0PJZo3k011600@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1933 ------- Comment #3 from mdehoon@ims.u-tokyo.ac.jp 2006-01-25 14:35 ------- Is there an example script demonstrating XML parsing of multiple blast query results? (Preferably, one that we can use as a test case). ------- 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 Fri Jan 27 22:20:01 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Jan 27 22:34:49 2006 Subject: [Biopython-dev] [Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601280320.k0S3K1o6002608@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 bill@barnard-engineering.com changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |bill@barnard-engineering.com OS/Version|Linux |All ------- Comment #1 from bill@barnard-engineering.com 2006-01-27 22:19 ------- I rewrote the Makefile for the Doc directory subtree. The gist of the work was to properly call pdflatex, hevea, & hacha to build the pdfs, htmls, & txt files from their .tex input files. I made a common.mk file to abstract the common parts from the subdirectory makefiles. I created a patch for the Doc/biopdb_faq.tex file, generated from Doc/biopdb_faq.lyx, which contained an error from the perspective of the doc-generating utilities. I modified MANIFEST.in to include the new files, and to exclude the files which will be subsequently generated by the make/build and hence included in the distribution. I added a one line mod to setup.py to call the Doc make [ os.system('make -C Doc') ]. I sent these changes to the mailing list http://www.biopython.org/pipermail/biopython/2005-September/002777.html Recently I retrieved updates from CVS and discovered a small change I needed to make. Doc/Makefile did not correctly clean the dirs and subdirs; I fixed that with a command line env target, e.g. "make TARGET=clean". I also modified the top level Makefile which called make clean for the Doc directory so it uses the new calling convention. (This is probably irrelevant to the purpose of that makefile however.) The associated patches and new files will be attached to this bug report. ------- 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 Fri Jan 27 22:25:10 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Jan 27 22:34:59 2006 Subject: [Biopython-dev] [Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601280325.k0S3PApg002647@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 ------- Comment #2 from bill@barnard-engineering.com 2006-01-27 22:25 ------- Created an attachment (id=274) --> (http://bugzilla.open-bio.org/attachment.cgi?id=274&action=view) common portions to all Doc directory makefiles to be included in Makefile(s) common.mk abstracts all common portions of Doc/Makefile and subdirectory Makefile(s) into a single place which can be included by those Makefiles. ------- 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 Fri Jan 27 22:13:10 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Jan 27 22:36:19 2006 Subject: [Biopython-dev] [Bug 1939] New: Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601280313.k0S3D9mj002565@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 Summary: Doc/Makefile does not build pdf, html, txt files completely correctly Product: Biopython Version: Not Applicable Platform: All OS/Version: Linux Status: NEW Severity: minor Priority: P2 Component: Documentation AssignedTo: biopython-dev@biopython.org ReportedBy: bill@barnard-engineering.com Existing Doc/Makefile does not correctly call all utilities for creating pdf, html, and txt outputs from the .tex inputs. In particular the hevea utility needs to be called twice the create the html outputs. The txt outputs can/should be created from the .tex inputs. Also the by-products (aux, log, out, toc, haux, htoc) of the build should be removed while doing the standard make so the overall build works from a clean, complete tree. The subdirectories Makefiles should be called from the Doc/Makefile in a recursive or similar manner, and the same issues apply to those directories. Finally the output files (html, pdf, txt) are currently checked into CVS; they should be removed from CVS and generated by the make/build process instead. ------- 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 Fri Jan 27 22:36:47 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Jan 27 23:34:42 2006 Subject: [Biopython-dev] [Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601280336.k0S3alTP002794@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 ------- Comment #3 from bill@barnard-engineering.com 2006-01-27 22:36 ------- Created an attachment (id=275) --> (http://bugzilla.open-bio.org/attachment.cgi?id=275&action=view) fix "improperly" generated biodb_faq.tex (output of biopdb_faq.lyx) Generating html from biopdb_faq.tex has a minor failure (resulting in a missing image file referenced in the html) due to lack of bounding box information in the .tex file. Since the .tex file is exported (I assume) from the .lyx file, I thought the "problem" should be fixed there. I did not figure it out, and didn't want to learn too much more about LyX in order to do so. Instead I created a patch file for the .tex file that permits proper html generation by hevea. The patch is applied in the Makefile. ------- 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 Fri Jan 27 22:42:28 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Jan 27 23:35:00 2006 Subject: [Biopython-dev] [Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601280342.k0S3gSp1002917@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 ------- Comment #4 from bill@barnard-engineering.com 2006-01-27 22:42 ------- Created an attachment (id=276) --> (http://bugzilla.open-bio.org/attachment.cgi?id=276&action=view) Fix all other Makefiles and related build files This completes all needed changes to all the Makefiles, and related build files to make required build changes. ------- 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 Fri Jan 27 22:44:39 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Fri Jan 27 23:35:19 2006 Subject: [Biopython-dev] [Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601280344.k0S3idrG002943@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 ------- Comment #5 from bill@barnard-engineering.com 2006-01-27 22:44 ------- Original bug reports were made in the following mailing list entries: http://www.biopython.org/pipermail/biopython/2005-September/002775.html http://www.biopython.org/pipermail/biopython/2005-September/002776.html http://www.biopython.org/pipermail/biopython/2005-September/002777.html http://www.biopython.org/pipermail/biopython/2006-January/002894.html ------- 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 Sat Jan 28 06:34:26 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Jan 28 07:34:55 2006 Subject: [Biopython-dev] [Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601281134.k0SBYPfd008350@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 ------- Comment #6 from biopython-bugzilla@maubp.freeserve.co.uk 2006-01-28 06:34 ------- In the orginal report: > Finally the output files (html, pdf, txt) are currently > checked into CVS; they should be removed from CVS and > generated by the make/build process instead. Having them in CVS can be very helpful for those just browsing the web interface to see what's changed recently. In comment 1 Bill wrote: > I added a one line mod to setup.py to call > the Doc make [ os.system('make -C Doc') ]. Will this work on the Windows platform? I have never tried to build BioPython on Windows, but I am fairly sure that make isn't present by default. ------- 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 Sat Jan 28 17:56:51 2006 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Jan 28 18:34:47 2006 Subject: [Biopython-dev] [Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly Message-ID: <200601282256.k0SMupYH015528@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1939 ------- Comment #7 from bill@barnard-engineering.com 2006-01-28 17:56 ------- In the original report: > > Finally the output files (html, pdf, txt) are currently > > checked into CVS; they should be removed from CVS and > > generated by the make/build process instead. > > Having them in CVS can be very helpful for those just > browsing the web interface to see what's changed recently. Agreed. Maybe it's best to leave them in CVS. Whoever checks in new doc source files will need to remember to run the make to update the outputs though. > > In comment 1 Bill wrote: > > I added a one line mod to setup.py to call > > the Doc make [ os.system('make -C Doc') ]. > > Will this work on the Windows platform? I have never tried to build BioPython > on Windows, but I am fairly sure that make isn't present by default. Good point. The system call returns a zero on my linux box. If make is not found in the path, as would be normal on a windows box, then the os.system call simply returns the exit status for the command and the code continues running. The Doc make calls the pdflatex, hevea, & hacha programs which are unlikely to be on a windows box either. In any case, if the Doc build programs are not present in the path then some error messages are written to stdout and setup.py continues to run. I think the worst case on Windows would be that the Doc build output files might be out of date with respect to the .tex source files. So I'd leave the new line in setup.py. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.