gotgenes (Chris Lasher)

Tiding up some warnings, and deprecating Bio.utils.ungap() function

Adding Seq object ungap method developed on one of my git branches plus explicit UnknownSeq support (see mailing list)

State the the legacy BLAST wrappers in Bio.Blast.Applications are obsolete

Removing deprecated module Bio.PubMed (use Bio.Entrez instead)

Deprecating the obsolete module Bio.listfns(most of this is covered by Python itself nowadays)

Remove Bio.pairwise2.py dependency on obsolete Bio.listfns (which used a naive Python implementation anyway, not C code)

More doctests in Bio/Seq.py

Include new Bio.SeqFeature doctests in test suite

Basic doctests for Bio.SeqFeature, and checking strand and location arguments

Adding a few PMC associated DTD files, http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/dtd/pmc-1.dtd and http://www.pubmedcentral.nih.gov/pmcdoc/dtd/nlm_lib/articleset/nlm-articleset-2.0.dtd

Parse atom element field in PDB files (Bug 2495)

Adding a small real PDB file containing some HETATM lines for use in unit tests

Unit test and fix for SeqFeature locations in new SeqRecord __radd__ method

Basic unit test for SeqRecord slicing with a full length source feature

Fixed SeqRecord slicing for SeqFeature with OneOfPosition

Adding final tests for the MAST parser

Fixed bug that left last term stanza unparsed.

Adding code to Ontology get/set functions. Added Bio.GO to setup.py build list.

The start of a obo parser. Currently will setup basic GOTerms.

Removing the deprecated module Bio.SCOP.FileIndex

Removing the deprecated function pairlist_to_dict from Bio.InterPro

Don't nag Jython users about NumPy not being installed. Fix from Kyle Ellrott on github

Tiding up some warnings, and deprecating Bio.utils.ungap() function

Adding Seq object ungap method developed on one of my git branches plus explicit UnknownSeq support (see mailing list)

State the the legacy BLAST wrappers in Bio.Blast.Applications are obsolete

Removing deprecated module Bio.PubMed (use Bio.Entrez instead)

Deprecating the obsolete module Bio.listfns(most of this is covered by Python itself nowadays)

Remove Bio.pairwise2.py dependency on obsolete Bio.listfns (which used a naive Python implementation anyway, not C code)

More doctests in Bio/Seq.py

Include new Bio.SeqFeature doctests in test suite

Basic doctests for Bio.SeqFeature, and checking strand and location arguments

Adding a few PMC associated DTD files, http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/dtd/pmc-1.dtd and http://www.pubmedcentral.nih.gov/pmcdoc/dtd/nlm_lib/articleset/nlm-articleset-2.0.dtd

Parse atom element field in PDB files (Bug 2495)

Adding a small real PDB file containing some HETATM lines for use in unit tests

Unit test and fix for SeqFeature locations in new SeqRecord __radd__ method

Basic unit test for SeqRecord slicing with a full length source feature

Fixed SeqRecord slicing for SeqFeature with OneOfPosition

Adding final tests for the MAST parser

Working on standalone BLAST section of the Tutorial

Starting work on the BLAST chapter of the tutorial. Moving online section to the start (simpler for beginners)

Should have all BLAST+ command line arguments supported now, except soft_masking and use_index where it is unclear from the documentation if they should be a 'switch' or an 'option' taking a boolean argument

Adding more missing NCBI BLAST+ options (guided by the new unit test), should be everything except for some blastn options

Adding more missing NCBI BLAST+ options (guided by the new unit test)

Adding more missing NCBI BLAST+ options (guided by the new unit test)

BLAST culling_limit, best_hit_overhang and best_hit_score_edge options

Aadding more missing BLAST+ command line tool arguments to wrappers

Adding unit test for new NCBI BLAST wrappers

Working on adding missing core BLAST+ command line tool arguments to wrappers

Fixed typo in new warning.

Update Bio.ExPASy.get_sprot_raw() to use URL http://www.uniprot.org/uniprot/XXX.txt as per http://www.expasy.ch/expasy_urls.html since the old URL http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?XXX is currently returning FASTA format. See report via mailing list. This fixes test_SeqIO_online.py

Adding a more explicit test for the MAST parser; skipping the parser code that does not work yet

Starting work on the BLAST chapter of the tutorial. Moving online section to the start (simpler for beginners)

Should have all BLAST+ command line arguments supported now, except soft_masking and use_index where it is unclear from the documentation if they should be a 'switch' or an 'option' taking a boolean argument

Adding more missing NCBI BLAST+ options (guided by the new unit test), should be everything except for some blastn options

Adding more missing NCBI BLAST+ options (guided by the new unit test)

Adding more missing NCBI BLAST+ options (guided by the new unit test)

BLAST culling_limit, best_hit_overhang and best_hit_score_edge options

Aadding more missing BLAST+ command line tool arguments to wrappers

Adding unit test for new NCBI BLAST wrappers

Working on adding missing core BLAST+ command line tool arguments to wrappers

Fixed typo in new warning.

Update Bio.ExPASy.get_sprot_raw() to use URL http://www.uniprot.org/uniprot/XXX.txt as per http://www.expasy.ch/expasy_urls.html since the old URL http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?XXX is currently returning FASTA format. See report via mailing list. This fixes test_SeqIO_online.py

Adding a more explicit test for the MAST parser; skipping the parser code that does not work yet

Adding sample XML output from new C++ BLAST blastx 2.2.22+

Updating BLAST plain text parser to cope with new C++ NCBI tools from NCBI, with unit test of blastx 2.2.22+ output

Progress with parsing plain text BLASTX 2.2.22+ output

New BLAST text output has no blank line after query and its length

Cope with new date-less first line in BLAST 2.2.22+ plain text output

Adding blastall 2.2.22 BLASTX output example

Reorder the test methods following file renumbering

Renumbering plain text BLAST files bt102 to bt105 to fit existing sequence

Renumbering plain text BLAST files in order to insert bt102 to bt105 in correct sequence

Removing unused HTML BLAST files, bt100 and bt101

Adding a BLASTP 2.2.21 plain text file

Updating the plain text NCBI BLAST parser to cope with a recent multi-query file.

Renaming plain text BLAST examples to have .txt extension

Whitespace fix in parsing database name from BLAST plain text output

These XML files don't need to be marked as executable (relevant only on Unix)

Adding two BLASTX examples to the unit tests

Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obsolete. Need to update the tutorial still...

Merge branch 'master' of git@github.com:biopython/biopython

Bio.Blast.NCBIXML.read() function was missing in module docstring

Be consistent with _current_ref versus _cur_reference in the two GenBank consumers

Cope with blank line in GenBank files after ORIGIN but before sequence

Fix for corner case with missing GenBank annotation

Expose the FASTA al_start and al_end information as private properties in the short term, pending proper support later on. See mailing list discussion

Installation document still talked about CVS not git

Update Bio.PDB.PDBList to cope with revised formatting of files ftp://ftp.wwpdb.org/pub/pdb/status/yyyymmdd/added.pdb .../modified.pdb and .../obsolete.pdb (Bug 2933)

Update Bio.PDB.PDBList to cope with revised formatting of file ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat (Bug 2929)

Fixed typo in warning message

Silence Bio.Application deprecation warnings in test_Clustalw_tool.py

Skip test_Entrez.py under Jython as the XML parser doesn't work. See Biopython Bug 2918 and the underlying Jython bug http://bugs.jython.org/issue1447

Update BLAST XML parser to work on Jython, based on a fix on github by Kyle Ellrott. Tested on Jython 2.5.1

Updating DEPRECATED file regarding Bio.Application and Bio.WWW

Deprecating Bio.Application.generic_run and ApplicationResult

Adding hook to help run the doctests during development

Working on adding the common BLAST+ arguments to the new wrappers

Working on adding the common BLAST+ arguments to the new wrappers

Working on the core of the new BLAST wrappers

Contribution from Chris Lasher to add verbose option to run_tests.py

Added -v;--verbosity option to run_tests.py.

The classic BLAST tool wrappers are obsolete now. We must write wrappers for the new BLAST+ tools instead...

Starting to update the Tutorial for BLAST+

Adding a BLASTP 2.2.22+ output file from new NCBI C++ blastx tool

Updated NEWS file with BLAST parsing work

Support database_sequences as well as num_sequences_in_database when parsing BLAST XML (see Bug 2176 for similar issues)

Adding sample XML output from new C++ BLAST blastx 2.2.22+

Updating BLAST plain text parser to cope with new C++ NCBI tools from NCBI, with unit test of blastx 2.2.22+ output

Progress with parsing plain text BLASTX 2.2.22+ output

New BLAST text output has no blank line after query and its length

Cope with new date-less first line in BLAST 2.2.22+ plain text output

Adding blastall 2.2.22 BLASTX output example

Reorder the test methods following file renumbering

Renumbering plain text BLAST files bt102 to bt105 to fit existing sequence

Renumbering plain text BLAST files in order to insert bt102 to bt105 in correct sequence

Removing unused HTML BLAST files, bt100 and bt101

Adding a BLASTP 2.2.21 plain text file

Updating the plain text NCBI BLAST parser to cope with a recent multi-query file.

Whitespace fix in parsing database name from BLAST plain text output

These XML files don't need to be marked as executable (relevant only on Unix)

Adding two BLASTX examples to the unit tests

Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obsolete. Need to update the tutorial still...

Merge branch 'master' of git@github.com:biopython/biopython

Bio.Blast.NCBIXML.read() function was missing in module docstring

Abstracted out some of the classes and methods.

Added GOTerm.__repr__()

Added verbosity option.