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revised gff3 code
2009-09-02 Christopher Leerevised gff3 code
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2009-09-02 Christopher Leeadded GFF3 example of gene building
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2009-09-01 Christopher LeeMerge commit 'remotes/mkszuba/xmlrpc_tutorial' into...
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2009-09-01 Christopher LeeMerge commit 'remotes/ctb/doc_annotations' into tutorial
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2009-09-01 Christopher Leeextracted material for separate database tutorial
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2009-08-29 Christopher Leeremoved unnecessary stat and shutil import from setup.py
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2009-08-14 Christopher Leefixed easy_install bug by protecting coordinator.ResourceFil...
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2009-08-04 Christopher Leefixed blast_test: renamed test_seq_without_db() to...
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2009-08-04 Christopher LeeMerge commit 'remotes/ctb/minor_fixes' into minor_fixes
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2009-08-04 Christopher Leefix port passing in testutil.TestXMLRPCServer
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2009-08-04 Christopher Leeuse pair_identity_tuple() for blast_test formatting...
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2009-08-04 Christopher Leeadded BlastBase.tearDown() to close seqdbs as they...
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2009-08-04 Christopher LeeMerge commit 'remotes/mkszuba/doc_make'
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2009-08-04 Christopher LeeMerge commit 'remotes/mkszuba/rpm'
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2009-07-29 Christopher Leegot rid of BlastMapping.warn_about_self_matches()
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2009-07-29 Christopher Leechanged NLMSA pairwiseMode to allow reporting of self...
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2009-07-29 Christopher LeeMerge commit 'remotes/mkszuba/debian'
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2009-07-29 Christopher Leeretry reading port_file in TestXMLRPCServer several...
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2009-07-29 Christopher Leeadded comments to process_blast()
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2009-07-29 Christopher Leefix problem introduced in process_blast() by commit...
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2009-07-28 Christopher Leehandle missing WINDIR case on Windows
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2009-07-28 Christopher Leeadded SeqTranslator.__repr__()
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2009-07-28 Christopher LeeMerge commit 'remotes/ctb/simpleframe_formatdb_cleanup...
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2009-07-28 Christopher LeeMerge branch 'master' into simpleframe
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2009-07-28 Christopher Leeadded SeqTranslator.iter_frames() method, used in BlastxMapp...
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2009-07-28 Christopher LeeMerge commit 'remotes/ctb/simpleframe_doc_align' into...
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2009-07-27 Christopher Leeprotect 2 more tests using blast_enabled() check
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2009-07-27 Christopher Leefixed syntax error
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2009-07-27 Christopher Leeadded python 2.3 code for FilePopen to detect bad exit...
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2009-07-27 Christopher LeeMerge branch 'no_edge_db'
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2009-07-27 Christopher LeeMerge branch 'silencio'
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2009-07-27 Christopher Leeadded showFormatdbMessages option to BlastMapping
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2009-07-25 Christopher Leeadded support for no-edgeDB case in mapping.Graph:...
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2009-07-23 Christopher Leeadded option for latex output of the reference manual
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2009-07-16 Christopher LeeMerge commit 'remotes/ctb/blast_test_rc' into simpleframe
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2009-07-16 Christopher Leeadded more docstrings for blast.py
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2009-07-16 Christopher Leeremoved old BlastxMapping code
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2009-07-16 Christopher Leenew, greatly simplified BlastxMapping
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2009-07-16 Christopher Leeswitched test_blastx_server to use new TranslationDB...
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2009-07-16 Christopher Leeadded read_blast_alignment() translateDest option
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2009-07-16 Christopher Leeadded NLMSA.edges() method
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2009-07-16 Christopher Leeswitched test_tblastn_parser to use new TranslationDB...
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2009-07-16 Christopher Leeswitch tblastn to use new TranslationDB approach
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2009-07-15 Christopher Leeadded translationDB.py
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2009-07-15 Christopher Leemoved dbname default into get_bound_subclass()
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2009-07-15 Christopher Leemake CoordsToIntervals / get_interval() use seq.absolute_sli...
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2009-07-15 Christopher Leecleaned up SeqPath.classySlice()
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2009-07-15 Christopher LeeMerge commit 'remotes/mkszuba/nlmsa_no_verbose' into...
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2009-07-15 Christopher LeeMerge commit 'remotes/mkszuba/cnestedlist_notice' into...
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2009-07-15 Christopher Leeincomplete new code for TranslationDB
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2009-07-15 Christopher Leecleaned up reversePath construction
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2009-07-15 Christopher Leeadd absolute_slice() method to SeqPath
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2009-07-14 Christopher LeeMerge commit 'remotes/mkszuba/cnestedlist_logger' into...
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2009-07-14 Christopher LeeMerge branch 'master' into megatests
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2009-07-03 Christopher LeeMerge branch 'formatdb_fail'
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2009-07-03 Christopher Leeimproved whitespace path warning
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2009-07-03 Christopher Leeadded warning for whitespace in path
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2009-07-01 Christopher LeeMerge commit 'remotes/mkszuba/megatests'
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2009-07-01 Christopher Leeuse glob.glob() instead of os.listdir(); cleaned up...
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2009-07-01 Christopher LeeMerge commit 'remotes/mkszuba/mimetext'
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2009-07-01 Christopher LeeMerge commit 'remotes/mkszuba/docfixes'
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2009-07-01 Christopher LeeMerge commit 'remotes/mkszuba/hashlib'
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2009-06-26 Christopher Leefixed caching bug introduced in commit 8d9966 in PrefixUnion...
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2009-06-20 Christopher Leedeprecated cursor argument to SQLTable
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2009-06-20 Christopher Leefixed issue 99
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2009-06-20 Christopher Leeadded test for issue 99
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2009-06-20 Christopher Leecleaned up SQLiteServerInfo
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2009-06-20 Christopher Leeadded DBServerInfo.new_cursor() method
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2009-06-13 Christopher LeeMerge commit 'remotes/mkszuba/issue97_test' into issue97_test
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2009-06-13 Christopher Leeremoved redundant and buggy rstrip(".py") call from...
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2009-06-12 Christopher Leefix issue97
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2009-06-12 Christopher Leeraised minimum identity for relaxed blast tests to 60%
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2009-06-09 Christopher Leereplaced a few remaining refs in the docs to pygr.Data...
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2009-06-09 Christopher LeeMerge commit 'remotes/mkszuba/deb'
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2009-06-09 Christopher LeeMerge commit 'remotes/mkszuba/renames'
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2009-06-09 Christopher LeeMerge branch 'interval_filters' into blast_tests
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2009-06-09 Christopher Leerelaxed-tests had a bug that made them pass the comparison...
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2009-06-04 Christopher Leemust close FilePopen object before exiting BlastxMapping...
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2009-06-04 Christopher Leemerged in ctb/blastx_database
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2009-06-04 Christopher LeeMerge commit 'remotes/ctb/blastx_generator' into ctb_tmp
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2009-06-04 Christopher LeePEP8 and whitespace fixes to nlmsa_utils.py; no functionalit...
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2009-06-04 Christopher Leeconverted add_aligned_intervals functionality into...
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2009-06-04 Christopher Leeclean up AttributeInterface according to Titus suggestions
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2009-06-04 Christopher LeeMerge commit 'remotes/ctb/ctb_intervals' into interval_filters
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2009-06-03 Christopher LeeMerge commit 'remotes/ctb/ctb_blast2' into ctb_tmp
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2009-06-03 Christopher LeeMerge commit 'remotes/ctb/minor_doc_fixes' into ctb_tmp
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2009-06-03 Christopher Leemerged in ctb/annotation
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2009-06-03 Christopher Leemerged in ctb/blast_skip conflict with ctb/blast_cache
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2009-06-03 Christopher LeeMerge commit 'remotes/ctb/blast_cache' into ctb_tmp
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2009-05-29 Christopher LeeMerge commit 'remotes/ctb/nlmsa_iter_repr'
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2009-05-29 Christopher Leeremoved unnecessary import
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2009-05-29 Christopher Leeconverted test_multiblast_single() back to test against...
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2009-05-29 Christopher Leerename to avoid false implication this test involves...
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2009-05-27 Christopher LeeMerge commit 'remotes/mkszuba/trove' into marek_tmp
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2009-05-27 Christopher Leeadded comparison with single seq blast in test_multiblast
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2009-05-27 Christopher Leeadded text file for checking long parser results
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2009-05-27 Christopher Leeput close() within try-finally as always
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2009-05-27 Christopher LeeMerge commit 'remotes/mkszuba/blast_test' into marek_tmp
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2009-05-27 Christopher LeeMerge commit 'remotes/mkszuba/ebuilds' into marek_tmp
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2009-05-23 Christopher Leeadded ResourceServer register() / serve_forever() docs
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Graph database interfaces in Python