| 2009-09-02 |
Titus Brown | blast now reports self-matches; updated alignment tutorial...
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commit | commitdiff | tree |
| 2009-08-04 |
Titus Brown | test for fix in commit 54a1ef (fixed BLASTs of sequences...
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commit | commitdiff | tree |
| 2009-08-04 |
Titus Brown | SixFrameInfo/KeyError should mention erroneous key...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | thoughts for future alignments tutorial work.
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | Added section on storing BLAST results on disk. Done?
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | minor cleanup
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | Merge branch 'simpleframe_blast_fixes' into simpleframe_doc_...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | changed BlastxMapping.__getitem__ to return a non-consumable...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | fixed bug that broke BlastxMapping.__getitem__: use...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | Merge branch 'simpleframe_tests' into simpleframe_blast_fixes
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | BlastxMapping.__getitem__ should not be a generator.
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | test for non-equivalent 'repr's for translationDB sequences...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | fixed bug with empty slices in translationDB.
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | Merge branch 'simpleframe_tests' into simpleframe_blast_fixes
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | some basic tests for translationDB.
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | only return NLMSASlices derived from the query sequence...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | Merge branch 'simpleframe_tests' into simpleframe_blast_fixes
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | fixes individual sequence queries of BlastxMappings...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | check that only NLMSASlices for the translated sequences...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | tests for presence of translationdb.annodb in NLMSA...
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | updated alignment tutorial for new BLAST API
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commit | commitdiff | tree |
| 2009-07-21 |
Titus Brown | cleanup after foobarbaz formatdb failure by removing...
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commit | commitdiff | tree |
| 2009-07-17 |
Titus Brown | mask deprecation warning output in test
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commit | commitdiff | tree |
| 2009-07-17 |
Titus Brown | ensure that tests using the XML-RPC server wait for...
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commit | commitdiff | tree |
| 2009-07-17 |
Titus Brown | eliminate bleed-through of formatdb failed output.
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commit | commitdiff | tree |
| 2009-07-17 |
Titus Brown | show dots again, at lowest verbosity level!
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commit | commitdiff | tree |
| 2009-07-17 |
Titus Brown | move 'disable_threshold' to module level, for import...
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commit | commitdiff | tree |
| 2009-07-12 |
Titus Brown | added more reverse complement tests for BLASTX
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commit | commitdiff | tree |
| 2009-07-12 |
Titus Brown | added a simple test for blastx w/negative frame matches.
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commit | commitdiff | tree |
| 2009-07-11 |
Titus Brown | renamed 'filepath' to 'testpath' where it might be...
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commit | commitdiff | tree |
| 2009-06-30 |
Titus Brown | added test for formatdb failure; fixed string.
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commit | commitdiff | tree |
| 2009-06-30 |
Titus Brown | initial patch to have failed formatdb be reported
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commit | commitdiff | tree |
| 2009-06-08 |
Titus Brown | minor updates to blast.py: make explicit __call__ in...
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commit | commitdiff | tree |
| 2009-06-08 |
Titus Brown | minor reformatting of docstrings and comments to 80...
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commit | commitdiff | tree |
| 2009-06-02 |
Titus Brown | moved the blast SkipTest stuff into the tests that...
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commit | commitdiff | tree |
| 2009-06-02 |
Titus Brown | fixed the expensive multiblast caching
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commit | commitdiff | tree |
| 2009-06-01 |
Titus Brown | introduced 'frame' descriptor for TranslationAnnot...
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commit | commitdiff | tree |
| 2009-06-01 |
Titus Brown | trapped IndexError for missing orientation in sliceAttr...
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commit | commitdiff | tree |
| 2009-05-31 |
Titus Brown | minor adjustment to hash test, to also test that AnnotationD...
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commit | commitdiff | tree |
| 2009-05-30 |
Titus Brown | refactored the AttributeInterface class to be less...
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commit | commitdiff | tree |
| 2009-05-30 |
Titus Brown | removed unused **kwargs passthru to groupIntervals...
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commit | commitdiff | tree |
| 2009-05-30 |
Titus Brown | spread out the read_aligned_coords and get_aligned_intervals...
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commit | commitdiff | tree |
| 2009-05-30 |
Titus Brown | removed unused/unnecessary third 'None' yielded from...
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commit | commitdiff | tree |
| 2009-05-30 |
Titus Brown | more whitespace & comment updates, no functional changes
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commit | commitdiff | tree |
| 2009-05-30 |
Titus Brown | some initial whitespacing of the read_aligned_intervals...
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commit | commitdiff | tree |
| 2009-05-30 |
Titus Brown | move all object generation into generate_intervals.
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | Merge branch 'master_master' into ctb_for_commit
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | Merge branch 'master_master' into blast_minor_changes
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | disallowed BOTH a sequence AND a db for BlastMapping...
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | used logger instead of sys.stdout/sys.stderr for BLAST...
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | made bidirectional=False the default for BlastMapping...
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | a bit of functional reformatting of blast_test.py to...
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | reformatted blast_test; no functional changes.
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | fixed bug in .py stripping in runtests
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | modified blast to alternate between seq=None and queryDB...
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | make repr on NLMSASlice informative
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | NLMSA.__iter__ now raises NotImplementedError
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commit | commitdiff | tree |
| 2009-05-29 |
Titus Brown | spacing & comment cleanup
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commit | commitdiff | tree |
| 2009-05-28 |
Titus Brown | ignore formatdb output files
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commit | commitdiff | tree |
| 2009-04-26 |
Titus Brown | switched clean to no-clean
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commit | commitdiff | tree |
| 2009-04-25 |
Titus Brown | default to using a random (guaranteed unbound) port...
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commit | commitdiff | tree |
| 2009-04-25 |
Titus Brown | changed get_server to bind to a random port when port...
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commit | commitdiff | tree |
| 2009-04-24 |
Titus Brown | added in SkipTest properly; fixed runtest to use it...
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commit | commitdiff | tree |
| 2009-04-24 |
Titus Brown | added SkipTest
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commit | commitdiff | tree |
| 2009-04-18 |
Titus Brown | switched runtest to using unittest.TestLoader().
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commit | commitdiff | tree |
| 2009-03-29 |
Titus Brown | 'set' must be imported from the 'sets' module in python...
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commit | commitdiff | tree |
| 2009-03-28 |
Titus Brown | removed debugging assert statement that causes failures ;)
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commit | commitdiff | tree |
| 2009-03-28 |
Titus Brown | fixed port assignment for XML-RPC server in runtest.
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commit | commitdiff | tree |
| 2009-03-28 |
Titus Brown | switched random.getrandbits to random.random for py2...
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commit | commitdiff | tree |
| 2009-03-28 |
Titus Brown | optparse fixes for python2.3
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commit | commitdiff | tree |
| 2009-03-28 |
Titus Brown | runtest now uses exit codes to signal success/failure.
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commit | commitdiff | tree |
| 2009-03-24 |
Titus Brown | Merge git://repo.or.cz/pygr into seqdb_review
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commit | commitdiff | tree |
| 2009-03-24 |
Titus Brown | fixed problem with __repr__ on SequenceDB trying to...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | moved coverage start into pathfix, which does the first...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | started figleaf code coverage recording ASAP, before...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | number of tests passed vs number of tests run is now...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | used existing hooks to implement stdout/stderr capture...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | Added tempdir and .DS_Store to appropriate .gitignore...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | altered runtest to output the test name, rather than...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | tests and associated bug fixes for NLMSA.add_aligned_interva...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | some more minor documentation updates to seqdb; no...
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commit | commitdiff | tree |
| 2009-03-22 |
Titus Brown | added module-level docs, and a few docstrings. no...
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | more docstring cleanup, no functionality changes.
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | moved seqLenDict creation into SequenceFileDB._create_seqLen...
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | made use of new logger functionality in seqdb module...
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | moved testlib.logger into pygr.logger
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | moved SQLSequence etc into sqlgraph.py
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | added classutil.lazy_create_invert and refactored seqdb...
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | removed SliceDB, VirtualSeq, and VirtualSeqDB.
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | removed idfilter and ifile mechanism in _store_seqlen_dict.
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | renamed set_seqtype to _set_seqtype to indicate private...
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | simplified set_seqtype behavior & removed read_fasta_one_lin...
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | removed 'ifile' mechanism on SequenceFileDB.
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | Merge branch 'master' into seqdb_review
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commit | commitdiff | tree |
| 2009-03-21 |
Titus Brown | integrated get_bound_class/_init_subclass changes from...
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commit | commitdiff | tree |
| 2009-03-15 |
Titus Brown | fixed missing itemClass problem in SequenceDB and added...
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commit | commitdiff | tree |
| 2009-03-15 |
Titus Brown | Removed points at top, cleaned up comments a bit.
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commit | commitdiff | tree |
| 2009-03-15 |
Titus Brown | fixed minor bugaboo issue with forcing seq id to str...
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commit | commitdiff | tree |
| 2009-03-15 |
Titus Brown | formatting changes and code review of PrefixUnionDict...
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commit | commitdiff | tree |
| 2009-03-15 |
Titus Brown | a bunch more seqdb tests, mostly for PrefixUnionDict...
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commit | commitdiff | tree |
