Commits

Author Commit Message Labels Comments Date
James Taylor
Added a method for accumulating scores along an alignment into an array. I also changed Bob's changes a little, making the code a bit more redundant but perhaps easier to follow for less programmer headed persons? I could go either way though.
Bob Harris
made gap/gap be ignored, and neighboring gaps on opposite strands incur two gap open penalties
James Taylor
Fixes noticed by Bob.
James Taylor
Scoring now handle alignments, including multiple. Should be exactly the same as multiz.
James Taylor
Basic module for scoring pairwise alignments. Table size and value type are variable. 128 and Int16 by default. HOX70 matrix included as a module level variable. Still needs to be able to take and Alignment object, and handle the more than 2 species case.
Bob Harris
changed binBitsSetRange to leave ALL_ONE bins as is; may reduce memory footprint when long ranges are set (longer than a bin)
James Taylor
Switched from distutils to setuptools. The setuptools egg will be automagically downloaded when you run setup.py if you do not have it installed locally. Test runner is gone since setuptools handles what we need (including getting extensions on the path), just run 'python setup.py test'
James Taylor
Merging David's changes from universe version of this file.
James Taylor
Added "bed_subtract_basewise" tool and fixed some bugs in and/or for binned bitsets (one case that occurs only after complementing the second set were not being handled correctly)
David King
Average was getting nan when sum < 0. Now it checks the denominator.
James Taylor
Binned arrays can now be written to a file. Only the bins that are set get written, and each bin is compressed with zlib. This allows pseudo random access to the data while still providing a reasonable amount of compression.
Bob Harris
line counting was incorrect
James Taylor
Remove some dead code from bed_complement.py
James Taylor
Added: - bed_complement.py: complements regions in a bed file (requires a LEN file) - bed_intersect_basewise: base-by-base 'AND' of two bed files Modified: - bed_intersect: Now takes upstream/downstream padding to duplicate the 'proximity' operation in galaxy. Ouput can be reversed (printing regions that do not overlap the bitset) - maf_tile: minor fixes, no longer u…
Bob Harris
making them more pythonic
Bob Harris
making it more pythonic
Bob Harris
score argument was being ignored
Bob Harris
Bob Harris
Bob Harris
added caller-supplied species names
Bob Harris
changed import paths to bx...
Bob Harris
changed import of interval_index_file
James Taylor
Binned bitsets now use two sentinals, ALL_ONE for bins containing all ones and ALL_ZERO for bins containing all zeros. Boolean operations (and, or, not) implemented (with tests).
James Taylor
Undo path change, need to make this more easily configurable
James Taylor
Added tests for Bitset and BinnedBitset covering set/clear, setrange, countrange, next_set/next_clear Added a hacky test runner that adds the build directories to the pythonpath. Long term this should read possible tests from a file, and allow a command line for just running some tests.
Bob Harris
completion of yesterday's correction; incorporating other 'lost' changes (which consists only of a comment)
James Taylor
More import fixes
James Taylor
Allow bed_merge_overlapping to take input from both stdin and files Import and other fixes for python 2.3 compatibility
Bob Harris
Added species_to_lengths argument to Alignment constructor.
James Taylor
Another bug fix for counting in binned bitsets bed_intersect now allows specifying a number of bases to overlap.
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