Commits

Author Commit Message Labels Comments Date
Bob Harris
(1) added support for floating-point matrix (2) added __str__ method
Bob Harris
tabs instead of spaces made methods become invisible
Bob Harris
(1) made note that no-gap scoring scheme is allowed (2) added score_xxx as methods (3) permitted extra carriage returns at end of the score matrix text blob
James Taylor
Cleaning and documenting some of these operations
James Taylor
Moved functions for building bitsets from files to a separate module (including some new ones from galaxyOps4)
David King
Added index to Scorer
David King
Added a maf reader for the pwm scorer
David King
added strand to variableStep
David King
same change for fixedStep as galaxy
James Taylor
Added a matplotlib Artist for drawing a whole bunch of characters at once (like, say, an alignment). This is much much faster than before.
James Taylor
A VERY ROUGH start on tools for building 'track' style user interfaces / plots.
David King
pwm has position_weight_matrix.py, which is similar to bob_weight_matrix stuff, but with some enhancements for formulas, alignments, and helper tools. All are in a single file for now but I might reorganize.
Bob Harris
(1) added matrix scores for upper to loweer as per blastz (2) added support for asymmetirc alphabets (different alphabet for text1 than text2) and symbols outside the normal ASCII character set
James Taylor
Moved the core of 'maf_tile' into a module, I will change the main script to use this later (after I write some tests). I anticipate slowly doing this with most of the scripts, to the point that some of them could even be automatically generated as just simple wrappers to library funtions.
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
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