Commits

Author Commit Message Labels Comments Date
Ian Schenk
Turns out Numeric is inactive, and we're supposed to move over to numpy. I guess I know what I'm doing tomorrow.
Ian Schenk
Small fixes. bx.intervals.io needed to be fixed to allow -1 to indicate no strand column. Setup.py was altered to automatically install dependencies (although these might be changed to optional dependencies). Lastly, LRUCache 0.2 was used for FileBinnedArray.
David King
Bad codes for some degeneracy symbols
Bob Harris
changed isUpper to isupper, &c.
Ian Schenk
Changed filters around to be more abstract. Made the CpG sitemask filter fit the Meunier paper's definitions, which required some C.
James Taylor
Bad imports.
Ian Schenk
Added sitemask package. Also added quality masker (Simple) and CpG masker (Strict, although now I think it's loose). FileBinnedArray now implements a lrucache, but a cheap one since I didn't implement a heap, but it should be ok since the cache will be small.
James Taylor
Removing pkg_resources, causes conflicts with setuptools installed version.
Bob Harris
spelling correction
Bob Harris
added command line note to describe the lengths file format
Ian Schenk
The coord_to_col scheme broke when looking up the col for the coordinate get_forward_strand_end because ends are excluded, but this was still necessary to do a proper slice, since python slices are [start, end).
Ian Schenk
I was told that the block numbers must be unique. axt.writer was updated to increment block numbers.
Ian Schenk
Sorry for the poor code... under pressure :). This should be better.
Ian Schenk
Made a hack to core.py that allows coord_to_col to work in constant time, which gave the alignment masker a 70-fold speed boost. I know C is faster, but this is very close.
James Taylor
Updated ez_setup.py
James Taylor
Adding some scripts that are used by ESPERR
David King
Added a small C extension for pwm score motif.
Bob Harris
added comment about gap scores
Ian Schenk
hasty typo
Ian Schenk
bx.align.core was not handling reverse strand components correctly in the method coord_to_col. Fixed to use forward strand; however, this might be slower because of the extra method lookup.
David King
ScoreMotif operates on a list or string. Added script for scoring motifs in intervals.
David King
bed_score_aligned_pwm.py: score intervals for motifs
Ian Schenk
Added qv_to_bqv.py, which converts an ascii fasta type quality file to a FileBinnedArray (binned_array.py). Note that this script takes hours to run... Comments welcome.
Ian Schenk
Updated binned_array to include a lite mode that deallocates bins, and also a BinnedArrayWriter for writing binned arrays too large for memmory. Comments welcome.
Bob Harris
corrected extract_name for unnamed sequences
Bob Harris
new method to read scores from a file was not tested
Bob Harris
set_score now optionally folds case; added method to read scores from a file
Ian Schenk
Implemented cluster in C/Pyrex. Criticism welcome.
David King
Fixed import statements
Ian Schenk
Subtract was ommitting chromosomes incorrectly.
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