Commits

Author Commit Message Labels Comments Date
James Taylor
Another script I had in several places so it is probably
David King
name change
David King
fourfold_degenerate_translate.py: bed-like output labels degenerate codon positions. Takes bed or gtf files.
David King
fixed indent errors-- sometimes I think I'm in C
David King
gene_reader.py: Readers for gtf files
David King
bitset_utils.py: basic utils for lists, taken semi-verbatim from bitset_builders that operate on files
James Taylor
Added a check in "_seqmapping.pyx" to ensure the input buffer
James Taylor
Updated pkg_resources.py
David King
move pwm to bx/pwm
James Taylor
Removed seq_numarray and alphabet.py, replaced with much better code
James Taylor
Moved maf tests into the conventional place, all tests except
James Taylor
Okay, tests all look good.
James Taylor
Moved a bunch of stuff that we didn't write into the 'bx_extras' package.
James Taylor
Phast tree model reader tests, pyrex optomization for alignments.
James Taylor
Tests work (except some pieces I haven't committed, will fix later)
James Taylor
Big partial commit, spring cleaning!
James Taylor
Fixing up phast reader, removing scipy dependency (need to abstract the linalg
James Taylor
Very rudimentary support for PHAST's tree model file format.
James Taylor
Newick format tree parser using pyparsing (sweet!). Some refactoring and
James Taylor
Tool for extracting colum counts from a MAF.
James Taylor
Adding the stats package which is used by a few things.
James Taylor
Refactored bx.intervals.io to extend the stuff from bx.tabular.io
James Taylor
Another script for adding columns to a table. Also, the expression is optional
James Taylor
Added classes for working with tabular data files. The intervals stuff should
James Taylor
Added a tool for joing two lists of intervals side by side.
James Taylor
first pass at a class for reading genomic intervals from a tabular
James Taylor
"aggregate_scores_in_intervals.py" now can read the scores either
James Taylor
Some fixes to various things.
James Taylor
UCSC's dependencies are a nightmare, something changed recently
David King
small additions
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