Commits

Author Commit Message Labels Comments Date
James Taylor
first pass at a class for reading genomic intervals from a tabular data file with (optional) headers and comments (bed is a specialization). moved interval intersection code to a new submodule aggregate_scores_in_intervals.py outputs tab separated now
James Taylor
"aggregate_scores_in_intervals.py" now can read the scores either from a wiggle file (using "bx.wiggle.Reader") or a directory of previously prepared FileBinnedArray format files (e.g. from "wiggle_to_chr_binned_array.py")
James Taylor
Some fixes to various things.
James Taylor
UCSC's dependencies are a nightmare, something changed recently and bitset pulled in a bunch more. So instead I've moved bits.c/h into our source directory and faked up the minimum of common.c/h to keep everything working nicely.
David King
small additions
James Taylor
Adding pkg_resources to the bx-python project.
James Taylor
Another fix
James Taylor
Okay, that did not work so well
James Taylor
Removing ez_setup (will make external shortly), bitset.c allows building without pyrex.
James Taylor
Couple of scripts, might or might not be any good, wrote these during ENCODE and forgot about them until now.
James Taylor
setuptools / egg related changes (incomplete)
Bob Harris
implemented DNA case folding when one side of a slaw-style scoring matrix is DNA
David King
binned arrays from wiggle by chromosome
David King
Added motif scorer for MAFs
James Taylor
KDTree from an old David Eppstein email, slightly hacked.
James Taylor
Various small changes to the bag of bed tools.
David King
maf_tile: added option parsing and missing data option
David King
Program for projecting pwm maf hits onto reference coordinates
James Taylor
Updated to deal with multiple datasets, both sampling methods now work correctly, but the gap list based one turns out to be slower. Might be a data structure issue though, needs optimization.
James Taylor
Moving this script for random intersections into svn, but it is still pretty young.
James Taylor
Right, bed format, always '+' coordinates.
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
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