Commits

Author Commit Message Labels Comments Date
Bob Harris
recommitting earlier change, involving correction of how intervals are handled on negative strand
Bob Harris
backing out latest change in lieu of testing
Bob Harris
fixed problem that occurred when the reference strand was negative
Bob Harris
fixed problem that occurred when the reference strand was negative
Daniel Blankenberg
Add an iterator to AbstractIndexedAccess and AbstractMultiIndexedAccess which returns the index and offset along with the value contained at the offset.
Nate Coraor
Per James, make the build-time numpy dependency conditional (this is so people building for their own platforms need not have numpy).
Daniel Blankenberg
Remove recursive call from interval.io.BitsetSafeReaderWrapper.next().
James Taylor
Fix for twobit on 64bit platforms (fixes ticket #7)
James Taylor
Make labels optional in newick parser, add tests from markd (fixes ticket #3)
James Taylor
Update pyparsing to latest version (1.5.0)
James Taylor
Fix comparisons operations (from markd@soe.ucsc.edu, fixes ticket #4)
James Taylor
Do not pkg_resource.require bx-python from inside bx-python
James Taylor
Include TY (type) lines in motif parsing
James Taylor
Fix package data (for template.ps)
James Taylor
Support for optional short options (specifying a long option only) in doc_optparse.
James Taylor
Writer for transfac format, parser now handles "BS" lines as produced by CREAD.
James Taylor
Use sorted alphabet for drawing logos.
James Taylor
Use static inline only. This gives the same effect in C89+GNU and C99, and compiles just fine on solaris with the sun pro compilers.
James Taylor
Fixes to seqmapping and associated tests (test problems, type ambiguity that Cython notices, and a bug when passing out-of-range inputs -- no problems with valid input).
James Taylor
motif.pwm: Scoring sequences with gaps,
James Taylor
bx.motif: Drawing sequence logos from count/frequency matrices in EPS format.
James Taylor
bx.align.tools.thread: Need to use a deepcopy here to avoid affecting the original Alignment.
James Taylor
motif.pwm.ScoringMatrix: unscored positions are set to nan.
James Taylor
Transfac Reader: requiring the matrix prefixes to always start at "01" was apparently too strict.
James Taylor
New motif/matrix classes. Includes a reader for TRANSFAC style databases (which can be easily extended), and position specific weight/frequency and scoring matrix code using numpy. Fast string scoring is provided through a Cython extension. This doesn't do everything the bx.pwm module does, but I think it is a little better organized, and includes more documentation and tests. It would be nice to see what we can move from bx.pwm into here.
James Taylor
table_filter.py: option to treat first line as header even if it does not start with "#"
Greg Von Kuster
Fix bug in binned_bitsets - now handling errors in incoming lens dictionary. Added a new subclass of NiceReaderWrapper to handle ValueError, IndexError and OverflowError exceptions thorwn when creating / using bitsets.
Greg Von Kuster
Added exception handling related to integer overflow for interval operations.
James Taylor
Bitsets now aggressively check all their arguments.
James Taylor
Make Cython optional.
  1. Prev
  2. Next