Author Commit Message Labels Comments Date
James Taylor avatarJames Taylor
Use sorted alphabet for drawing logos.
James Taylor avatarJames 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 avatarJames Taylor
Fixes to seqmapping and associated tests (test problems, type
James Taylor avatarJames Taylor
motif.pwm: Scoring sequences with gaps,
James Taylor avatarJames Taylor
bx.motif: Drawing sequence logos from count/frequency matrices in EPS format.
James Taylor avatarJames Taylor
bx.align.tools.thread: Need to use a deepcopy here to avoid affecting the original Alignment.
James Taylor avatarJames Taylor
motif.pwm.ScoringMatrix: unscored positions are set to nan.
James Taylor avatarJames Taylor
Transfac Reader: requiring the matrix prefixes to always start at "01" was
James Taylor avatarJames Taylor
New motif/matrix classes. Includes a reader for TRANSFAC style databases
James Taylor avatarJames Taylor
table_filter.py: option to treat first line as header even if it does not
Greg Von Kuster avatarGreg 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 avatarGreg Von Kuster
Added exception handling related to integer overflow for interval operations.
James Taylor avatarJames Taylor
Bitsets now aggressively check all their arguments.
James Taylor avatarJames Taylor
Make Cython optional.
James Taylor avatarJames Taylor
This fixes the fasta test for me, was in an infinite loop, Bob?
James Taylor avatarJames Taylor
Add a "do_mask" flag for 2bit files. This is by far the slowest part of
James Taylor avatarJames Taylor
Get script_tests working again. All tests should be passing.
James Taylor avatarJames Taylor
Require Cython (Pyrex evolved) to build.
James Taylor avatarJames Taylor
Fix for write_with_synteny, I think the score should always be formatted
Guru Ananda avatarGuru Ananda
Adding a new attribute called "minend" to IntervalNode.
Default avatar David King
typo
Default avatar David King
The refindex parameter may now be given a species name instead, and need not be the reference species of the MAF file.
James Taylor avatarJames Taylor
NibFile now checks for negative lengths (+ tests and some doc cleanup)
Daniel Blankenberg avatarDaniel Blankenberg
Rework wiggle readers. These now return zero-based (half-open) coordinates.
Daniel Blankenberg avatarDaniel Blankenberg
Update align.core.src_split() to split species, chrom from the left.
Bob Harris avatarBob Harris
changed assertion so that, on failure, the mismatched alignment blocks are shown
Daniel Blankenberg avatarDaniel Blankenberg
Fix iterator when using fixedStep in wiggle.Reader().
Daniel Blankenberg avatarDaniel Blankenberg
Fix for table reader returning comments for blank lines when return_comments is False.
James Taylor avatarJames Taylor
Changed default for mincols from 10 to 0
James Taylor avatarJames Taylor
Fix for maf_extract_ranged_indexed.py (and a test!)
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