Commits

Author Commit Message Labels Comments Date
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.
James Taylor
This fixes the fasta test for me, was in an infinite loop, Bob?
James Taylor
Add a "do_mask" flag for 2bit files. This is by far the slowest part of working with these files, so if you aren't using the soft masking you can turn it off. However 'N' masking is always done, since the data is invalid without it.
James Taylor
Get script_tests working again. All tests should be passing.
James Taylor
Require Cython (Pyrex evolved) to build.
James Taylor
Fix for write_with_synteny, I think the score should always be formatted this way, has someone seen something different?
Guru Ananda
Adding a new attribute called "minend" to IntervalNode. This attribute will contain the minimum end value for a node's subtree.
David King
typo
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
NibFile now checks for negative lengths (+ tests and some doc cleanup)
Daniel Blankenberg
Rework wiggle readers. These now return zero-based (half-open) coordinates. Add tests for wiggle readers.
Daniel Blankenberg
Update align.core.src_split() to split species, chrom from the left.
Bob Harris
changed assertion so that, on failure, the mismatched alignment blocks are shown
Daniel Blankenberg
Fix iterator when using fixedStep in wiggle.Reader().
Daniel Blankenberg
Fix for table reader returning comments for blank lines when return_comments is False.
James Taylor
Changed default for mincols from 10 to 0
James Taylor
Fix for maf_extract_ranged_indexed.py (and a test!)
Daniel Blankenberg
Fix for retrieving lists of blocks from indexes.
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