1. James Taylor
  2. bx-python

Commits

Author Commit Message Date Builds
Bob Harris
(missed commit for this on Apr/7/2006), species_to_length now is more forgiving of certain alignment src names
Bob Harris
sequence readers are now supported (i.e. iterate over sequences in a fasta file)
Ian Schenk
Added find_clusters.
Bob Harris
script to convert lav file to maf, name changes in maf_to_axt
Ian Schenk
Fixed merge to maintain proper columns throughout file
Bob Harris
incorporated NIB into the LAV test, added some more error checking
Ian Schenk
Concat added.
Ian Schenk
Added base coverage and coverage operations.
Ian Schenk
fixed an error where an entire chromosome could be missed.
Bob Harris
introductory LAV support
Bob Harris
removing some debug prints
Bob Harris
specific sequence formats are now subclasses of SeqFile, which provides common functionality like reverse-complement
Ian Schenk
small change in merge.py
Ian Schenk
Added subtract and merge, updated intersect and __init__
James Taylor
Add C files so pyrex not needed to build (still a good idea...)
David King
fixed import statements for pwm libs
Bob Harris
added fasta format
Bob Harris
sequence formats have a commonality now, like alignment formats (will add fasta later)
Bob Harris
paths to sample files now (allegedly) platform independent
Bob Harris
sample file for qdna_tests
Bob Harris
added qdna_tests.py
Bob Harris
support for quantum DNA files
Bob Harris
has been renamed to nib_tests.py
Bob Harris
added nib_tests.py
Bob Harris
(used to be test_nib.py), updated for inclusion with other bx tests
Bob Harris
wasn't looking in correct path for support modules
Bob Harris
documentation conformity
Bob Harris
axt writer incorrectly assumed score is an integer
Ian Schenk
New intersect operation, hopefully for real this time.
Ian Schenk
New intersect operation along with modifications to io, etc.
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