1. pombredanne
  2. biostuff

Commits

Author Commit Message Date Builds
Brent Pedersen
merge.
Brent Pedersen
update to new numpy semantics where we cant use 'c' for dtype, must use 'S1'
Brent Pedersen
only require r+ for memory map.
Brent Pedersen
fix cases where there are ambiguous, equal scoring paths through the backtrack matrix. always choose the path where gaps are pushed to the ends if possible. much thanks to marcin ceslik for careful examples and discussion of the problem.
Brent Pedersen
close file handles.
Brent Pedersen
update docstring about where to get the scoring matrices
Brent Pedersen
split-fasta: handle case where have a lot of headers, dont open the filehandles until actually writing to them (and close immediately after) other wise get a too many-open file-handles.
Brent Pedersen
Added tag nwalign-0.3.1 for changeset d576e3d9686e
Brent Pedersen
handle cases where zero-length strings are passed in. thanks to richard christen for reporting.
Brent Pedersen
Added tag nwalign-0.3.0 for changeset a8ceeac6b465
Brent Pedersen
fix up docs, prep for upload to pypi.
Brent Pedersen
update c code and init.py
Brent Pedersen
add updated c code and fix setup.py
Brent Pedersen
add commandline interface for the socket server.
Brent Pedersen
major speed improvment trading space for speed. direct lookup into scoring matrix, instead of requiring a 3 lookups.
Brent Pedersen
some cleanup.
Brent Pedersen
remove extra crap for fixing ends. solved by sorting the input seqs based on length.
Brent Pedersen
use less memory storing the gap info as we only need 1 level back.
Brent Pedersen
Added tag nwalign-0.2.2 for changeset c798f2d56257
Brent Pedersen
up version.
Brent Pedersen
fix test
Brent Pedersen
add a scoring function for matrix alignments. clean up tests.
Brent Pedersen
try to keep gaps at end of sequence. still need to push them to the beginning as well.
Brent Pedersen
fix one bug, still finding a few more.
Brent Pedersen
um. fix bug again. change kwargs to be more intuitive. remove 'mismatch' kwargs as it's the same as gap.
Brent Pedersen
some speed changes (> 15% improvement for matrix case, 10% when using match/mismatch)
Brent Pedersen
Added tag 0.2 for changeset 054a2e648e47
Brent Pedersen
fix bug reported by Richard Christen (thanks).
Tags
0.2
Brent Pedersen
Added tag 0.2 for changeset 40123c237f7e
Brent Pedersen
fix bug in gap_open when not using a matrix to calculate substitutions.
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