Source

bx-python / lib / bx / align / core.py

Author Commit Message Labels Comments Date
mruffalo
Raise exceptions instead of raw strings for issue #35
Bob Harris
Corrected problem in maf_extract_ranges_indexed, which failed when a maf block contains more than one line with the desired reference sequence. The failure manifested as an abort, from the range error test in coord_to_col() in align/core.py. The correction is two-fold. First, we add a test in the script co that coord_to_col is not called with an empty interval. Second, we change the script to loop over *all* interesting reference intervals, rather than the first.
Bob Harris
fixed slicing for -strand reference again; last time I did not get it right; have also added self-test this time
Bob Harris
many fixes related to negative strand components
Bob Harris
fixed problem that occurred when the reference strand was negative
Daniel Blankenberg
Update align.core.src_split() to split species, chrom from the left.
Daniel Blankenberg
Fix memory issues when dealing with alignments.
Daniel Blankenberg
Better (hopefully) fix for remove_all_gap_columns() where component.text is not of type sequence.
Daniel Blankenberg
Fix for remove_all_gap_columns() when the one of the component's sequence is not the proper
Bob Harris
separated read_lengths_file into its own module
Bob Harris
make score a number only if it's a string
Bob Harris
make score a number if at all possible
James Taylor
Support for q rows.
James Taylor
Working around empty components and slicing.
James Taylor
Support for 'i' and 'e' rows when reading/writing mafs (and in
James Taylor
Deal with 'None' in equality test (fixes LAV tests which probably are using
James Taylor
Define equality for Alignment objects.
James Taylor
Support for 'e' rows in MAF files. This is off by default since empty
James Taylor
Adding module / package level doc comments to everything.
Bob Harris
contigs are now supported for lav and fasta; my fasta contig implementaton leaves much room for improvement
Bob Harris
LAV module doesn't currently support as much as ZXT and MAF; rather than add that support I am taking the lazy approach and blocking the calls to it
Bob Harris
corrected errors in import paths
Bob Harris
import lav was missing
Ian Schenk
The coord_to_col scheme broke when looking up the col for the coordinate get_forward_strand_end because ends are excluded, but this was still necessary to do a proper slice, since python slices are [start, end).
Ian Schenk
Sorry for the poor code... under pressure :). This should be better.
Ian Schenk
Made a hack to core.py that allows coord_to_col to work in constant time, which gave the alignment masker a 70-fold speed boost. I know C is faster, but this is very close.
Ian Schenk
hasty typo
Ian Schenk
bx.align.core was not handling reverse strand components correctly in the method coord_to_col. Fixed to use forward strand; however, this might be slower because of the extra method lookup.
James Taylor
Fixes. Aggregate now takes a mask.
James Taylor
Yay, debug statements that corrupt my output!
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