Bio.Compass package
Module contents
Code to deal with COMPASS output, a program for profile/profile comparison.
Compass is described in:
Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol. 2003 Feb 7;326(1):317-36.
Tested with COMPASS 1.24.
- Bio.Compass.read(handle)
Read a COMPASS file containing one COMPASS record.
- Bio.Compass.parse(handle)
Iterate over records in a COMPASS file.
- class Bio.Compass.Record
Bases:
object
Hold information from one compass hit.
Ali1 is the query, Ali2 the hit.
- __init__()
Initialize the class.
- query_coverage()
Return the length of the query covered in the alignment.
- hit_coverage()
Return the length of the hit covered in the alignment.
- __firstlineno__ = 96
- __static_attributes__ = ('evalue', 'gap_threshold', 'hit', 'hit_aln', 'hit_filtered_length', 'hit_length', 'hit_neffseqs', 'hit_nseqs', 'hit_start', 'positives', 'query', 'query_aln', 'query_filtered_length', 'query_length', 'query_neffseqs', 'query_nseqs', 'query_start', 'sw_score')