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__(self)

Initialize the class.

query_coverage(self)

Return the length of the query covered in the alignment.

hit_coverage(self)

Return the length of the hit covered in the alignment.