# 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')

Biopython v: 1.85

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