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.
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Bio.Compass.
read
(handle)¶ Read a COMPASS file containing one COMPASS record.
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Bio.Compass.
parse
(handle)¶ Iterate over records in a COMPASS file.
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class
Bio.Compass.
Record
¶ Bases:
object
Hold information from one compass hit.
Ali1 is the query, Ali2 the hit.
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__init__
(self)¶ Initialize the class.
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query_coverage
(self)¶ Return the length of the query covered in the alignment.
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hit_coverage
(self)¶ Return the length of the hit covered in the alignment.
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