Package Bio :: Package Compass
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Package Compass

source code

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.

Classes [hide private]
  Record
Hold information from one compass hit.
Functions [hide private]
 
read(handle)
Reads a COMPASS file containing one COMPASS record.
source code
 
parse(handle)
Iterates over records in a COMPASS file.
source code
 
__read_names(record, line) source code
 
__read_threshold(record, line) source code
 
__read_lengths(record, line) source code
 
__read_profilewidth(record, line) source code
 
__read_scores(record, line) source code
 
__read_query_alignment(record, line) source code
 
__read_positive_alignment(record, line) source code
 
__read_hit_alignment(record, line) source code
Variables [hide private]
  __regex = {'align': re.compile(r'^.{15}(\S+)'), 'lengths': re....
  __package__ = 'Bio.Compass'
Variables Details [hide private]

__regex

Value:
{'align': re.compile(r'^.{15}(\S+)'),
 'lengths': re.compile(r'length1=(\S+)\s+filtered_length1=(\S+)\s+leng\
th2=(\S+)\s+filtered_length2=(\S+)'),
 'names': re.compile(r'Ali1:\s+(\S+)\s+Ali2:\s+(\S+)\s+'),
 'positive_alignment': re.compile(r'^.{15}(.+)'),
 'profilewidth': re.compile(r'Nseqs1=(\S+)\s+Neff1=(\S+)\s+Nseqs2=(\S+\
)\s+Neff2=(\S+)'),
 'scores': re.compile(r'Smith-Waterman score = (\S+)\s+Evalue = (\S+)'\
...