Package Bio :: Package Compass

Package Compass

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.

Functions: read Reads a COMPASS file containing one COMPASS record parse Iterates over records in a COMPASS file.

Classes: Record One result of a COMPASS file

DEPRECATED CLASSES:

_Scanner Scan compass results _Consumer Consume scanner events RecordParser Parse one compass record Iterator Iterate through a number of compass records

Classes

[hide private]

Record
Hold information from one compass hit.

_Scanner
Reads compass output and generate events (DEPRECATED)

_Consumer

RecordParser
Parses compass results into a Record object (DEPRECATED).

Iterator
Iterate through a file of compass results (DEPRECATED).

Functions

[hide private]

read(handle)

source code

parse(handle)

source code

__read_names(record, line)
Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln...

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....

StringTypes = (<type 'str'>, <type 'unicode'>)

__package__ = 'Bio.Compass'

xml_support = 1

Function Details

[hide private]

__read_names(record, line)

source code


Ali1: 60456.blo.gz.aln  Ali2: allscop//14984.blo.gz.aln
      ------query-----        -------hit-------------

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+)'
...