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.
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
OBSOLETE CLASSES:
_Scanner Scan compass results _Consumer Consume scanner
events RecordParser Parse one compass record Iterator Iterate
through a number of compass records
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Record
Hold information from one compass hit.
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_Scanner
Reads compass output and generate events (OBSOLETE)
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_Consumer
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RecordParser
Parses compass results into a Record object (OBSOLETE).
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Iterator
Iterate through a file of compass results (OBSOLETE).
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__regex = { ' align ' : re.compile(r'^.{15} ( \S+ ) '), ' lengths ' : re....
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StringTypes = ( <type 'str'>, <type 'unicode'>)
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__package__ = ' Bio.Compass '
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xml_support = 1
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Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln
------query----- -------hit-------------
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__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+ ) '
...
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