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Sourcecode: python-biopython version File versions  Download package

transfac.py

00001 """A Martel format to parse the output from transfac.

Formats:
format             Format for a whole file.

"""
import sys

from Martel import *
from Martel import RecordReader

blank_line = Opt(Spaces()) + AnyEol()

MATRIX_LINE = Str("Search for sites by WeightMatrix library:") + Spaces() + \
              UntilEol("matrix_file") + AnyEol()
SEQUENCE_LINE = Str("Sequence file:") + Spaces() + \
                UntilEol("sequence_file") + AnyEol()
PROFILE_LINE = Str("Site selection profile:") + Spaces() + \
               UntilSep("profile_file", sep=" ") + Spaces() + \
               UntilEol("profile_description") + AnyEol()

TITLE_LINE = Str("Inspecting sequence ID") + Spaces() + \
             UntilSep("entryname", sep=" ") + Spaces() + \
             UntilSep("dataclass", sep=";") + Str(";") + Spaces() + \
             UntilSep("molecule", sep=";") + Str(";") + Spaces() + \
             UntilSep("division", sep=";") + Str(";") + Spaces() + \
             UntilSep("sequencelength", sep=" ") + Spaces() + Str("BP") + \
             UntilEol() + AnyEol()

def SS(exp):  # expression surrounded by optional spaces.
    return Opt(Spaces()) + exp + Opt(Spaces())


DATA_LINE = \
    SS(UntilSep("matrix_identifier", sep=" |")) + \
    Str("|") + \
    SS(UntilSep("position", sep=" ")) + \
    SS(Str("(") + Group("strand", Any("+-")) + Str(")")) + \
    Str("|") + \
    SS(Float("core_match")) + \
    Str("|") + \
    SS(Float("matrix_match")) + \
    Str("|") + \
    Opt(Spaces()) + UntilEol("sequence") + AnyEol()

SEQUENCES_LENGTH_LINE = \
    Spaces() + Str("Total sequences length=") + Integer("sequences_length") + \
    AnyEol()

FOUND_SITES_LINE = \
    Spaces() + Str("Total number of found sites=") + Integer("found_sites") + \
    AnyEol()

SITE_FREQUENCY_LINE = \
    Spaces() + Str("Frequency of sites per nucleotide=") + \
    Float("sites_per_nucleotide") + AnyEol()
    
format = MATRIX_LINE + \
         SEQUENCE_LINE + \
         PROFILE_LINE + \
         blank_line + \
         TITLE_LINE + \
         blank_line + \
         Rep(DATA_LINE) + \
         blank_line + \
         SEQUENCES_LENGTH_LINE + \
         blank_line + \
         FOUND_SITES_LINE + \
         blank_line + \
         SITE_FREQUENCY_LINE 

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