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# Copyright 2003 by Bartek Wilczynski. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This module provides code to work with the standalone version of AlignACE,
for motif search in DNA sequences.
AlignACE homepage:
http://atlas.med.harvard.edu/
AlignACE Citations:
Computational identification of cis-regulatory elements associated with
groups of functionally related genes in Saccharomyces cerevisiae,
Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular
Biology 2000 Mar 10;296(5):1205-14.
Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences
Clustered by Whole-Genome mRNA Quantitation,
Roth, FR, Hughes, JD, Estep, PE & GM Church, Nature Biotechnology
1998 Oct;16(10):939-45.
functions:
AlignAce - runs the AlignACE standalone prgram and returns the
ApplicationResult object
"""
import os
import string
import re
from Bio import File
from Bio.ParserSupport import *
from Applications import AlignAceCommandline
import Scanner
import Parser
def AlignAce(infile, cmd="AlignACE", **keywds):
"""Runs AlignACE and returns data.
cmd == AlignACE executable
infile == sequence file to process
You may pass more parameters to **keywds to change the behavior of
the search. Otherwise, optional values will be chosen by blastall.
numcols number of columns to align (10)
expect number of sites expected in model (10)
gcback background fractional GC content of input sequence (0.38)
minpass minimum number of non-improved passes in phase 1 (200)
seed set seed for random number generator (time)
undersample possible sites / (expect * numcols * seedings) (1)
oversample 1/undersample (1)
"""
if not os.path.exists(cmd):
raise IOError, "Executable does not exist at %s" % cmd
if not os.path.exists(infile):
raise IOError, "Input file does not exist at %s" % infile
AlignCmd = AlignAceCommandline(cmd)
AlignCmd.set_parameter("input",infile)
for (par,val) in keywds.iteritems():
AlignCmd.set_parameter(par,val)
return AlignCmd.run()
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