def test_2():
failure = 1
try:
motility.find_iupac("R", "N");
failure = 0
except Exception, e:
pass
def test_2():
failure = 1
try:
motility.find_iupac("R", "N")
failure = 0
except Exception, e:
pass
def main():
usage="%prog [options]"
parser = OptionParser(usage,version="%prog " + __version__)
parser.add_option("-s","--sequence",action="store",type="string",dest="dna_seq",help="DNA sequence in fasta format")
parser.add_option("-m","--motif",action="store",type="string",dest="motif_iupac",help="Tab (space) separated two-column file: Motif_ID <space> Motif_IUPAC. Motif_ID should be unique. For example:Motif.7.4 TGTWCHH\nMotif.6.3 RGWACA\nMotif.6.2 TGTWCW")
parser.add_option("-o","--out-prefix",action="store",type="string",dest="output",help="Output file")
parser.add_option("-n","--mismatch",action="store",type="int",dest="mismatch_num",default=0, help="Number of mismaatch. default=%default")
(options,args)=parser.parse_args()
if not (options.dna_seq and options.output and options.motif_iupac):
parser.print_help()
sys.exit(0)
FOUT1 = open(options.output + '.seq2motif.xls','w')
FOUT2 = open(options.output + '.motif2seq.xls','w')
motifs={}
print >>sys.stderr, "Reading motif file " + options.motif_iupac
for line in open(options.motif_iupac,'r'):
line=line.strip()
if line.startswith(('#',' ','\n')):continue
id,iupac = line.split()
motifs[id] = iupac
print >>sys.stderr, "Search motifs for each sequence "
for line in open(options.dna_seq,'r'):
line=line.strip()
if line.startswith(('#',' ','\n')):continue
if line.startswith('>'):
print >>FOUT1, line[1:] + '\t',
continue
print >>FOUT1, line + '\t',
for motif in sorted(motifs):
if len(motifs[motif]) > len(line):
continue
found = mt.find_iupac(line, motifs[motif], options.mismatch_num)
print >>FOUT1, motif + ";" + motifs[motif] + ';' + str(len(found)) + '\t',
print >>FOUT1
print >>sys.stderr, "Search sequences for each motif"
for motif in sorted(motifs):
count = 0
SEQ = open(options.dna_seq,'r')
for line in SEQ:
line=line.strip()
if line.startswith(('#',' ','\n','>')):continue
if len(motifs[motif]) > len(line): continue
found = mt.find_iupac(line, motifs[motif], options.mismatch_num)
if len(found)>0:count +=1
SEQ.close()
print >>FOUT2, motif + '\t' + motifs[motif] + '\t' + str(count)
def test_4():
"""
Test misc coord handling / match str extraction
"""
motif = 'ACGG'
pwm = motility.make_pwm([motif])
pwm_match = pwm.find(motif, 4)
iupac_match = motility.find_iupac(motif, motif)
exact_match = motility.find_exact(motif, motif)
assert pwm_match == iupac_match
assert pwm_match == exact_match
rcmotif = 'CCGT'
pwm_match = pwm.find(rcmotif, 4)
iupac_match = motility.find_iupac(rcmotif, motif)
exact_match = motility.find_exact(rcmotif, motif)
assert pwm_match == iupac_match
def test_4():
"""
Test misc coord handling / match str extraction
"""
motif = 'ACGG'
pwm = motility.make_pwm([motif])
pwm_match = pwm.find(motif, 4)
iupac_match = motility.find_iupac(motif, motif)
exact_match = motility.find_exact(motif, motif)
assert pwm_match == iupac_match
assert pwm_match == exact_match
rcmotif = 'CCGT'
pwm_match = pwm.find(rcmotif, 4)
iupac_match = motility.find_iupac(rcmotif, motif)
exact_match = motility.find_exact(rcmotif, motif)
assert pwm_match == iupac_match
def test_g(self):
motif = 'G'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 0
assert len(motif_obj.find('A')) == 0
assert motif_obj.calc_score('A') == 0
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 0 # DOES NOT do RC
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 0
assert len(motif_obj.find('T')) == 0
assert motif_obj.calc_score('T') == 0
assert len(find_iupac('N', motif)) == 0
assert len(motif_obj.find('N')) == 0
assert motif_obj.calc_score('N') == 0
def test_n(self):
motif = 'N'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 1
assert len(motif_obj.find('A')) == 1
assert motif_obj.calc_score('A') == 1
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 1
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 1
assert len(motif_obj.find('T')) == 1
assert motif_obj.calc_score('T') == 1
assert len(find_iupac('N', motif)) == 1
assert len(motif_obj.find('N')) == 1
assert motif_obj.calc_score('N') == 1
def test_g(self):
motif = 'G'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 0
assert len(motif_obj.find('A')) == 0
assert motif_obj.calc_score('A') == 0
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 0 # DOES NOT do RC
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 0
assert len(motif_obj.find('T')) == 0
assert motif_obj.calc_score('T') == 0
assert len(find_iupac('N', motif)) == 0
assert len(motif_obj.find('N')) == 0
assert motif_obj.calc_score('N') == 0
def test_n(self):
motif = 'N'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 1
assert len(motif_obj.find('A')) == 1
assert motif_obj.calc_score('A') == 1
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 1
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 1
assert len(motif_obj.find('T')) == 1
assert motif_obj.calc_score('T') == 1
assert len(find_iupac('N', motif)) == 1
assert len(motif_obj.find('N')) == 1
assert motif_obj.calc_score('N') == 1
#! /usr/bin/env python
import motility
print '\n---------------------------------\n'
##############################################################################
#
# example 1: use an IUPAC motif with and without mismatches.
#
motif = "AR" # R = A or G
seq = "ATCT" # sequence to search
### 0 mismatches
matches = motility.find_iupac(seq, motif) # search with zero mismatches
print "found %d match(es) to '%s' in '%s' with 0 mismatches:" \
% (len(matches), motif, seq)
for (start, end, o, match) in matches:
print '\t%d to %d in %d orientation; match is %s' % (start, end, o, match)
### 1 mismatch allowed
matches = motility.find_iupac(seq, motif, 1) # search with 1 mismatch
print "\nfound %d match(es) to '%s' in '%s' with 1 mismatch allowed:" \
% (len(matches), motif, seq)
for (start, end, o, match) in matches:
#! /usr/bin/env python
import sys
sys.path.append('/u/t/dev/motility/python/build/lib.linux-i686-2.3/')
import motility
sys.path.append('/u/t/dev/slippy/lib')
import fasta
if len(sys.argv) != 3:
sys.stderr.write('Usage:\n\t%s <motif> <FASTA file to search>\n' % (sys.argv[0],))
sys.exit(0)
motif = sys.argv[1]
filename = sys.argv[2]
sys.stderr.write('searching file %s with motif %s\n' % (filename, motif,))
seq = fasta.load_single(filename)
results = motility.find_iupac(seq, motif)
for (start, end, orientation, match) in results:
print 'MATCH: %d --> %d, orientation %d; match is %s' % (start, end,
orientation,
match,)
sys.exit(0)
#! /usr/bin/env python
import motility
print "\n---------------------------------\n"
##############################################################################
#
# example 1: use an IUPAC motif with and without mismatches.
#
motif = "AR" # R = A or G
seq = "ATCT" # sequence to search
### 0 mismatches
matches = motility.find_iupac(seq, motif) # search with zero mismatches
print "found %d match(es) to '%s' in '%s' with 0 mismatches:" % (len(matches), motif, seq)
for (start, end, o, match) in matches:
print "\t%d to %d in %d orientation; match is %s" % (start, end, o, match)
### 1 mismatch allowed
matches = motility.find_iupac(seq, motif, 1) # search with 1 mismatch
print "\nfound %d match(es) to '%s' in '%s' with 1 mismatch allowed:" % (len(matches), motif, seq)
for (start, end, o, match) in matches:
print "\t%d to %d in %d orientation; match is %s" % (start, end, o, match)
def test_1():
assert len(motility.find_iupac("ACTGNX", "N")) == 6
def test_1():
assert len(motility.find_iupac("ACTGNX", "N")) == 6
