def run(self):
title1 = self.title1
title2 = self.title2
working1 = working_directory.Working(self.working_dir1)
working2 = working_directory.Working(self.working_dir2)
cutoff = self.cutoff
sequence_names = [
name for name, length in working1.get_reference().get_lengths()
]
if title1 is None:
title1 = working1.name
if title2 is None:
title2 = working2.name
n = 1
while significance([('A', n)], [('T', n)], 1.0) > cutoff:
n += 1
f = open(self.prefix + '.txt', 'wb')
print >> f, '%g\tsignificance cutoff' % cutoff
print >> f, '%d\tdepth required to call substitution (greater if there are errors in the reads)' % n
print >> f, 'Sequence\tPosition in reference\tChange type\tReference\t%s\t%s\tp-value (no correction for multiple testing)\t%s\t%s' % (
title1, title2, title1, title2)
for sequence_name in sequence_names:
filename1 = working1 / (
grace.filesystem_friendly_name(sequence_name) +
'-evidence.txt')
filename2 = working2 / (
grace.filesystem_friendly_name(sequence_name) +
'-evidence.txt')
for (pos1, ins1, sub1, ref1, conins1,
consub1), (pos2, ins2, sub2, ref2, conins2,
consub2) in itertools.izip(read_file(filename1),
read_file(filename2)):
assert pos1 == pos2 and ref1 == ref2
if pos1 % 1000 == 0:
grace.status('Testing %s %d' % (sequence_name, pos1))
dec_ins1 = io.decode_evidence(ins1)
dec_ins2 = io.decode_evidence(ins2)
if dec_ins1 and dec_ins2:
sig = significance(io.decode_evidence(ins1),
io.decode_evidence(ins2), cutoff)
if sig is not None and sig <= cutoff:
print >> f, '%s\t%d\t%s\t\t%s\t%s\t%g\t%s\t%s' % (
sequence_name, pos1, 'insertion-before', ins1,
ins2, sig, conins1, conins2)
f.flush()
dec_sub1 = io.decode_evidence(sub1)
dec_sub2 = io.decode_evidence(sub2)
if dec_sub1 and dec_sub2:
sig = significance(dec_sub1, dec_sub2, cutoff)
if sig is not None and sig <= cutoff:
if dec_sub1[0][0] == '-' or dec_sub2[0][0] == '-':
what = 'deletion'
elif dec_sub1[0][0] != dec_sub2[0][0]:
what = 'substitution'
else:
what = 'different mix'
print >> f, '%s\t%d\t%s\t%s\t%s\t%s\t%g\t%s\t%s' % (
sequence_name, pos1, what, ref1, sub1, sub2, sig,
consub1, consub2)
f.flush()
f.close()
grace.status('')
return 0
def main(args):
title1, args = grace.get_option_value(args, "--title1", str, None)
title2, args = grace.get_option_value(args, "--title2", str, None)
grace.expect_no_further_options(args)
if len(args) != 3:
print >> sys.stderr, USAGE
return 1
working_dir1 = args[0]
working_dir2 = args[1]
cutoff = float(args[2])
sequence_names = [name for name, sequence in io.read_sequences(os.path.join(working_dir1, "reference.fa"))]
if title1 is None:
title1 = working_dir1
if title2 is None:
title2 = working_dir2
n = 1
while significance([("A", n)], [("T", n)], 1.0) > cutoff:
n += 1
print "%g\tsignificance cutoff" % cutoff
print "%d\tdepth required to call substitution (greater if there are errors in the reads)" % n
print "Sequence\tPosition in reference\tChange type\tReference\t%s\t%s\tp-value (no correction for multiple testing)\t%s\t%s" % (
title1,
title2,
title1,
title2,
)
for sequence_name in sequence_names:
filename1 = os.path.join(working_dir1, grace.filesystem_friendly_name(sequence_name) + "-evidence.txt")
filename2 = os.path.join(working_dir2, grace.filesystem_friendly_name(sequence_name) + "-evidence.txt")
for (pos1, ins1, sub1, ref1, conins1, consub1), (pos2, ins2, sub2, ref2, conins2, consub2) in itertools.izip(
read_file(filename1), read_file(filename2)
):
assert pos1 == pos2 and ref1 == ref2
if pos1 % 1000 == 0:
grace.status("Testing %s %d" % (sequence_name, pos1))
dec_ins1 = io.decode_evidence(ins1)
dec_ins2 = io.decode_evidence(ins2)
if dec_ins1 and dec_ins2:
sig = significance(io.decode_evidence(ins1), io.decode_evidence(ins2), cutoff)
if sig is not None and sig <= cutoff:
grace.status("")
print "%s\t%d\t%s\t\t%s\t%s\t%g\t%s\t%s" % (
sequence_name,
pos1,
"insertion-before",
ins1,
ins2,
sig,
conins1,
conins2,
)
dec_sub1 = io.decode_evidence(sub1)
dec_sub2 = io.decode_evidence(sub2)
if dec_sub1 and dec_sub2:
sig = significance(dec_sub1, dec_sub2, cutoff)
if sig is not None and sig <= cutoff:
if dec_sub1[0][0] == "-" or dec_sub2[0][0] == "-":
what = "deletion"
elif dec_sub1[0][0] != dec_sub2[0][0]:
what = "substitution"
else:
what = "different mix"
grace.status("")
print "%s\t%d\t%s\t%s\t%s\t%s\t%g\t%s\t%s" % (
sequence_name,
pos1,
what,
ref1,
sub1,
sub2,
sig,
consub1,
consub2,
)
grace.status("")
return 0
def run(self):
title1 = self.title1
title2 = self.title2
working1 = working_directory.Working(self.working_dir1)
working2 = working_directory.Working(self.working_dir2)
cutoff = self.cutoff
sequence_names = [ name
for name, length
in working1.get_reference().get_lengths() ]
if title1 is None:
title1 = working1.name
if title2 is None:
title2 = working2.name
n = 1
while significance([('A',n)],[('T',n)],1.0) > cutoff:
n += 1
f = open(self.prefix + '.txt','wb')
print >> f, '%g\tsignificance cutoff' % cutoff
print >> f, '%d\tdepth required to call substitution (greater if there are errors in the reads)' % n
print >> f, 'Sequence\tPosition in reference\tChange type\tReference\t%s\t%s\tp-value (no correction for multiple testing)\t%s\t%s' % (title1, title2, title1, title2)
for sequence_name in sequence_names:
filename1 = working1/(grace.filesystem_friendly_name(sequence_name) + '-evidence.txt')
filename2 = working2/(grace.filesystem_friendly_name(sequence_name) + '-evidence.txt')
for (pos1, ins1, sub1, ref1, conins1, consub1), (pos2, ins2, sub2, ref2, conins2, consub2) in itertools.izip(read_file(filename1), read_file(filename2)):
assert pos1 == pos2 and ref1 == ref2
if pos1 % 1000 == 0:
grace.status('Testing %s %d' % (sequence_name, pos1))
dec_ins1 = io.decode_evidence(ins1)
dec_ins2 = io.decode_evidence(ins2)
if dec_ins1 and dec_ins2:
sig = significance(io.decode_evidence(ins1), io.decode_evidence(ins2), cutoff)
if sig is not None and sig <= cutoff:
print >> f, '%s\t%d\t%s\t\t%s\t%s\t%g\t%s\t%s' % (sequence_name, pos1, 'insertion-before', ins1, ins2, sig, conins1, conins2)
f.flush()
dec_sub1 = io.decode_evidence(sub1)
dec_sub2 = io.decode_evidence(sub2)
if dec_sub1 and dec_sub2:
sig = significance(dec_sub1, dec_sub2, cutoff)
if sig is not None and sig <= cutoff:
if dec_sub1[0][0] == '-' or dec_sub2[0][0] == '-':
what = 'deletion'
elif dec_sub1[0][0] != dec_sub2[0][0]:
what = 'substitution'
else:
what = 'different mix'
print >> f, '%s\t%d\t%s\t%s\t%s\t%s\t%g\t%s\t%s' % (sequence_name, pos1, what, ref1, sub1, sub2, sig, consub1, consub2)
f.flush()
f.close()
grace.status('')
return 0
def main(args):
title1, args = grace.get_option_value(args, '--title1', str, None)
title2, args = grace.get_option_value(args, '--title2', str, None)
grace.expect_no_further_options(args)
if len(args) != 3:
print >> sys.stderr, USAGE
return 1
working_dir1 = args[0]
working_dir2 = args[1]
cutoff = float(args[2])
sequence_names = [
name for name, sequence in io.read_sequences(
os.path.join(working_dir1, 'reference.fa'))
]
if title1 is None:
title1 = working_dir1
if title2 is None:
title2 = working_dir2
n = 1
while significance([('A', n)], [('T', n)], 1.0) > cutoff:
n += 1
print '%g\tsignificance cutoff' % cutoff
print '%d\tdepth required to call substitution (greater if there are errors in the reads)' % n
print 'Sequence\tPosition in reference\tChange type\tReference\t%s\t%s\tp-value (no correction for multiple testing)\t%s\t%s' % (
title1, title2, title1, title2)
for sequence_name in sequence_names:
filename1 = os.path.join(
working_dir1,
grace.filesystem_friendly_name(sequence_name) + '-evidence.txt')
filename2 = os.path.join(
working_dir2,
grace.filesystem_friendly_name(sequence_name) + '-evidence.txt')
for (pos1, ins1, sub1, ref1, conins1,
consub1), (pos2, ins2, sub2, ref2, conins2,
consub2) in itertools.izip(read_file(filename1),
read_file(filename2)):
assert pos1 == pos2 and ref1 == ref2
if pos1 % 1000 == 0:
grace.status('Testing %s %d' % (sequence_name, pos1))
dec_ins1 = io.decode_evidence(ins1)
dec_ins2 = io.decode_evidence(ins2)
if dec_ins1 and dec_ins2:
sig = significance(io.decode_evidence(ins1),
io.decode_evidence(ins2), cutoff)
if sig is not None and sig <= cutoff:
grace.status('')
print '%s\t%d\t%s\t\t%s\t%s\t%g\t%s\t%s' % (
sequence_name, pos1, 'insertion-before', ins1, ins2,
sig, conins1, conins2)
dec_sub1 = io.decode_evidence(sub1)
dec_sub2 = io.decode_evidence(sub2)
if dec_sub1 and dec_sub2:
sig = significance(dec_sub1, dec_sub2, cutoff)
if sig is not None and sig <= cutoff:
if dec_sub1[0][0] == '-' or dec_sub2[0][0] == '-':
what = 'deletion'
elif dec_sub1[0][0] != dec_sub2[0][0]:
what = 'substitution'
else:
what = 'different mix'
grace.status('')
print '%s\t%d\t%s\t%s\t%s\t%s\t%g\t%s\t%s' % (
sequence_name, pos1, what, ref1, sub1, sub2, sig,
consub1, consub2)
grace.status('')
return 0
