def main():
usage = """%prog [options] <input> <input format> <output dir>
This program reads in an input sequence in any format supported by BioPython
and writes out a preprocessed file ready for use with zipHMM.
Also supports gzipped input files, if the name ends with `.gz`.
Assumption #1: Either the file is a pairwise alignment, or you have provided
exactly two names to the `--names` option.
Assumption #2: The file uses a simple ACGT format (and N/-). Anything else will
be interpreted as N and a warning will be given with all unknown symbols.
Warning: This program uses SeqIO.to_dict to read in the entire alignment, you
may want to split the alignment first if it's very large.
"""
parser = OptionParser(usage=usage, version="%prog 1.0")
parser.add_option(
"--names",
dest="names",
type="string",
default=None,
help="A comma-separated list of names to use from the source file",
)
parser.add_option("-v", "--verbose", dest="verbose", action="store_true", default=False, help="Print some stuff")
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error("Needs input file, input format and output file")
in_filename = args.pop(0)
in_format = args.pop(0)
output_dirname = args.pop(0)
assert os.path.exists(in_filename), "Must use an existing input file"
if in_filename.endswith(".gz"):
if options.verbose:
print "Assuming '%s' is a gzipped file." % in_filename
inf = gzip.open(in_filename)
else:
inf = open(in_filename)
if options.verbose:
print "Loading data...",
sys.stdout.flush()
alignments = SeqIO.to_dict(SeqIO.parse(inf, in_format))
if options.verbose:
print "done"
if options.names:
names = options.names.split(",")
else:
names = list(alignments.keys())
assert len(names) == 2, "Must be a pairwise alignment."
if options.verbose:
print "Assuming pairwise alignment between '%s' and '%s'" % (names[0], names[1])
srcs = [alignments[name].seq for name in names]
clean = set("ACGT")
A = srcs[0]
B = srcs[1]
assert len(A) == len(B)
L = len(A)
fd, foutname = tempfile.mkstemp()
if options.verbose:
print "Writing temp file readable by zipHMM to '%s'..." % (foutname),
sys.stdout.flush()
seen = set()
with os.fdopen(fd, "w", 64 * 1024) as f:
for i in xrange(L):
s1, s2 = A[i].upper(), B[i].upper()
seen.add(s1)
seen.add(s2)
if s1 not in clean or s2 not in clean:
print >> f, 2,
elif s1 == s2:
print >> f, 0,
else:
print >> f, 1,
if options.verbose:
print "done"
if len(seen - set("ACGTN-")) > 1:
print >> sys.stderr, "I didn't understand the following symbols form the input sequence: %s" % (
"".join(list(seen - set("ACGTN-")))
)
if options.verbose:
print "zipHMM is preprocessing...",
sys.stdout.flush()
f = Forwarder.fromSequence(seqFilename=foutname, alphabetSize=3, minNoEvals=500)
if options.verbose:
print "done"
if options.verbose:
print "Writing zipHMM data to '%s'..." % (output_dirname),
sys.stdout.flush()
if not os.path.exists(output_dirname):
os.makedirs(output_dirname)
f.writeToDirectory(output_dirname)
os.rename(foutname, os.path.join(output_dirname, "original_sequence"))
if options.verbose:
print "done"
def main():
usage = """%prog [options] <input> <input format> <output dir>
This program reads in an input sequence in any format supported by BioPython
and writes out a preprocessed file ready for use with zipHMM.
Also supports gzipped input files, if the name ends with `.gz`.
Assumption #1: Either the file is a pairwise alignment, or you have provided
exactly two names to the `--names` option.
Assumption #2: The file uses a simple ACGT format (and N/-). Anything else will
be interpreted as N and a warning will be given with all unknown symbols.
Warning: This program uses SeqIO.to_dict to read in the entire alignment, you
may want to split the alignment first if it's very large.
"""
parser = OptionParser(usage=usage, version="%prog 1.0")
parser.add_option(
"--names",
dest="names",
type="string",
default=None,
help="A comma-separated list of names to use from the source file")
parser.add_option("-v",
"--verbose",
dest="verbose",
action="store_true",
default=False,
help="Print some stuff")
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error("Needs input file, input format and output file")
in_filename = args.pop(0)
in_format = args.pop(0)
output_dirname = args.pop(0)
assert os.path.exists(in_filename), "Must use an existing input file"
if in_filename.endswith('.gz'):
if options.verbose:
print "Assuming '%s' is a gzipped file." % in_filename
inf = gzip.open(in_filename)
else:
inf = open(in_filename)
if options.verbose:
print "Loading data...",
sys.stdout.flush()
alignments = SeqIO.to_dict(SeqIO.parse(inf, in_format))
if options.verbose:
print "done"
if options.names:
names = options.names.split(',')
else:
names = list(alignments.keys())
assert len(names) == 2, "Must be a pairwise alignment."
if options.verbose:
print "Assuming pairwise alignment between '%s' and '%s'" % (names[0],
names[1])
srcs = [alignments[name].seq for name in names]
clean = set('ACGT')
A = srcs[0]
B = srcs[1]
assert len(A) == len(B)
L = len(A)
fd, foutname = tempfile.mkstemp()
if options.verbose:
print "Writing temp file readable by zipHMM to '%s'..." % (foutname),
sys.stdout.flush()
seen = set()
with os.fdopen(fd, 'w', 64 * 1024) as f:
for i in xrange(L):
s1, s2 = A[i].upper(), B[i].upper()
seen.add(s1)
seen.add(s2)
if s1 not in clean or s2 not in clean:
print >> f, 2,
elif s1 == s2:
print >> f, 0,
else:
print >> f, 1,
if options.verbose:
print "done"
if len(seen - set('ACGTN-')) > 1:
print >> sys.stderr, "I didn't understand the following symbols form the input sequence: %s" % (
''.join(list(seen - set('ACGTN-'))))
if options.verbose:
print "zipHMM is preprocessing...",
sys.stdout.flush()
f = Forwarder.fromSequence(seqFilename=foutname,
alphabetSize=3,
minNoEvals=500)
if options.verbose:
print "done"
if options.verbose:
print "Writing zipHMM data to '%s'..." % (output_dirname),
sys.stdout.flush()
if not os.path.exists(output_dirname):
os.makedirs(output_dirname)
f.writeToDirectory(output_dirname)
os.rename(foutname, os.path.join(output_dirname, 'original_sequence'))
if options.verbose:
print "done"
