def pslAddSequence(query_fasta, sbjct_fasta, options):
iterator = Blat.BlatIterator(sys.stdin)
ninput, noutput, ndiscarded, nskipped = 0, 0, 0, 0
while 1:
match = next(iterator)
if not match:
break
ninput += 1
if options.test and ninput >= options.test:
break
if ninput % options.report_step == 0:
E.info("progress: ninput=%i, noutput=%i" % (ninput, noutput))
new = Blat.MatchPSLX()
new.fromPSL(match,
query_fasta.getSequence(
match.mQueryId, "+", match.mQueryFrom, match.mQueryTo),
sbjct_fasta.getSequence(
match.mSbjctId, "+", match.mSbjctFrom, match.mSbjctTo))
options.stdout.write(str(new) + "\n")
noutput += 1
E.info("ninput=%i, noutput=%i, nskipped=%i, ndiscarded=%i" %
(ninput, noutput, nskipped, ndiscarded))
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: psl2table.py 2891 2010-04-07 08:59:18Z andreas $",
usage=globals()["__doc__"])
parser.add_option(
"--mask-lowercase",
dest="mask_lowercase",
action="store_true",
help=
"mask lowercase characters before computing properties [default=%default]"
)
parser.add_option("--with-match",
dest="with_match",
action="store_true",
help="echo the match in output [default=%default]")
parser.add_option(
"--without-match",
dest="with_match",
action="store_false",
help="do not echo the match in output [default=%default]")
parser.add_option(
"-m",
"--method",
dest="methods",
type="choice",
action="append",
choices=("counts", "baseml", "match", "query-counts", "sbjct-counts"),
help="methods to compute properties between sequence pairs.")
WrapperCodeML.BaseML().AddOptions(parser)
parser.set_defaults(
methods=[],
mask_lowercase=False,
is_pslx=True,
with_match=True,
)
(options, args) = E.Start(parser)
counters_plain = []
counters = []
for method in options.methods:
if method == "counts":
counters.append(
SequencePairProperties.SequencePairPropertiesCountsNa())
elif method == "query-counts":
counters.append(QueriesCounter())
elif method == "sbjct-counts":
counters.append(SbjctsCounter())
elif method == "baseml":
counters.append(
SequencePairProperties.SequencePairPropertiesBaseML(options))
elif method == "match":
counters_plain.append(CounterMatch(options))
if counters:
iterator = Blat.iterator_pslx(options.stdin)
header = "\t".join(Blat.MatchPSLX().getHeaders())
else:
iterator = Blat.iterator(options.stdin)
header = "\t".join(Blat.Match().getHeaders())
if not options.with_match:
header = "qName"
options.stdout.write(
"\t".join([
header,
] + ["\t".join(x.getHeaders()) for x in counters] +
["\t".join(x.getHeaders()) for x in counters_plain]) + "\n")
ninput, noutput, nskipped = 0, 0, 0
for match in iterator:
ninput += 1
if options.with_match:
options.stdout.write(str(match))
else:
options.stdout.write(match.mQueryId)
if counters:
qseq = match.mQuerySequence
sseq = match.mSbjctSequence
# mask non printable characters - sometimes
# appear after using pslToPslX
qseq = [re.sub("[^a-zA-Z]", "N", x) for x in qseq]
sseq = [re.sub("[^a-zA-Z]", "N", x) for x in sseq]
if options.mask_lowercase:
qseq = [re.sub("[a-z]", "N", x) for x in qseq]
sseq = [re.sub("[a-z]", "N", x) for x in sseq]
match.mQuerySequence = qseq
match.mSbjctSequence = sseq
qseq = "".join(match.mQuerySequence).upper()
sseq = "".join(match.mSbjctSequence).upper()
if len(qseq) != len(sseq):
if options.loglevel >= 1:
options.stdlog.write(
"# WARNING: two sequences of unequal length in match\n# %s\n"
% str(match))
nskipped += 1
continue
for counter in counters:
counter(qseq, sseq)
options.stdout.write(
"\t" + "\t".join([str(counter) for counter in counters]))
if counters_plain:
for counter in counters_plain:
counter(match)
options.stdout.write(
"\t" + "\t".join([str(counter) for counter in counters_plain]))
options.stdout.write("\n")
noutput += 1
if options.loglevel >= 1:
options.stdlog.write("# ninput=%i, noutput=%i, nskipped=%i\n" %
(ninput, noutput, nskipped))
E.Stop()
