def main():
args = get_args()
regex = re.compile("[N,n]{20,}")
if args.dupefile:
dupes = get_dupes(args.dupefile, longfile=False)
else:
dupes = None
matches, probes = get_matches(args.lastz, args.splitchar, args.components,
args.fish)
#unique_matches = sum([1 for uce, map_pos in matches.iteritems() if len(map_pos) == probes[uce]])
if args.fasta:
tb = bx.seq.twobit.TwoBitFile(file(args.genome))
count = 0
for k, v in matches.iteritems():
chromo, strand, start, end, skip = quality_control_matches(
matches, probes, dupes, k, v, args.verbose)
if not skip and args.fasta:
prep_and_write_fasta(tb, regex, args.fasta, chromo, strand, start,
end, count, args.flank)
if not skip and args.bed:
args.bed.write("{0} {1} {2} {3} 1000 {4}\n".format(
chromo, start - args.flank, end + args.flank, k, strand))
count += 1
#pdb.set_trace()
args.fasta.close()
def main():
args = get_args()
uces = set([
get_name(read.identifier, "|", 1)
for read in fasta.FastaReader(args.query)
])
files = glob.glob(os.path.join(args.lastz, '*.lastz'))
# this prob. needs to be more robust
organisms = [
os.path.splitext(os.path.basename(f).split('-')[-1])[0].replace(
'-', "_") for f in files
]
conn, c = create_match_database(args.db, organisms, uces)
if args.dupefile:
dupes = get_dupes(args.dupefile)
else:
dupes = None
#pdb.set_trace()
for f in files:
critter = os.path.splitext(os.path.basename(f).split('-')[-1])[0]
matches, probes = get_matches(f, args.splitchar, args.components)
count = 0
for k, v in matches.iteritems():
skip = False
if len(v) > 1:
if run_checks(k, v, probes, args.verbose):
# sort by match position
v_sort = sorted(v, key=itemgetter(2))
start, end = v_sort[0][2], v_sort[-1][3]
diff = end - start
# ensure our range is less than N(probes) * probe_length - this
# still gives us a little wiggle room because probes are ~ 2X tiled
if diff > (probes[k] * 120):
skip = True
if args.verbose:
print "range longer than expected"
else:
skip = True
elif args.dupefile and k in dupes:
skip = True
if args.verbose: print "{0} is in dupefile".format(k)
else:
pass
if not skip:
store_lastz_results_in_db(c, critter, k)
count += 1
print "Entered {} matches for {}".format(count, critter)
conn.commit()
c.close()
conn.close()
def main():
args = get_args()
uces = set([get_name(read.identifier, "|", 1) for read in fasta.FastaReader(args.query)])
files = glob.glob(os.path.join(args.lastz, '*.lastz'))
# this prob. needs to be more robust
organisms = [os.path.splitext(os.path.basename(f).split('-')[-1])[0].replace('-',"_") for f in files]
conn, c = create_match_database(args.db, organisms, uces)
if args.dupefile:
dupes = get_dupes(args.dupefile)
else:
dupes = None
#pdb.set_trace()
for f in files:
critter = os.path.splitext(os.path.basename(f).split('-')[-1])[0]
matches, probes = get_matches(f, args.splitchar, args.components)
count = 0
for k,v in matches.iteritems():
skip = False
if len(v) > 1:
if run_checks(k, v, probes, args.verbose):
# sort by match position
v_sort = sorted(v, key = itemgetter(2))
start, end = v_sort[0][2], v_sort[-1][3]
diff = end - start
# ensure our range is less than N(probes) * probe_length - this
# still gives us a little wiggle room because probes are ~ 2X tiled
if diff > (probes[k] * 120):
skip = True
if args.verbose:
print "range longer than expected"
else:
skip = True
elif args.dupefile and k in dupes:
skip = True
if args.verbose:print "{0} is in dupefile".format(k)
else:
pass
if not skip:
store_lastz_results_in_db(c, critter, k)
count += 1
print "Entered {} matches for {}".format(count, critter)
conn.commit()
c.close()
conn.close()
def main():
args = get_args()
regex = re.compile("[N,n]{20,}")
if args.dupefile:
dupes = get_dupes(args.dupefile, longfile=False)
else:
dupes = None
matches, probes = get_matches(args.lastz, args.splitchar, args.components, args.fish)
#unique_matches = sum([1 for uce, map_pos in matches.iteritems() if len(map_pos) == probes[uce]])
if args.fasta:
tb = bx.seq.twobit.TwoBitFile(file(args.genome))
count = 0
for k, v in matches.iteritems():
chromo, strand, start, end, skip = quality_control_matches(matches, probes, dupes, k, v, args.verbose)
if not skip and args.fasta:
prep_and_write_fasta(tb, regex, args.fasta, chromo, strand, start, end, count, args.flank)
if not skip and args.bed:
args.bed.write("{0} {1} {2} {3} 1000 {4}\n".format(chromo, start - args.flank, end + args.flank, k, strand))
count += 1
#pdb.set_trace()
args.fasta.close()