def get_matches(lastz_file):
matches = defaultdict(list)
probes = defaultdict(int)
for lz in lastz.Reader(lastz_file, long_format=True):
uce_name = get_uce_name(lz.name2)
probe_number = get_uce_num(lz.name2)
if probe_number > probes[uce_name]:
probes[uce_name] = probe_number
matches[uce_name].append([get_name(lz.name1).lower(), lz.strand2, lz.zstart1, lz.end1])
return matches, probes
def get_bgi_matches(lastz_file, stripnum):
matches = defaultdict(list)
probes = defaultdict(int)
for lz in lastz.Reader(lastz_file, long_format=True):
uce_name = re.sub(stripnum, 's', lz.name2).lower()
probe_number = int(lz.name2.split('_')[-1])
if probe_number > probes[uce_name]:
probes[uce_name] = probe_number
matches[uce_name].append(
[get_name(lz.name1).lower(), lz.strand2, lz.zstart1, lz.end1])
return matches, probes
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 get_matches(lastz_file):
matches = defaultdict(list)
probes = defaultdict(int)
for lz in lastz.Reader(lastz_file, long_format=True):
uce_name = get_uce_name(lz.name2)
probe_number = get_uce_num(lz.name2)
if probe_number > probes[uce_name]:
probes[uce_name] = probe_number
matches[uce_name].append(
[
get_name(lz.name1).lower(),
lz.strand2,
lz.zstart1,
lz.end1
]
)
return matches, probes
def get_bgi_matches(lastz_file, stripnum):
matches = defaultdict(list)
probes = defaultdict(int)
for lz in lastz.Reader(lastz_file, long_format=True):
uce_name = re.sub(stripnum, 's', lz.name2).lower()
probe_number = int(lz.name2.split('_')[-1])
if probe_number > probes[uce_name]:
probes[uce_name] = probe_number
matches[uce_name].append(
[
get_name(lz.name1).lower(),
lz.strand2,
lz.zstart1,
lz.end1
]
)
return matches, probes
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()
config = ConfigParser.RawConfigParser(allow_no_value=True)
config.read(args.config)
conn = sqlite3.connect(args.db)
c = conn.cursor()
if args.extend_db:
query = "ATTACH DATABASE '{0}' AS extended".format(args.extend_db)
c.execute(query)
organisms = get_names_from_config(config, "Organisms")
uces = get_names_from_config(config, "Loci")
# pdb.set_trace()
uce_fasta_out = fasta.FastaWriter(args.output)
regex = re.compile("[N,n]{1,21}")
for organism in organisms:
print "Getting {0} reads...".format(organism)
written = []
# going to need to do something more generic w/ suffixes
# pdb.set_trace()
name = organism.replace("_", "-")
if args.notstrict:
if not organism.endswith("*"):
reads = find_file(args.contigs, name)
node_dict, missing = get_nodes_for_uces(c, organism, uces, extend=False, notstrict=True)
elif args.extend_dir:
# remove the asterisk
name = name.rstrip("*")
reads = find_file(args.extend_dir, name)
node_dict, missing = get_nodes_for_uces(c, organism.rstrip("*"), uces, extend=True, notstrict=True)
else:
if not name.endswith("*"):
reads = find_file(args.contigs, name)
node_dict, missing = get_nodes_for_uces(c, organism, uces)
elif name.endswith("*") and args.extend_dir:
# remove the asterisk
name = name.rstrip("*")
reads = find_file(args.extend_dir, name)
node_dict, missing = get_nodes_for_uces(c, organism.rstrip("*"), uces, extend=True)
for read in fasta.FastaReader(reads):
name = get_name(read.identifier).lower()
coverage = get_coverage(read.identifier)
if name in node_dict.keys():
uce_seq = fasta.FastaSequence()
uce_seq.identifier = ">{0}_{1} |{0}|{2}".format(node_dict[name][0], organism.rstrip("*"), coverage)
# deal with strandedness because aligners dont, which
# is annoying
if node_dict[name][1] == "-":
uce_seq.sequence = transform.DNA_reverse_complement(read.sequence)
else:
uce_seq.sequence = read.sequence
# replace any occurrences of <21 Ns in a given sequence with
# blanks. These should gap out during alignment.
if regex.search(uce_seq.sequence):
uce_seq.sequence = re.sub(regex, "", uce_seq.sequence)
print "\tReplaced < 20 ambiguous bases in {0}".format(uce_seq.identifier.split(" ")[0])
# Replace and leading/trailing lowercase bases from velvet
# assemblies. Lowercase bases indicate low coverage, and these
# have been problematic in downstream alignments).
uce_seq.sequence = re.sub("^[acgtn]+", "", uce_seq.sequence)
uce_seq.sequence = re.sub("[acgtn]+$", "", uce_seq.sequence)
uce_fasta_out.write(uce_seq)
written.append(str(node_dict[name][0]))
else:
pass
# pdb.set_trace()
if args.notstrict and missing:
args.notstrict.write("[{0}]\n".format(organism))
for name in missing:
args.notstrict.write("{0}\n".format(name))
written.append(name)
assert set(written) == set(uces), "UCE names do not match"
# assert set(written) == set(uces), pdb.set_trace()
uce_fasta_out.close()
def main():
args = get_args()
config = ConfigParser.RawConfigParser(allow_no_value=True)
config.read(args.config)
conn = sqlite3.connect(args.db)
c = conn.cursor()
if args.extend_db:
query = "ATTACH DATABASE '{0}' AS extended".format(args.extend_db)
c.execute(query)
organisms = get_names_from_config(config, 'Organisms')
uces = get_names_from_config(config, 'Loci')
#pdb.set_trace()
uce_fasta_out = fasta.FastaWriter(args.output)
regex = re.compile("[N,n]{1,21}")
for organism in organisms:
print "Getting {0} reads...".format(organism)
written = []
# going to need to do something more generic w/ suffixes
#pdb.set_trace()
name = organism.replace('_', '-')
if args.notstrict:
if not organism.endswith('*'):
reads = find_file(args.contigs, name)
node_dict, missing = get_nodes_for_uces(c, organism, uces, extend=False, notstrict=True)
elif args.extend_dir:
# remove the asterisk
name = name.rstrip('*')
reads = find_file(args.extend_dir, name)
node_dict, missing = get_nodes_for_uces(c, organism.rstrip('*'), uces, extend=True, notstrict=True)
else:
if not name.endswith('*'):
reads = find_file(args.contigs, name)
node_dict, missing = get_nodes_for_uces(c, organism, uces)
elif name.endswith('*') and args.extend_dir:
# remove the asterisk
name = name.rstrip('*')
reads = find_file(args.extend_dir, name)
node_dict, missing = get_nodes_for_uces(c, organism.rstrip('*'), uces, extend=True)
for read in fasta.FastaReader(reads):
name = get_name(read.identifier).lower()
coverage = get_coverage(read.identifier)
if name in node_dict.keys():
uce_seq = fasta.FastaSequence()
uce_seq.identifier = ">{0}_{1} |{0}|{2}".format(node_dict[name][0], organism, coverage)
# deal with strandedness because aligners dont, which
# is annoying
if node_dict[name][1] == '-':
uce_seq.sequence = transform.DNA_reverse_complement(read.sequence)
else:
uce_seq.sequence = read.sequence
# replace any occurrences of <21 Ns
if regex.search(uce_seq.sequence):
uce_seq.sequence = re.sub(regex, "", uce_seq.sequence)
print "\tReplaced < 20 ambiguous bases in {0}".format(uce_seq.identifier.split(' ')[0])
uce_fasta_out.write(uce_seq)
written.append(str(node_dict[name][0]))
else:
pass
#pdb.set_trace()
if args.notstrict and missing:
args.notstrict.write("[{0}]\n".format(organism))
for name in missing:
args.notstrict.write("{0}\n".format(name))
written.append(name)
assert set(written) == set(uces), "UCE names do not match"
#assert set(written) == set(uces), pdb.set_trace()
uce_fasta_out.close()