def dump_hmm_matches(fasta_file, hits_file, dbpath, port, scantype, idmap, args):
hits_header = ("#query_name", "hit", "evalue", "sum_score", "query_length",
"hmmfrom", "hmmto", "seqfrom", "seqto", "query_coverage")
# Cache previous results if resuming is enabled
VISITED = set()
if args.resume and pexists(hits_file):
print colorify("Resuming previous run. Reading computed output from %s" % hits_file, 'yellow')
VISITED = set([line.split('\t')[0].strip()
for line in open(hits_file) if not line.startswith('#')])
print len(VISITED), 'queries skipped'
OUT = open(hits_file, 'a')
else:
OUT = open(hits_file, 'w')
print colorify("Sequence mapping starts now!", 'green')
if not args.no_file_comments:
print >>OUT, get_call_info()
print >>OUT, '# ' + '\t'.join(hits_header)
total_time = 0
last_time = time.time()
start_time = time.time()
qn = 0
for qn, (name, elapsed, hits, querylen, seq) in enumerate(search.iter_hits(
fasta_file,
args.translate,
args.qtype,
args.dbtype,
scantype,
dbpath,
port,
evalue_thr=args.evalue,
score_thr=args.score,
qcov_thr=args.qcov,
fixed_Z=args.Z,
max_hits=args.maxhits,
skip=VISITED,
maxseqlen=args.maxseqlen,
cpus=args.cpu)):
if elapsed == -1:
# error occurred
print >>OUT, '\t'.join(
[name] + ['ERROR'] * (len(hits_header) - 1))
elif not hits:
print >>OUT, '\t'.join([name] + ['-'] * (len(hits_header) - 1))
else:
for hitindex, (hid, heval, hscore, hmmfrom, hmmto, sqfrom, sqto, domscore) in enumerate(hits):
hitname = hid
if idmap:
hitname = idmap[hid][0]
print >>OUT, '\t'.join(map(str, [name, hitname, heval, hscore,
int(querylen), int(hmmfrom),
int(hmmto), int(sqfrom),
int(sqto),
float(sqto - sqfrom) / querylen]))
OUT.flush()
# monitoring
total_time += time.time() - last_time
last_time = time.time()
if qn and (qn % 25 == 0):
print >>sys.stderr, qn + \
1, total_time, "%0.2f q/s" % ((float(qn + 1) / total_time))
sys.stderr.flush()
# Writes final stats
elapsed_time = time.time() - start_time
if not args.no_file_comments:
print >>OUT, '# %d queries scanned' % (qn + 1)
print >>OUT, '# Total time (seconds):', elapsed_time
print >>OUT, '# Rate:', "%0.2f q/s" % ((float(qn + 1) / elapsed_time))
OUT.close()
print colorify(" Processed queries:%s total_time:%s rate:%s" %\
(qn+1, elapsed_time, "%0.2f q/s" % ((float(qn+1) / elapsed_time))), 'lblue')
def dump_hmm_matches(fasta_file, hits_file, dbpath, port, scantype, idmap,
args):
hits_header = ("#query_name", "hit", "evalue", "sum_score", "query_length",
"hmmfrom", "hmmto", "seqfrom", "seqto", "query_coverage")
# Cache previous results if resuming is enabled
VISITED = set()
if args.resume and pexists(hits_file):
print colorify(
"Resuming previous run. Reading computed output from %s" %
hits_file, 'yellow')
VISITED = set([
line.split('\t')[0].strip() for line in open(hits_file)
if not line.startswith('#')
])
print len(VISITED), 'queries skipped'
OUT = open(hits_file, 'a')
else:
OUT = open(hits_file, 'w')
print colorify("Sequence mapping starts now!", 'green')
if not args.no_file_comments:
print >> OUT, get_call_info()
print >> OUT, '# ' + '\t'.join(hits_header)
total_time = 0
last_time = time.time()
start_time = time.time()
qn = 0 # in case nothing to loop bellow
for qn, (name, elapsed, hits, querylen, seq) in enumerate(
search.iter_hits(fasta_file,
args.translate,
args.qtype,
args.dbtype,
scantype,
dbpath,
port,
evalue_thr=args.evalue,
score_thr=args.score,
qcov_thr=args.qcov,
fixed_Z=args.Z,
max_hits=args.maxhits,
skip=VISITED,
maxseqlen=args.maxseqlen,
cpus=args.cpu,
base_tempdir=args.temp_dir)):
if elapsed == -1:
# error occurred
print >> OUT, '\t'.join([name] + ['ERROR'] *
(len(hits_header) - 1))
elif not hits:
print >> OUT, '\t'.join([name] + ['-'] * (len(hits_header) - 1))
else:
for hitindex, (hid, heval, hscore, hmmfrom, hmmto, sqfrom, sqto,
domscore) in enumerate(hits):
hitname = hid
if idmap:
hitname = idmap[hid][0]
print >> OUT, '\t'.join(
map(str, [
name, hitname, heval, hscore,
int(querylen),
int(hmmfrom),
int(hmmto),
int(sqfrom),
int(sqto),
float(sqto - sqfrom) / querylen
]))
OUT.flush()
# monitoring
total_time += time.time() - last_time
last_time = time.time()
if qn and (qn % 25 == 0):
print >>sys.stderr, qn + \
1, total_time, "%0.2f q/s" % ((float(qn + 1) / total_time))
sys.stderr.flush()
# Writes final stats
elapsed_time = time.time() - start_time
if not args.no_file_comments:
print >> OUT, '# %d queries scanned' % (qn + 1)
print >> OUT, '# Total time (seconds):', elapsed_time
print >> OUT, '# Rate:', "%0.2f q/s" % ((float(qn + 1) / elapsed_time))
OUT.close()
print colorify(" Processed queries:%s total_time:%s rate:%s" %\
(qn+1, elapsed_time, "%0.2f q/s" % ((float(qn+1) / elapsed_time))), 'lblue')