print ''
if submit:
fork_self(samplename, fragment, VERBOSE=VERBOSE, PCR=PCR,
block_len=block_len, n_reads_per_ali=n_reads_per_ali)
continue
sample = SamplePat(sample)
pname = sample.patient
refseq = SeqIO.read(get_initial_reference_filename(pname, fragment), 'fasta')
refm = np.array(refseq)
len_reference = len(refseq)
# NOTE: we need consensi to decontaminate, so
bamfilename = sample.get_mapped_filtered_filename(fragment,
PCR=PCR,
decontaminated=(not use_raw_reads))
if not os.path.isfile(bamfilename):
continue
if VERBOSE >= 1:
print 'PCR', PCR,
if VERBOSE >= 2:
print ''
cons = build_consensus(bamfilename, len_reference, VERBOSE=VERBOSE,
block_len=block_len,
reads_per_alignment=n_reads_per_ali,
deltamax=deltamax)
consm = np.fromstring(cons, 'S1')
if not fragments:
fragments = ['F' + str(i) for i in xrange(1, 7)]
if VERBOSE >= 3:
print 'fragments', fragments
if submit:
for fragment in fragments:
for samplename, sample in samples_focal.iterrows():
sample = SamplePat(sample)
if PCR is None:
PCRs_sample = (1, 2)
else:
PCRs_sample = [PCR]
for PCR_sample in PCRs_sample:
bamfilename = sample.get_mapped_filtered_filename(
fragment, PCR=PCR_sample, decontaminated=False)
if not os.path.isfile(bamfilename):
continue
#if check_already_decontaminated(sample, fragment, PCR_sample):
# continue
fork_self(samplename,
fragment,
VERBOSE=VERBOSE,
maxreads=maxreads,
summary=summary,
PCR=PCR_sample)
sys.exit()
if not fragments:
fragments = ["F" + str(i) for i in xrange(1, 7)]
if VERBOSE >= 3:
print "fragments", fragments
if submit:
for fragment in fragments:
for samplename, sample in samples_focal.iterrows():
sample = SamplePat(sample)
if PCR is None:
PCRs_sample = (1, 2)
else:
PCRs_sample = [PCR]
for PCR_sample in PCRs_sample:
bamfilename = sample.get_mapped_filtered_filename(fragment, PCR=PCR_sample, decontaminated=False)
if not os.path.isfile(bamfilename):
continue
# if check_already_decontaminated(sample, fragment, PCR_sample):
# continue
fork_self(samplename, fragment, VERBOSE=VERBOSE, maxreads=maxreads, summary=summary, PCR=PCR_sample)
sys.exit()
for fragment in fragments:
consensi = {refname: "".join(load_custom_reference(refname + "_" + fragment)) for refname in refnames}
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
try:
fragment,
VERBOSE=VERBOSE,
PCR=PCR,
block_len=block_len,
n_reads_per_ali=n_reads_per_ali)
continue
sample = SamplePat(sample)
pname = sample.patient
refseq = SeqIO.read(
get_initial_reference_filename(pname, fragment), 'fasta')
refm = np.array(refseq)
len_reference = len(refseq)
# NOTE: we need consensi to decontaminate, so
bamfilename = sample.get_mapped_filtered_filename(
fragment, PCR=PCR, decontaminated=(not use_raw_reads))
if not os.path.isfile(bamfilename):
continue
if VERBOSE >= 1:
print 'PCR', PCR,
if VERBOSE >= 2:
print ''
cons = build_consensus(bamfilename,
len_reference,
VERBOSE=VERBOSE,
block_len=block_len,
reads_per_alignment=n_reads_per_ali,
deltamax=deltamax)
consm = np.fromstring(cons, 'S1')
