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:
consensi[samplename] = sample.get_consensus(fragment, PCR=1)
except IOError:
print samplename, "file not found"
continue
for samplename, sample in samples_focal.iterrows():
sample = SamplePat(sample)
pname = sample.patient
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)
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:
consensi[samplename] = sample.get_consensus(fragment, PCR=1)
except IOError:
print samplename, 'file not found'
continue
for samplename, sample in samples_focal.iterrows():
sample = SamplePat(sample)
pname = sample.patient
if PCR is None:
PCRs_sample = (1, 2)
else:
PCRs_sample = [PCR]
for PCR_sample in PCRs_sample:
bamfilename = sample.get_mapped_filtered_filename(
samples_pat = samples_pat.loc[samples_pat.index.isin(samplenames)]
if VERBOSE >= 2:
print 'samples', samples_pat.index.tolist()
consensi = []
for samplename_pat, sample_pat in samples_pat.iterrows():
sample_pat = SamplePat(sample_pat)
if VERBOSE >= 1:
print sample_pat.name,
consensi_pat = {}
try:
for i in xrange(6):
fragment = 'F'+str(i+1)
consensi_pat[fragment] = sample_pat.get_consensus(fragment)
except IOError:
if VERBOSE >= 1:
print 'warning: some consensus not found: skipping'
continue
except ValueError:
if VERBOSE >= 1:
print 'warning: some consensus is not clean (e.g. contamination): skipping'
continue
if VERBOSE >= 1:
print 'ok: all 6 consensi found'
consensus = merge_fragments(consensi_pat, name=sample_pat.patient,
samples_pat = samples_pat.loc[samples_pat.index.isin(samplenames)]
if VERBOSE >= 2:
print 'samples', samples_pat.index.tolist()
consensi = []
for samplename_pat, sample_pat in samples_pat.iterrows():
sample_pat = SamplePat(sample_pat)
if VERBOSE >= 1:
print sample_pat.name,
consensi_pat = {}
try:
for i in xrange(6):
fragment = 'F' + str(i + 1)
consensi_pat[fragment] = sample_pat.get_consensus(fragment)
except IOError:
if VERBOSE >= 1:
print 'warning: some consensus not found: skipping'
continue
except ValueError:
if VERBOSE >= 1:
print 'warning: some consensus is not clean (e.g. contamination): skipping'
continue
if VERBOSE >= 1:
print 'ok: all 6 consensi found'
consensus = merge_fragments(consensi_pat,
