if VERBOSE >= 2:
print 'samples', samples_groups.groups
# If the script is called with no fragment, iterate over all
if not fragments:
fragments = ['F' + str(i) for i in xrange(1, 7)]
if VERBOSE >= 3:
print 'fragments', fragments
for (samplename_pat,
PCR), samplenames_seq in samples_groups.groups.iteritems():
sample_pat = samples_pat.loc[samplename_pat].copy()
samples_seq_group = samples_seq.loc[samples_seq.index.isin(
samplenames_seq)]
sample_pat.samples_seq = samples_seq_group
pname = sample_pat.patient
PCR = int(PCR)
for fragment in fragments:
if submit:
fork_self(samplename_pat,
fragment,
VERBOSE=VERBOSE,
n_pairs=n_pairs,
PCR=PCR,
summary=summary)
continue
if summary:
sfn = get_filter_mapped_init_summary_filename(pname,
samples_groups = samples_seq.groupby(['patient sample', 'PCR'])
if VERBOSE >= 2:
print 'samples', samples_groups.groups
# If the script is called with no fragment, iterate over all
if not fragments:
fragments = ['F'+str(i) for i in xrange(1, 7)]
if VERBOSE >= 3:
print 'fragments', fragments
for (samplename_pat, PCR), samplenames_seq in samples_groups.groups.iteritems():
sample_pat = samples_pat.loc[samplename_pat].copy()
samples_seq_group = samples_seq.loc[samples_seq.index.isin(samplenames_seq)]
sample_pat.samples_seq = samples_seq_group
pname = sample_pat.patient
PCR = int(PCR)
for fragment in fragments:
if submit:
fork_self(samplename_pat, fragment,
VERBOSE=VERBOSE,
n_pairs=n_pairs,
PCR=PCR,
summary=summary)
continue
if summary:
sfn = get_filter_mapped_init_summary_filename(pname, samplename_pat, fragment, PCR=PCR)
with open(sfn, 'w') as f:
