if VERBOSE >= 2:
print "samples", samples.index.tolist()
for samplename, sample in samples.iterrows():
if VERBOSE >= 1:
print samplename
sample = SamplePat(sample)
pname = sample.patient
ref = sample.get_reference("genomewide", "gb")
# Collect the insertions (where possible)
ics = {}
for fragment in ["F" + str(i) for i in xrange(1, 7)]:
try:
ic = sample.get_insertions(fragment, merge_read_types=False)
except IOError:
continue
start = find_annotation(ref, fragment).location.nofuzzy_start
ics[(fragment, start)] = ic
if not len(ics):
if VERBOSE >= 1:
print "No data found: skipping"
continue
# Merge insertions
ic = merge_insertions(ics, VERBOSE=VERBOSE)
if save_to_file:
fn_out = sample.get_insertions_filename("genomewide")
save_insertions(fn_out, ic)
if VERBOSE >= 2:
print 'samples', samples.index.tolist()
for samplename, sample in samples.iterrows():
if VERBOSE >= 1:
print samplename
sample = SamplePat(sample)
pname = sample.patient
ref = sample.get_reference('genomewide', 'gb')
# Collect the insertions (where possible)
ics = {}
for fragment in ['F' + str(i) for i in xrange(1, 7)]:
try:
ic = sample.get_insertions(fragment, merge_read_types=False)
except IOError:
continue
start = find_annotation(ref, fragment).location.nofuzzy_start
ics[(fragment, start)] = ic
if not len(ics):
if VERBOSE >= 1:
print 'No data found: skipping'
continue
# Merge insertions
ic = merge_insertions(ics, VERBOSE=VERBOSE)
if save_to_file:
fn_out = sample.get_insertions_filename('genomewide')
save_insertions(fn_out, ic)
