for fragment in fragments:
inses = []
for samplename, sample in samples.iterrows():
if submit:
fork_self(samplename, fragment, VERBOSE=VERBOSE, qual_min=qual_min)
continue
if VERBOSE >= 1:
print fragment, samplename
sample = SamplePat(sample)
pname = sample.patient
refseq = SeqIO.read(get_initial_reference_filename(pname, fragment), 'fasta')
fn = sample.get_mapped_filtered_filename(fragment, PCR=PCR)
if not os.path.isfile(fn):
warn('No BAM file found', NoDataWarning)
continue
_, inse = gac(fn, len(refseq), qual_min=qual_min, VERBOSE=VERBOSE)
inses.append(inse)
if save_to_file:
fn_out = sample.get_insertions_filename(fragment, PCR=PCR,
qual_min=qual_min)
save_insertions(fn_out, inse)
if VERBOSE >= 2:
print 'Insertions saved:', samplename, fragment
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 >= 1:
print "Genomewide insertions saved to:", fn_out
fork_self(samplename,
fragment,
VERBOSE=VERBOSE,
qual_min=qual_min)
continue
if VERBOSE >= 1:
print fragment, samplename
sample = SamplePat(sample)
pname = sample.patient
refseq = SeqIO.read(
get_initial_reference_filename(pname, fragment), 'fasta')
fn = sample.get_mapped_filtered_filename(fragment, PCR=PCR)
if not os.path.isfile(fn):
warn('No BAM file found', NoDataWarning)
continue
_, inse = gac(fn, len(refseq), qual_min=qual_min, VERBOSE=VERBOSE)
inses.append(inse)
if save_to_file:
fn_out = sample.get_insertions_filename(fragment,
PCR=PCR,
qual_min=qual_min)
save_insertions(fn_out, inse)
if VERBOSE >= 2:
print 'Insertions saved:', samplename, fragment
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 >= 1:
print 'Genomewide insertions saved to:', fn_out
