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
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
counts = []
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
pname = sample.patient
if VERBOSE >= 2:
print pname, fragment, samplename
refseq = SeqIO.read(
get_initial_reference_filename(pname, fragment), 'fasta')
fn_out = sample.get_allele_cocounts_filename(fragment,
PCR=PCR,
qual_min=qual_min,
compressed=True)
fn = sample.get_mapped_filtered_filename(
fragment, PCR=PCR, decontaminated=True) #FIXME
if save_to_file:
cocount = gac(fn,
len(refseq),
maxreads=maxreads,
VERBOSE=VERBOSE,
qual_min=qual_min,
use_tests=use_tests)
np.savez_compressed(fn_out, cocounts=cocount)
if VERBOSE >= 2:
print 'Allele cocounts saved:', samplename, fragment
counts.append(cocount)
counts_all = []
for fragment in fragments:
counts = []
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
pname = sample.patient
if VERBOSE >= 2:
print pname, fragment, samplename
refseq = SeqIO.read(get_initial_reference_filename(pname, fragment), 'fasta')
fn_out = sample.get_allele_cocounts_filename(fragment, PCR=PCR,
qual_min=qual_min,
compressed=True)
fn = sample.get_mapped_filtered_filename(fragment, PCR=PCR,
decontaminated=True) #FIXME
if save_to_file:
cocount = gac(fn, len(refseq),
maxreads=maxreads,
VERBOSE=VERBOSE,
qual_min=qual_min,
use_tests=use_tests)
np.savez_compressed(fn_out, cocounts=cocount)
if VERBOSE >= 2:
print 'Allele cocounts saved:', samplename, fragment
counts.append(cocount)
elif os.path.isfile(fn_out):
