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
fork_self(samplename, fragment, VERBOSE=VERBOSE,
qual_min=qual_min, PCR=PCR)
sys.exit()
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
pname = sample.patient
for fragment in fragments:
if VERBOSE >= 1:
print pname, samplename, fragment
fn = sample.get_allele_cocounts_filename(fragment, PCR=PCR,
qual_min=qual_min,
compressed=False)
fn_out = sample.get_allele_cocounts_filename(fragment, PCR=PCR,
qual_min=qual_min,
compressed=True)
if not os.path.isfile(fn):
if VERBOSE >= 2:
print 'Input file not found, skipping'
continue
if VERBOSE >= 2:
print 'Loading cocounts'
cocount = np.load(fn)
