def main(args):
if args.v: print args
print 'reading %s...' % args.variant_fn
pos2var=VariantPositions(args.variant_fn)
try: os.mkdir(args.output_dir)
except OSError: pass
for f in os.listdir(args.output_dir):
os.unlink(os.path.join(args.output_dir, f))
dots=ProgressDots(args.dot_counter)
stats={'n_reads':0,
'n_variants':0}
print 'reading %s...' % args.rnaseq_fn
with open(args.rnaseq_fn) as f:
for line in f:
dots.ping()
if line.startswith('@'):
continue
stats['n_reads']+=1
row=line.split('\t')
var=pos2var.variant_for(row[2], int(row[3]), len(row[9]))
if not var: continue
stats['n_variants']+=1
try:
var.reads.append(line)
except AttributeError:
var.reads=[line]
print
# write out all reads for each variant:
for var in pos2var.values():
try:
fn=os.path.join(args.output_dir, '%s.fastq' % var.symbol)
with open(fn, 'w') as var_f:
for line in var.reads:
var_f.write(line)
except AttributeError: # on var.reads
pass
print stats
return 0
def test_read_variant_file(self):
var_fn=os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'triple_negativ_mut_seq'))
pos2var=VariantPositions(var_fn)
stats=pos2var.stats
self.assertEqual(stats['n_variants'], 1128)
self.assertEqual(stats['n_snp'], 1022)
self.assertEqual(stats['n_ins'], 1)
self.assertEqual(stats['n_del'], 105)
self.assertEqual(stats['n_ignored'], 264)
self.assertEqual(stats['n_variant_errors'], 13)
self.assertEqual(stats['n_genes'], 496)
self.assertEqual(len(pos2var), 740)
print stats
# check that all variants bracket the alignments assigned to them:
for k, var in pos2var.items():
(chr, pos)=k.split('_')
nchr=chr[3:]
self.assertEqual(nchr, var.chrom)
self.assertTrue(int(pos) >= int(var.start), '%s: %s <= %s' % (var, pos, var.start))
self.assertTrue(int(pos) <= int(var.stop), '%s: %s >= %s' % (var, pos, var.stop))
