def xsq_list(filename, count=False, minreads=-1, total=False):
xsq = XSQFile(filename)
print 'Tags: '
for tag in xsq.tags:
t = xsq.tags[tag]
if t.is_colorspace:
print ' %s[cs/%s]' % (tag, t.prefix)
else:
print ' %s[nt]' % (tag,)
print ''
print 'Samples: '
acc = 0
try:
for sample in xsq.get_samples():
desc = xsq.get_sample_desc(sample).strip()
if count:
readcount = xsq.get_read_count(sample)
if readcount > minreads:
pn = pretty_number(readcount)
if sample != 'Unclassified':
acc += readcount
if desc:
print ' %s (%s) %s' % (sample, desc, pn)
else:
print ' %s %s' % (sample, pn)
else:
if desc:
print ' %s (%s)' % (sample, desc)
else:
print ' %s' % (sample, )
except KeyboardInterrupt:
pass
if count and total:
print ''
print ' Total reads => %s' % pretty_number(acc)
print ''
xsq.close()
def xsq_convert_all(filename, tags=None, force=False, suffix=None, noz=False, usedesc=False, minreads=0, fsuffix=None, unclassified=False, procs=1, tmpdir=None):
xsq = XSQFile(filename)
samples = []
for sample in xsq.get_samples():
fname = sample
if not fsuffix:
fsuffix = ''
if usedesc:
fname = xsq.get_sample_desc(sample)
if not fname:
fname = sample
if fname == sample:
sys.stderr.write('Sample: %s... ' % fname)
else:
sys.stderr.write('Sample: (%s) %s... ' % (sample, fname))
if noz:
outname = '%s%s.fastq' % (fname, fsuffix)
else:
outname = '%s%s.fastq.gz' % (fname, fsuffix)
if force or not os.path.exists(outname):
if sample == 'Unclassified' and not unclassified:
sys.stderr.write(' Skipping unclassified\n')
continue
count = xsq.get_read_count(sample)
if count < minreads:
sys.stderr.write(' Too few reads (%s)\n' % count)
continue
samples.append((sample, outname))
sys.stderr.write('\n')
xsq.close()
for sample, outname in samples:
xsq_convert(filename, sample, tags, suffix, procs=procs, outname=outname, noz=noz, tmpdir=tmpdir)
