def _prep_bam_input(f, i, base):
if not os.path.exists(f):
raise ValueError("Could not find input file: %s" % f)
cur = copy.deepcopy(base)
cur["files"] = [os.path.abspath(f)]
cur["description"] = sample_name(f) or os.path.splitext(os.path.basename(f))[0]
return cur
def _prep_bam_input(f, i, base):
if not os.path.exists(f):
raise ValueError("Could not find input file: %s" % f)
cur = copy.deepcopy(base)
cur["files"] = [os.path.abspath(f)]
cur["description"] = ((sample_name(f) if f.endswith(".bam") else None)
or os.path.splitext(os.path.basename(f))[0])
return cur
def _get_bam_samples(f, data):
have_full_file = False
if have_full_file:
return [bam.sample_name(f)]
else:
if os.path.basename(f).startswith("%s-" % dd.get_sample_name(data)):
return [dd.get_sample_name(data)]
else:
return []
def _get_bam_samples(f, items):
have_full_file = False
if have_full_file:
return [bam.sample_name(f)]
else:
for data in items:
if os.path.basename(f).startswith(("%s-" % dd.get_sample_name(data),
"%s." % dd.get_sample_name(data))):
return [dd.get_sample_name(data)]
return []
def _get_bam_samples(f, items):
have_full_file = False
if have_full_file:
return [bam.sample_name(f)]
else:
for data in items:
if os.path.basename(f).startswith(("%s-" % dd.get_sample_name(data),
"%s." % dd.get_sample_name(data))):
return [dd.get_sample_name(data)]
return []
def _prep_bam_input(f, i, base):
if not os.path.exists(f) and not objectstore.is_remote(f):
raise ValueError("Could not find input file: %s" % f)
cur = copy.deepcopy(base)
if objectstore.is_remote(f):
cur["files"] = [f]
cur["description"] = os.path.splitext(os.path.basename(f))[0]
else:
cur["files"] = [os.path.abspath(f)]
cur["description"] = ((sample_name(f) if f.endswith(".bam") else None)
or os.path.splitext(os.path.basename(f))[0])
return cur
def _get_bam_samples(f):
return [bam.sample_name(f)]