def _indexes_to_secondary_files(gresources, genome_build):
"""Convert a list of genome indexes into a single file plus secondary files.
This ensures that all indices are staged together in a single directory.
"""
out = {}
for refname, val in gresources.items():
if isinstance(val, dict) and "indexes" in val:
# list of indexes -- aligners
if len(val.keys()) == 1:
indexes = sorted(val["indexes"])
if len(indexes) == 0:
if refname not in alignment.allow_noindices():
raise ValueError("Did not find indexes for %s: %s" %
(refname, val))
elif len(indexes) == 1:
val = {"indexes": indexes[0]}
else:
val = {
"indexes": {
"base": indexes[0],
"indexes": indexes[1:]
}
}
# directory plus indexes -- snpEff
elif "base" in val and os.path.isdir(
val["base"]) and len(val["indexes"]) > 0:
indexes = val["indexes"]
val = {"base": indexes[0], "indexes": indexes[1:]}
elif isinstance(val, dict) and genome_build in val:
val = _indexes_to_secondary_files(val, genome_build)
out[refname] = val
return out
def _indexes_to_secondary_files(gresources, genome_build):
"""Convert a list of genome indexes into a single file plus secondary files.
This ensures that all indices are staged together in a single directory.
"""
out = {}
for refname, val in gresources.items():
if isinstance(val, dict) and "indexes" in val:
# list of indexes -- aligners
if len(val.keys()) == 1:
indexes = sorted(val["indexes"])
if len(indexes) == 0:
if refname not in alignment.allow_noindices():
raise ValueError("Did not find indexes for %s: %s" % (refname, val))
elif len(indexes) == 1:
val = {"indexes": indexes[0]}
else:
val = {"indexes": {"base": indexes[0], "indexes": indexes[1:]}}
# directory plus indexes -- snpEff
elif "base" in val and os.path.isdir(val["base"]) and len(val["indexes"]) > 0:
indexes = val["indexes"]
val = {"base": indexes[0], "indexes": indexes[1:]}
elif isinstance(val, dict) and genome_build in val:
val = _indexes_to_secondary_files(val, genome_build)
out[refname] = val
return out