def build_table(args, handle, counts):
references = collect_references(args, handle)
table = {}
for (key, readgroup) in collect_readgroups(args, handle).iteritems():
sample = readgroup["SM"]
library = readgroup["LB"]
# Exclude counts for reads with no read-groups, if none such were seen
if key is None and not args.ignore_readgroups:
for reference in references:
subtable = counts.get(reference, {}).get(key)
if subtable is not None and subtable.has_values():
break
else:
continue
for (reference, size) in references.iteritems():
subtable_key = (args.target_name, sample, library, reference)
subtable = create_or_get_subtable(table, subtable_key, size)
statistics = counts.get(reference, {}).get(key)
if statistics is not None:
subtable.add(statistics)
return table
def build_table(args, handle, counts):
references = collect_references(args, handle)
table = {}
for (key, readgroup) in collect_readgroups(args, handle).iteritems():
sample = readgroup["SM"]
library = readgroup["LB"]
# Exclude counts for reads with no read-groups, if none such were seen
if key is None and not args.ignore_readgroups:
for reference in references:
subtable = counts.get(reference, {}).get(key)
if subtable is not None and subtable.has_values():
break
else:
continue
for (reference, size) in references.iteritems():
subtable_key = (args.target_name, sample, library, reference)
subtable = create_or_get_subtable(table, subtable_key, size)
statistics = counts.get(reference, {}).get(key)
if statistics is not None:
subtable.add(statistics)
return table
def build_key_struct(args, handle):
structure = collections.defaultdict(set)
for readgroup in collect_readgroups(args, handle).itervalues():
lb_key = readgroup["LB"]
sm_key = readgroup["SM"]
structure[sm_key].add(lb_key)
return structure
def build_key_struct(args, handle):
structure = collections.defaultdict(set)
for readgroup in collect_readgroups(args, handle).itervalues():
lb_key = readgroup["LB"]
sm_key = readgroup["SM"]
structure[sm_key].add(lb_key)
return structure
def build_table(args, handle, counts):
table = {}
for (key, readgroup) in collect_readgroups(args, handle).iteritems():
sample = readgroup["SM"]
library = readgroup["LB"]
for (reference, size) in collect_references(args, handle).iteritems():
subtable_key = (args.target_name, sample, library, reference)
subtable = create_or_get_subtable(table, subtable_key, size)
statistics = counts.get(reference, {}).get(key, {})
for (stat, value) in statistics.iteritems():
subtable[stat] += value
return table
def build_rg_to_smlbid_keys(args, handle):
"""Returns a dictionary which maps a readgroup ID to an index value,
as well as a list containing a tuple (samples, library) corresponding
to each index. Typically, this list will be shorter than the map of read-
groups, as multiple read-groups will map to the same sample / library.
"""
rg_to_lbsmid = {}
lbsm_to_lbsmid = {}
lbsmid_to_smlb = []
for (key_rg, readgroup) in collect_readgroups(args, handle).iteritems():
key_sm = readgroup["SM"]
key_lb = readgroup["LB"]
key_lbsm = (key_sm, key_lb)
if key_lbsm not in lbsm_to_lbsmid:
lbsm_to_lbsmid[key_lbsm] = len(lbsm_to_lbsmid)
lbsmid_to_smlb.append(key_lbsm)
rg_to_lbsmid[key_rg] = lbsm_to_lbsmid[key_lbsm]
return rg_to_lbsmid, lbsmid_to_smlb
def build_rg_to_smlbid_keys(args, handle):
"""Returns a dictionary which maps a readgroup ID to an index value,
as well as a list containing a tuple (samples, library) corresponding
to each index. Typically, this list will be shorter than the map of read-
groups, as multiple read-groups will map to the same sample / library.
"""
rg_to_lbsmid = {}
lbsm_to_lbsmid = {}
lbsmid_to_smlb = []
for (key_rg, readgroup) in collect_readgroups(args, handle).iteritems():
key_sm = readgroup["SM"]
key_lb = readgroup["LB"]
key_lbsm = (key_sm, key_lb)
if key_lbsm not in lbsm_to_lbsmid:
lbsm_to_lbsmid[key_lbsm] = len(lbsm_to_lbsmid)
lbsmid_to_smlb.append(key_lbsm)
rg_to_lbsmid[key_rg] = lbsm_to_lbsmid[key_lbsm]
return rg_to_lbsmid, lbsmid_to_smlb
def build_region_template(args, handle):
template = {}
for key in collect_readgroups(args, handle):
template[key] = dict(READGROUP_TEMPLATE)
return template
def build_region_template(args, handle):
template = {}
for key in collect_readgroups(args, handle):
template[key] = ReadGroup()
return template
def build_region_template(args, handle):
template = {}
for key in collect_readgroups(args, handle):
template[key] = ReadGroup()
return template