def build_totals_dict(args, handle):
references = tuple(collect_references(args, handle))
structure = build_key_struct(args, handle)
totals = {}
for (sm_key, libraries) in structure.iteritems():
for lb_key in libraries:
if len(references) == 1:
key = references[0]
counts = collections.defaultdict(int)
totals[(sm_key, lb_key, key)] = counts
totals[(sm_key, lb_key, '*')] = counts
else:
build_new_dicts(totals, sm_key, lb_key, references)
if len(libraries) == 1:
key = list(libraries)[0]
reuse_dicts(totals, sm_key, '*', sm_key, key, references)
else:
build_new_dicts(totals, sm_key, '*', references)
if len(structure) == 1:
key = list(structure)[0]
reuse_dicts(totals, '*', '*', key, '*', references)
else:
build_new_dicts(totals, '*', '*', references)
return totals
def build_totals_dict(args, handle):
references = tuple(collect_references(args, handle))
structure = build_key_struct(args, handle)
totals = {}
for (sm_key, libraries) in structure.iteritems():
for lb_key in libraries:
if len(references) == 1:
key = references[0]
counts = collections.defaultdict(int)
totals[(sm_key, lb_key, key)] = counts
totals[(sm_key, lb_key, '*')] = counts
else:
build_new_dicts(totals, sm_key, lb_key, references)
if len(libraries) == 1:
key = list(libraries)[0]
reuse_dicts(totals, sm_key, '*', sm_key, key, references)
else:
build_new_dicts(totals, sm_key, '*', references)
if len(structure) == 1:
key = list(structure)[0]
reuse_dicts(totals, '*', '*', key, '*', references)
else:
build_new_dicts(totals, '*', '*', references)
return totals
def print_table(handle, args, totals):
lengths = collect_references(args, handle)
if args.outfile == "-":
output_handle = sys.stdout
else:
output_handle = open(args.outfile, "w")
with output_handle:
rows = build_table(args.target_name, totals, lengths)
output_handle.write(_HEADER % datetime.datetime.now().isoformat())
output_handle.write("\n")
for line in padded_table(rows):
output_handle.write(line)
output_handle.write("\n")
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 print_table(handle, args, totals):
lengths = collect_references(args, handle)
if args.outfile == "-":
output_handle = sys.stdout
else:
output_handle = open(args.outfile, "w")
with output_handle:
rows = build_table(args.target_name, totals, lengths)
output_handle.write(_HEADER % datetime.datetime.now().isoformat())
output_handle.write("\n")
for line in padded_table(rows):
output_handle.write(line)
output_handle.write("\n")
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
