def read_table(table, filename):
with open(filename) as table_file:
for record in parse_padded_table(table_file):
key = (record["Name"], record["Sample"], record["Library"],
record["Contig"])
if "*" in key:
continue
subtable = get_in(table, key, {"Size": int(record["Size"])})
assert int(subtable["Size"]) == int(record["Size"])
for field in ("Hits", "SE", "PE_1", "PE_2", "Collapsed", "M", "I",
"D"):
subtable[field] = subtable.get(field, 0) + int(
record.get(field, 0))
set_in(table, key, subtable)
def _read_max_depths(filename, prefix, sample):
if filename in _DEPTHS_CACHE:
return _DEPTHS_CACHE[filename]
max_depth = None
try:
with open(filename) as handle:
for row in parse_padded_table(handle):
if row["Name"] == sample and row["Sample"] == "*" and row["Library"] == "*" and row["Contig"] == "*":
max_depth = row["MaxDepth"]
break
else:
raise MakefileError("Could not find MaxDepth in " "depth-histogram: %r" % (filename,))
except (OSError, IOError), error:
raise MakefileError("Error reading depth-histogram (%s): %s" % (filename, error))
def read_table(table, filename):
with open(filename) as table_file:
for record in parse_padded_table(table_file):
key = (record["Name"], record["Sample"], record["Library"], record["Contig"])
if "*" in key:
continue
subtable = get_in(table, key)
if subtable is None:
subtable = dict(READGROUP_TEMPLATE)
subtable["Size"] = int(record["Size"])
set_in(table, key, subtable)
assert int(subtable["Size"]) == int(record["Size"])
for key in READGROUP_TEMPLATE:
if key != "Size":
subtable[key] += int(record.get(key, 0))
def read_table(table, filename):
with open(filename) as table_file:
for record in parse_padded_table(table_file):
key = (record["Name"], record["Sample"], record["Library"],
record["Contig"])
if "*" in key:
continue
subtable = get_in(table, key)
if subtable is None:
subtable = dict(READGROUP_TEMPLATE)
subtable["Size"] = int(record["Size"])
set_in(table, key, subtable)
assert int(subtable["Size"]) == int(record["Size"])
for key in READGROUP_TEMPLATE:
if key != "Size":
subtable[key] += int(record.get(key, 0))
def _read_max_depths(filename, prefix, sample):
if filename in _DEPTHS_CACHE:
return _DEPTHS_CACHE[filename]
max_depth = None
try:
with open(filename) as handle:
for row in parse_padded_table(handle):
if row["Name"] == sample and \
row["Sample"] == "*" and \
row["Library"] == "*" and \
row["Contig"] == "*":
max_depth = row["MaxDepth"]
break
else:
raise MakefileError("Could not find MaxDepth in "
"depth-histogram: %r" % (filename, ))
except (OSError, IOError), error:
raise MakefileError("Error reading depth-histogram (%s): %s" %
(filename, error))
def _parse_padded_table(*args, **kwargs):
return list(parse_padded_table(*args, **kwargs))
def _parse_padded_table(*args, **kwargs):
return list(parse_padded_table(*args, **kwargs))
