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 = ReadGroup()
subtable.Size = int(record["Size"])
set_in(table, key, subtable)
assert int(subtable.Size) == int(record["Size"])
for key in ReadGroup.__slots__:
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 = ReadGroup()
subtable.Size = int(record["Size"])
set_in(table, key, subtable)
assert int(subtable.Size) == int(record["Size"])
for key in ReadGroup.__slots__:
if key != "Size":
subtable[key] += int(record.get(key, 0))
def _read_max_depth(filename, prefix, sample):
if filename in _DEPTHS_CACHE:
return _DEPTHS_CACHE[filename]
max_depth = None
max_depths = {}
try:
with open(filename) as handle:
for row in parse_padded_table(handle):
if row["Name"] != "*" and \
row["Sample"] == "*" and \
row["Library"] == "*" and \
row["Contig"] == "*":
if row["Name"] in max_depths:
raise MakefileError("Depth histogram %r contains "
"multiple 'MaxDepth' records for "
"sample %r; please rebuild!"
% (filename, row["Name"]))
max_depths[row["Name"]] = row["MaxDepth"]
except (OSError, IOError), error:
raise MakefileError("Error reading depth-histogram (%s): %s"
% (filename, error))
def _read_max_depth(filename, prefix, sample):
if filename in _DEPTHS_CACHE:
return _DEPTHS_CACHE[filename]
max_depth = None
max_depths = {}
try:
with open(filename) as handle:
for row in parse_padded_table(handle):
if row["Name"] != "*" and \
row["Sample"] == "*" and \
row["Library"] == "*" and \
row["Contig"] == "*":
if row["Name"] in max_depths:
raise MakefileError("Depth histogram %r contains "
"multiple 'MaxDepth' records for "
"sample %r; please rebuild!"
% (filename, row["Name"]))
max_depths[row["Name"]] = row["MaxDepth"]
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))
def _read_max_depth(filename, prefix, sample):
if filename in _DEPTHS_CACHE:
return _DEPTHS_CACHE[filename]
max_depth = None
max_depths = {}
try:
with open(filename) as handle:
for row in parse_padded_table(handle):
if (row["Name"] != "*" and row["Sample"] == "*"
and row["Library"] == "*" and row["Contig"] == "*"):
if row["Name"] in max_depths:
raise MakefileError("Depth histogram %r contains "
"multiple 'MaxDepth' records for "
"sample %r; please rebuild!" %
(filename, row["Name"]))
max_depths[row["Name"]] = row["MaxDepth"]
except (OSError, IOError) as error:
raise MakefileError("Error reading depth-histogram (%s): %s" %
(filename, error))
log = logging.getLogger(__name__)
if sample in max_depths:
max_depth = max_depths[sample]
else:
name_counts = {}
name_mapping = {}
for cand_sample in max_depths:
name = cand_sample.split(".", 1)[0]
name_mapping[name] = cand_sample
name_counts[name] = name_counts.get(name, 0) + 1
if name_mapping.get(sample) == 1:
# Sample name (with some extensions) found
# This is typical if 'paleomix depths' has been run manually.
max_depth = max_depths[name_mapping[sample]]
elif len(max_depths) == 1:
# Just one sampel in the depth histogram; even though it does not
# match, we assuem that this is the correct table. This is because
# manually generating files / renaming files would otherwise cause
# failure when using 'MaxDepth: auto'.
((cand_sample, max_depth), ) = max_depths.items()
log.warning(
"Name in depths file not as expected; found %r, not %r:",
cand_sample,
sample,
)
if max_depth is None:
raise MakefileError(
"MaxDepth for %r not found in depth-histogram: %r" %
(sample, filename))
elif max_depth == "NA":
raise MakefileError("MaxDepth is not calculated for sample %r; "
"cannot determine MaxDepth values automatically." %
(filename, ))
elif not max_depth.isdigit():
raise MakefileError("MaxDepth is not a valid for sample %r in %r; "
"expected integer, found %r." %
(sample, filename, max_depth))
max_depth = int(max_depth)
log.info("%s.%s = %i", sample, prefix, max_depth)
_DEPTHS_CACHE[filename] = max_depth
return max_depth