def get_attr_list(
inputfile=None,
outputfile=None,
separator="\n"):
"""
Get the list of attributes from a GTF file.
"""
gtf = GTF(inputfile, check_ensembl_format=False)
attr_list = gtf.get_attr_list()
n = 0
for i in attr_list:
if n != len(attr_list) - 1:
outputfile.write(i + separator)
else:
outputfile.write(i)
n += 1
gc.disable()
close_properly(outputfile, inputfile)
def count_key_values(inputfile=None,
outputfile=None,
keys="gene_id,transcript_id",
uniq=True,
additional_text=None):
"""
Count the number values for a set of keys.
"""
gtf = GTF(inputfile, check_ensembl_format=False)
if uniq:
val_list = defaultdict(set)
else:
val_list = defaultdict(list)
if keys == "*":
key_list = gtf.get_attr_list()
keys = ",".join(key_list)
else:
key_list = keys.split(",")
for i in gtf.extract_data(keys, as_list_of_list=True):
for k, v in zip(key_list, i):
if v in ['.', '?']:
continue
if uniq:
val_list[k].add(v)
else:
val_list[k] += [v]
for i in key_list:
if additional_text is None:
outputfile.write(i + "\t" + str(len(val_list[i])) + "\n")
else:
outputfile.write(i + "\t" + str(len(val_list[i])) + "\t" +
additional_text + "\n")
gc.disable()
close_properly(outputfile, inputfile)
def get_attr_value_list(inputfile=None,
outputfile=None,
key_name="gene_id",
print_key_name=False,
separator="\n",
count=False):
"""
Get the list of values observed for an attributes.
"""
gtf = GTF(inputfile, check_ensembl_format=False)
if key_name == '*':
key_name = ",".join(gtf.get_attr_list(add_basic=True))
if not count:
for akey in key_name.split(","):
for i in gtf.get_attr_value_list(akey):
if print_key_name:
outputfile.write(akey + separator + i + "\n")
else:
outputfile.write(i + "\n")
gc.disable()
close_properly(outputfile, inputfile)
else:
if separator == "\n":
separator = "\t"
for akey in key_name.split(","):
for i in gtf.get_attr_value_list(akey, count=True):
if print_key_name:
outputfile.write(akey + separator + i[0] + separator +
i[1] + "\n")
else:
outputfile.write(i[0] + separator + i[1] + "\n")
gc.disable()
close_properly(outputfile, inputfile)
def tabulate(inputfile=None,
outputfile=None,
key=None,
no_unset=False,
unique=False,
no_basic=False,
accept_undef=False,
select_gene_ids=False,
select_gene_names=False,
select_transcript_ids=False,
select_exon_ids=False,
separator="\t",
no_header=False):
"""Convert a GTF to tabulated format.
"""
# ----------------------------------------------------------------------
# Check mode
# ----------------------------------------------------------------------
if select_transcript_ids:
key = "transcript_id"
elif select_gene_ids:
key = "gene_id"
elif select_gene_names:
key = "gene_id"
elif select_exon_ids:
key = "exon_id"
no_undef = False
if not accept_undef:
no_undef = True
# ----------------------------------------------------------------------
# REad GTF and process
# ----------------------------------------------------------------------
gtf = GTF(inputfile, check_ensembl_format=False)
if key in ["all", "*"]:
if no_basic:
attr_list = gtf.get_attr_list(add_basic=False)
else:
attr_list = gtf.get_attr_list(add_basic=True)
tab = gtf.extract_data(attr_list)
else:
tab = gtf.extract_data(key)
if not no_header:
message("Writing header")
write_properly(separator.join(tab.colnames),
outputfile)
message("Writing")
try:
if not unique:
if no_unset:
if no_undef:
for i in tab:
if any([True for x in i.fields if x in [".", "?"]]):
continue
i.write(outputfile, separator)
else:
for i in tab:
if any([True for x in i.fields if x in ["."]]):
continue
i.write(outputfile, separator)
else:
if no_undef:
for i in tab:
if any([True for x in i.fields if x in ["?"]]):
continue
i.write(outputfile, separator)
else:
for i in tab:
i.write(outputfile, separator)
else:
printed = {}
if no_unset:
if no_undef:
for i in tab:
t = tuple(i)
if t not in printed:
if any([True for x in i.fields if x in [".", "?"]]):
continue
i.write(outputfile, separator)
printed[t] = 1
else:
for i in tab:
t = tuple(i)
if t not in printed:
if any([True for x in i.fields if x in ["."]]):
continue
i.write(outputfile, separator)
printed[t] = 1
else:
if no_undef:
for i in tab:
t = tuple(i)
if t not in printed:
if any([True for x in i.fields if x in ["?"]]):
continue
i.write(outputfile, separator)
printed[t] = 1
else:
for i in tab:
t = tuple(i)
if t not in printed:
i.write(outputfile, separator)
printed[t] = 1
except (BrokenPipeError, IOError):
def _void_f(*args, **kwargs):
pass
message("Received a boken pipe signal", type="WARNING")
sys.stdout.write = _void_f
sys.stdout.flush = _void_f
gc.disable()
close_properly(outputfile, inputfile)