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raise GTFtkError("Input_file should contain two columns.")
if not token[0].isdigit():
raise GTFtkError("Column 1 of intput file should be an int.")
new_data = self._dll.add_attr_to_pos(self._data,
native_str(input_file.name),
native_str(new_key))
return self._clone(new_data)
if __name__ == "__main__":
from pygtftk.utils import get_example_file
a = get_example_file()
gtf = GTF(a[0])
for i in gtf["feature", "transcript"]:
i.write(sys.stdout)
"data",
dataset)
file_dataset = os.listdir(path_dataset)
for i in file_dataset:
print("\t" + i)
else:
if format == "gtf":
example_file = get_example_file(datasetname=dataset,
ext=format)
if example_file:
example_file = example_file[0]
else:
example_file = get_example_file(datasetname=dataset,
ext=format + ".gz")
if example_file:
example_file = example_file[0]
else:
message("No GTF file found for this dataset.",
type="ERROR")
GTF(example_file, check_ensembl_format=False).write(outputfile, gc_off=True)
elif format in ["fa", "join", "join_mat", "genome", "chromInfo", "genes", "geneList"]:
try:
infile = open(get_example_file(datasetname=dataset,
ext=format)[0], "r")
except:
message("Unable to find example file.", type="ERROR")
for line in infile:
for i in dataset_list:
print("\t- " + os.path.basename(i))
elif list:
path_dataset = os.path.join(pygtftk.__path__[0],
"data",
dataset)
file_dataset = os.listdir(path_dataset)
for i in file_dataset:
print("\t" + i)
else:
if format == "gtf":
example_file = get_example_file(datasetname=dataset,
ext=format)
if example_file:
example_file = example_file[0]
else:
example_file = get_example_file(datasetname=dataset,
ext=format + ".gz")
if example_file:
example_file = example_file[0]
else:
message("No GTF file found for this dataset.",
type="ERROR")
GTF(example_file, check_ensembl_format=False).write(outputfile, gc_off=True)
elif format in ["fa", "join", "join_mat", "genome", "chromInfo", "genes", "geneList"]:
try:
if example_file:
example_file = example_file[0]
else:
example_file = get_example_file(datasetname=dataset,
ext=format + ".gz")
if example_file:
example_file = example_file[0]
else:
message("No GTF file found for this dataset.",
type="ERROR")
GTF(example_file, check_ensembl_format=False).write(outputfile, gc_off=True)
elif format in ["fa", "join", "join_mat", "genome", "chromInfo", "genes", "geneList"]:
try:
infile = open(get_example_file(datasetname=dataset,
ext=format)[0], "r")
except:
message("Unable to find example file.", type="ERROR")
for line in infile:
outputfile.write(line)
elif format == "*":
file_path = glob.glob(os.path.join(pygtftk.__path__[0],
'data',
dataset,
"*"))
file_path = [x for x in file_path if "__" not in x]
target_path = os.path.join(pygtftk.__path__[0], 'data', dataset)
if not quiet: