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#!/usr/bin/env python
#Author: Duy Tin Truong (duytin.truong@unitn.it)
# at CIBIO, University of Trento, Italy
import sys
import argparse as ap
import bz2
import gzip
import tarfile
#import logging.config
#sys.path.append('../pyphlan')
#sys.path.append('pyphlan')
import ooSubprocess
#logging.config.fileConfig('logging.ini', disable_existing_loggers=False)
#logger = logging.getLogger(__name__)
def read_params():
p = ap.ArgumentParser()
p.add_argument('--input_file', required=True, default=None, type=str)
return vars(p.parse_args())
def dump_file(ifn):
file_ext = ''
if ifn.endswith('.tar.bz2'):
ifile = tarfile.open(ifn, 'r:bz2')
file_ext = '.tar.bz2'
elif ifn.endswith('.tar.gz'):
ifile = tarfile.open(ifn, 'r:gz')
file_ext = '.tar.gz'
elif ifn.endswith('.bz2'):
ifile = bz2.BZ2File(ifn, 'r')
file_ext = '.bz2'
elif ifn.endswith('.gz'):
ifile = gzip.GzipFile(ifn, 'r')
file_ext = '.gz'
elif ifn.endswith('.fastq'):
ifile = open(ifn, 'r')
file_ext = '.fastq'
elif ifn.endswith('.sam'):
ifile = open(ifn, 'r')
file_ext = '.sam'
elif ifn.endswith('.sra'):
oosp = ooSubprocess.ooSubprocess()
ifile = oosp.ex(
'fastq-dump',
args=[
'-Z', ifn,
'--split-spot'],
get_out_pipe=True)
file_ext = '.sra'
else:
raise Exception('Unrecognized format! The format should be .bz2, .gz'\
'.tar.bz2, .tar.gz, .sra, .sam.bz2, .sam, or .fastq\n')
try:
if file_ext in ['.tar.bz2', '.tar.gz']:
for tar_info in ifile:
ifile2 = ifile.extractfile(tar_info)
if ifile2 != None:
for line in ifile2:
sys.stdout.write(line)
else:
for line in ifile:
sys.stdout.write(line)
except:
sys.stderr.write('Error while dumping file %s\n'%ifn)
raise
if __name__ == "__main__":
args = read_params()
dump_file(args['input_file'])
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