#######################################################################
# Main program
#######################################################################
if __name__ == "__main__":
# Create command line parser
p = optparse.OptionParser(usage="%prog OPTIONS R1.fastq R2.fastq",
version="%prog "+__version__,
description="Check that read headers for R1 and R2 fastq files "
"are in agreement, and that the files form an R1/2 pair.")
# Parse command line
options,args = p.parse_args()
# Get data directory name
if len(args) != 2:
p.error("expected two arguments (R1 and R2 fastq files to compare)")
fastq_file_r1 = args[0]
fastq_file_r2 = args[1]
# Process the data
if FASTQFile.fastqs_are_pair(fastq_file_r1,fastq_file_r2):
sys.exit(0)
else:
logging.error("Not R1/R2 pair")
sys.exit(1)
SHARE_DIR = os.path.abspath(
os.path.normpath(os.path.join(os.path.dirname(sys.argv[0]), '..')))
sys.path.append(SHARE_DIR)
import bcftbx.FASTQFile as FASTQFile
#######################################################################
# Main program
#######################################################################
if __name__ == "__main__":
# Create command line parser
p = optparse.OptionParser(
usage="%prog OPTIONS R1.fastq R2.fastq",
version="%prog " + __version__,
description="Check that read headers for R1 and R2 fastq files "
"are in agreement, and that the files form an R1/2 pair.")
# Parse command line
options, args = p.parse_args()
# Get data directory name
if len(args) != 2:
p.error("expected two arguments (R1 and R2 fastq files to compare)")
fastq_file_r1 = args[0]
fastq_file_r2 = args[1]
# Process the data
if FASTQFile.fastqs_are_pair(fastq_file_r1, fastq_file_r2):
sys.exit(0)
else:
logging.error("Not R1/R2 pair")
sys.exit(1)
#######################################################################
# Main program
#######################################################################
if __name__ == "__main__":
# Create command line parser
p = argparse.ArgumentParser(
version="%(prog)s "+__version__,
description="Check that read headers for R1 and R2 fastq files "
"are in agreement, and that the files form an R1/2 pair.")
p.add_argument('fastq_file_r1',metavar="R1.fastq",
help="Fastq file with R1 reads")
p.add_argument('fastq_file_r2',metavar="R2.fastq",
help="Fastq file with R2 reads to check against "
"R1 reads")
# Parse command line
args = p.parse_args()
# Process the data
if FASTQFile.fastqs_are_pair(args.fastq_file_r1,args.fastq_file_r2):
sys.exit(0)
else:
logging.error("Not R1/R2 pair")
sys.exit(1)