comparison extract_bcs.py @ 50:0b9aab6aaebf draft

Uploaded 16cfcafe8b42055c5dd64e62c42b82b455027a40

49:303f6402a035

#!/usr/bin/env python

tool_description = """
Exract barcodes from a FASTQ file according to a user-specified pattern.

By default output is written to stdout.

Copyright: 2015
License: Apache
Email: [e-mail]
Status: Testing
"""

import argparse
import logging
import re
from sys import stdout
from Bio.SeqIO.QualityIO import FastqGeneralIterator

# avoid ugly python IOError when stdout output is piped into another program
# and then truncated (such as piping to head)
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE, SIG_DFL)

# parse command line arguments
parser = argparse.ArgumentParser(description=tool_description,
                                 epilog=epilog,
                                 formatter_class=argparse.RawDescriptionHelpFormatter)

50:0b9aab6aaebf

#!/usr/bin/env python

import argparse
import logging
import re
from sys import stdout
from Bio.SeqIO.QualityIO import FastqGeneralIterator
# avoid ugly python IOError when stdout output is piped into another program
# and then truncated (such as piping to head)
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE, SIG_DFL)

tool_description = """
Exract barcodes from a FASTQ file according to a user-specified pattern.

By default output is written to stdout.

Copyright: 2015
License: Apache
Email: [e-mail]
Status: Testing
"""

# parse command line arguments
parser = argparse.ArgumentParser(description=tool_description,
                                 epilog=epilog,
                                 formatter_class=argparse.RawDescriptionHelpFormatter)