comparison extract_aln_ends.py @ 50:0b9aab6aaebf draft

Uploaded 16cfcafe8b42055c5dd64e62c42b82b455027a40

49:303f6402a035

#!/usr/bin/env python

tool_description = """
Extract alignment ends from sam file.

The resulting bed file contains the outer coordinates of the alignments. The

License: Apache
Email: [e-mail]
Status: Development
"""

import argparse
import logging
from sys import stdout
from shutil import rmtree
from tempfile import mkdtemp
from pybedtools import BedTool
import pysam


class DefaultsRawDescriptionHelpFormatter(argparse.ArgumentDefaultsHelpFormatter,
                                          argparse.RawDescriptionHelpFormatter):
    # To join the behaviour of RawDescriptionHelpFormatter with that of ArgumentDefaultsHelpFormatter
    pass

# 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=DefaultsRawDescriptionHelpFormatter)

50:0b9aab6aaebf

#!/usr/bin/env python

import argparse
import logging
from sys import stdout
from shutil import rmtree
from tempfile import mkdtemp
from pybedtools import BedTool
import pysam
# 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 = """
Extract alignment ends from sam file.

The resulting bed file contains the outer coordinates of the alignments. The

License: Apache
Email: [e-mail]
Status: Development
"""


class DefaultsRawDescriptionHelpFormatter(argparse.ArgumentDefaultsHelpFormatter,
                                          argparse.RawDescriptionHelpFormatter):
    # To join the behaviour of RawDescriptionHelpFormatter with that of ArgumentDefaultsHelpFormatter
    pass

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