comparison coords2clnt.py @ 50:0b9aab6aaebf draft

Uploaded 16cfcafe8b42055c5dd64e62c42b82b455027a40

49:303f6402a035

#!/usr/bin/env python

tool_description = """
Given coordinates of the aligned reads, calculate positions of the crosslinked
nucleotides. Crosslinked nts are assumed to be one nt upstream of the 5'-end of
the read.

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

import argparse
import logging
from sys import stdout
from pybedtools import BedTool
from pybedtools.featurefuncs import five_prime
# 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
from sys import stdout
from pybedtools import BedTool
from pybedtools.featurefuncs import five_prime
# 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 = """
Given coordinates of the aligned reads, calculate positions of the crosslinked
nucleotides. Crosslinked nts are assumed to be one nt upstream of the 5'-end of
the read.

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)