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comparison coords2clnt.py @ 50:0b9aab6aaebf draft

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Uploaded 16cfcafe8b42055c5dd64e62c42b82b455027a40
author rnateam
date Tue, 26 Jan 2016 04:38:27 -0500
parents de4ea3aa1090
children
comparison
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49:303f6402a035 50:0b9aab6aaebf
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2
3 import argparse
4 import logging
5 from sys import stdout
6 from pybedtools import BedTool
7 from pybedtools.featurefuncs import five_prime
8 # avoid ugly python IOError when stdout output is piped into another program
9 # and then truncated (such as piping to head)
10 from signal import signal, SIGPIPE, SIG_DFL
11 signal(SIGPIPE, SIG_DFL)
2 12
3 tool_description = """ 13 tool_description = """
4 Given coordinates of the aligned reads, calculate positions of the crosslinked 14 Given coordinates of the aligned reads, calculate positions of the crosslinked
5 nucleotides. Crosslinked nts are assumed to be one nt upstream of the 5'-end of 15 nucleotides. Crosslinked nts are assumed to be one nt upstream of the 5'-end of
6 the read. 16 the read.
22 Copyright: 2015 32 Copyright: 2015
23 License: Apache 33 License: Apache
24 Email: maticzkd@informatik.uni-freiburg.de 34 Email: maticzkd@informatik.uni-freiburg.de
25 Status: Testing 35 Status: Testing
26 """ 36 """
27
28 import argparse
29 import logging
30 from sys import stdout
31 from pybedtools import BedTool
32 from pybedtools.featurefuncs import five_prime
33 # avoid ugly python IOError when stdout output is piped into another program
34 # and then truncated (such as piping to head)
35 from signal import signal, SIGPIPE, SIG_DFL
36 signal(SIGPIPE, SIG_DFL)
37 37
38 # parse command line arguments 38 # parse command line arguments
39 parser = argparse.ArgumentParser(description=tool_description, 39 parser = argparse.ArgumentParser(description=tool_description,
40 epilog=epilog, 40 epilog=epilog,
41 formatter_class=argparse.RawDescriptionHelpFormatter) 41 formatter_class=argparse.RawDescriptionHelpFormatter)