Mercurial > repos > drosofff > msp_sr_signature

comparison signature.py @ 11:b1a15b5a3f1b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
author drosofff
date Wed, 07 Jun 2017 17:54:01 -0400
parents 2b30861d95f4
children
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10:d5106e27df0e 11:b1a15b5a3f1b
1 #!/usr/bin/python 1 #!/usr/bin/python
2 # script for computing overlap signatures from a bowtie output 2 # script for computing overlap signatures from a bowtie output
3 # Christophe Antoniewski <drosofff@gmail.com> 3 # Christophe Antoniewski <drosofff@gmail.com>
4 # Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target> 4 # Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target>
5 # <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedure option> <12: graph (global or lattice)> 5 # <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedure option> <12: graph (global or lattice)>
6 # <13: R code> 6 # <13: R code>
7 # version 2.0.0 7 # version 2.0.0
8 8
9 import sys
10 import subprocess 9 import subprocess
11 import argparse 10 import argparse
12 from smRtools import * 11 from smRtools import HandleSmRNAwindows
13 from collections import defaultdict # test whether it is required
14 12
15 13
16 def Parser(): 14 def Parser():
17 the_parser = argparse.ArgumentParser() 15 the_parser = argparse.ArgumentParser()
18 the_parser.add_argument( 16 the_parser.add_argument(