Mercurial > repos > drosofff > msp_sr_signature
comparison signature.py @ 1:6218b518cd16 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
author | drosofff |
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date | Wed, 07 Jun 2017 17:53:44 -0400 |
parents | a2f293717ce3 |
children |
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0:a2f293717ce3 | 1:6218b518cd16 |
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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( |