Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/MrepsToSet.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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1 from commons.core.parsing.FindRep import FindRep | |
2 from xml.sax import make_parser | |
3 from xml.sax.handler import feature_namespaces | |
4 import os | |
5 | |
6 | |
7 class MrepsToSet(object): | |
8 | |
9 def __init__(self, mrepsInputFileName="", mrepsOuputFileName="", outputFileName=None, errorFilter=0): | |
10 self._mrepsInputFileName = mrepsInputFileName | |
11 self._mrepsOuputFileName = mrepsOuputFileName | |
12 self._outputFileName = outputFileName or "%s.Mreps.set" % mrepsOuputFileName | |
13 self._errorFilter = errorFilter | |
14 | |
15 def run(self): | |
16 xmlParser = make_parser() | |
17 xmlParser.setFeature( feature_namespaces, 0 ) | |
18 xmlParser.setContentHandler( FindRep( self._outputFileName, self._errorFilter, 0 ) ) | |
19 xmlParser.parse( self._mrepsOuputFileName ) | |
20 | |
21 def clean( self ): | |
22 """ | |
23 Remove the output file (xml) from Mreps to keep only the 'set' file. | |
24 """ | |
25 if os.path.exists(self._mrepsOuputFileName): | |
26 os.remove(self._mrepsOuputFileName) | |
27 | |
28 | |
29 | |
30 | |
31 |