Mercurial > repos > yufei-luo > s_mart
view 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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from commons.core.parsing.FindRep import FindRep from xml.sax import make_parser from xml.sax.handler import feature_namespaces import os class MrepsToSet(object): def __init__(self, mrepsInputFileName="", mrepsOuputFileName="", outputFileName=None, errorFilter=0): self._mrepsInputFileName = mrepsInputFileName self._mrepsOuputFileName = mrepsOuputFileName self._outputFileName = outputFileName or "%s.Mreps.set" % mrepsOuputFileName self._errorFilter = errorFilter def run(self): xmlParser = make_parser() xmlParser.setFeature( feature_namespaces, 0 ) xmlParser.setContentHandler( FindRep( self._outputFileName, self._errorFilter, 0 ) ) xmlParser.parse( self._mrepsOuputFileName ) def clean( self ): """ Remove the output file (xml) from Mreps to keep only the 'set' file. """ if os.path.exists(self._mrepsOuputFileName): os.remove(self._mrepsOuputFileName)