Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/VarscanFile.py @ 36:44d5973c188c
Uploaded
author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/VarscanFile.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,145 @@ +# Copyright INRA (Institut National de la Recherche Agronomique) +# http://www.inra.fr +# http://urgi.versailles.inra.fr +# +# This software is governed by the CeCILL license under French law and +# abiding by the rules of distribution of free software. You can use, +# modify and/ or redistribute the software under the terms of the CeCILL +# license as circulated by CEA, CNRS and INRIA at the following URL +# "http://www.cecill.info". +# +# As a counterpart to the access to the source code and rights to copy, +# modify and redistribute granted by the license, users are provided only +# with a limited warranty and the software's author, the holder of the +# economic rights, and the successive licensors have only limited +# liability. +# +# In this respect, the user's attention is drawn to the risks associated +# with loading, using, modifying and/or developing or reproducing the +# software by the user in light of its specific status of free software, +# that may mean that it is complicated to manipulate, and that also +# therefore means that it is reserved for developers and experienced +# professionals having in-depth computer knowledge. Users are therefore +# encouraged to load and test the software's suitability as regards their +# requirements in conditions enabling the security of their systems and/or +# data to be ensured and, more generally, to use and operate it in the +# same conditions as regards security. +# +# The fact that you are presently reading this means that you have had +# knowledge of the CeCILL license and that you accept its terms. + + +from commons.core.parsing.VarscanHit import VarscanHit +from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag +from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8 +from commons.core.checker.CheckerException import CheckerException +from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag + +class VarscanFile(object): + + def __init__(self, varscanFileName = ""): + self._varscanFileName = varscanFileName + self._varscanFieldSeparator = "\t" + self._lVarscanHits = [] + self._typeOfVarscanFile = "" + + def __eq__(self, o): + return self._varscanFieldSeparator == o._varscanFieldSeparator and self._lVarscanHits == o._lVarscanHits and self._varscanFileName == o._varscanFileName + + def setVarscanHitsList(self, lVarscanHits): + self._lVarscanHits = lVarscanHits + + def setHeaderVarcanFile(self, headerVarcanFile): + self._headerVarcanFile = headerVarcanFile + + def setTypeOfVarscanFile(self, type): + if type == "Varscan_2_2" or type == "Varscan_2_2_WithTag" or type == "Varscan_2_2_8" or type == "Varscan_2_2_8_WithTag": + self._typeOfVarscanFile = type + else: + self._typeOfVarscanFile = "" + + def getVarscanHitsList(self): + return self._lVarscanHits + + def getHeaderVarcanFile(self): + return self._headerVarcanFile + + def getListOfVarscanHits(self): + return self._lVarscanHits + + def getTypeOfVarscanFile(self): + return self._typeOfVarscanFile + + def parse(self): + varscanFile = open(self._varscanFileName, "r") + currentLineNumber = 0 + line = varscanFile.readline() + if "Chrom\tPosition" in line: + self.setHeaderVarcanFile(line) + line = varscanFile.readline() + while line != "": + if not "Chrom\tPosition" in line: + currentLineNumber += 1 + line = line.strip() + lResults = line.split(self._varscanFieldSeparator) + if len(lResults) == 12: + currentVarscanLine = self.createVarscanHit(line, currentLineNumber) + self._typeOfVarscanFile = "Varscan_2_2" + elif len(lResults) == 13: + currentVarscanLine = self.createVarscanHitWithTag(line, currentLineNumber) + self._typeOfVarscanFile = "Varscan_2_2_WithTag" + elif len(lResults) == 19: + currentVarscanLine = self.createVarscanHit_v2_2_8(line, currentLineNumber) + self._typeOfVarscanFile = "Varscan_2_2_8" + elif len(lResults) == 20: + currentVarscanLine = self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber) + self._typeOfVarscanFile = "Varscan_2_2_8_WithTag" + else: + raise CheckerException ("Warning: this line (l.%s) is not a valid varscan line !" % currentLineNumber) + self._lVarscanHits.append(currentVarscanLine) + line = varscanFile.readline() + varscanFile.close() + + def createVarscanObjectFromLine(self, line, currentLineNumber): + if self._typeOfVarscanFile == "Varscan_2_2": + VarscanHit = self.createVarscanHit(line, currentLineNumber) + return VarscanHit + elif self._typeOfVarscanFile == "Varscan_2_2_WithTag": + return self.createVarscanHitWithTag(line, currentLineNumber) + elif self._typeOfVarscanFile == "Varscan_2_2_8": + return self.createVarscanHit_v2_2_8(line, currentLineNumber) + elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag": + return self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber) + + def createVarscanHit(self, line, currentLineNumber): + iVarscanHit = VarscanHit() + iVarscanHit.setAttributesFromString(line, currentLineNumber) + return iVarscanHit + + def createVarscanHitWithTag(self, line, currentLineNumber): + iVarscanHitWithTag = VarscanHit_WithTag() + iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber) + return iVarscanHitWithTag + + def createVarscanHit_v2_2_8(self, line, currentLineNumber): + iVarscanHit = VarscanHit_v2_2_8() + iVarscanHit.setAttributesFromString(line, currentLineNumber) + return iVarscanHit + + def createVarscanHit_v2_2_8_WithTag(self, line, currentLineNumber): + iVarscanHitWithTag = VarscanHit_v2_2_8_WithTag() + iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber) + return iVarscanHitWithTag + + def selectTypeOfVarscanHitObject(self): + if self._typeOfVarscanFile == "": + raise CheckerException ("Error: no varscan object found !") + elif self._typeOfVarscanFile == "Varscan_2_2": + return VarscanHit() + elif self._typeOfVarscanFile == "Varscan_2_2_WithTag": + return VarscanHit_WithTag() + elif self._typeOfVarscanFile == "Varscan_2_2_8": + return VarscanHit_v2_2_8() + elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag": + return VarscanHit_v2_2_8_WithTag() + \ No newline at end of file