Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/SsrParser.py @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/SsrParser.py Thu May 02 09:56:47 2013 -0400 @@ -0,0 +1,170 @@ +# 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. + +import sys + +## this class can parse a Ssr results output file. SSR.pl is developped by S.Cartinhour. (5/2000) +# +class SsrParser(object): + + + def __init__(self, BES_name='', BES_redundancy='', SSR_nbNucleotides='', SSR_Motif='', SSR_Motif_number='', SSR_start='', SSR_end='', BES_size=''): + self._BesName = BES_name + self._BesRedundancy = BES_redundancy + self._SsrNbNucleotides = SSR_nbNucleotides + self._SsrMotif = SSR_Motif + self._SsrMotifNumber = SSR_Motif_number + self._SsrStart = SSR_start + self._SsrEnd = SSR_end + self._BesSize = BES_size + + def __eq__(self, o): + return self._BesName == o._BesName and self._BesRedundancy == o._BesRedundancy and self._SsrNbNucleotides == o._SsrNbNucleotides and self._SsrMotif == o._SsrMotif and self._SsrMotifNumber == o._SsrMotifNumber and self._SsrStart == o._SsrStart and self._SsrEnd == o._SsrEnd and self._BesSize == o._BesSize + + def setBesName(self, BES_Name): + self._BesName = BES_Name + + def setBesRedundancy(self, BES_redundancy): + self._BesRedundancy = BES_redundancy + + def setSsrNbNucleotides(self, SSR_nbNucleotides): + self._SsrNbNucleotides = SSR_nbNucleotides + + def setSsrMotif(self, SSR_Motif): + self._SsrMotif = SSR_Motif + + def setSsrMotifNumber(self, SSR_Motif_number): + self._SsrMotifNumber = SSR_Motif_number + + def setSsrStart(self, SSR_start): + self._SsrStart = SSR_start + + def setSsrEnd(self, SSR_end): + self._SsrEnd = SSR_end + + def setBesSize(self, BES_size): + self._BesSize = BES_size + + def getBesName(self): + return self._BesName + + def getBesRedundancy(self): + return self._BesRedundancy + + def getSsrNbNucleotides(self): + return self._SsrNbNucleotides + + def getSsrMotif(self): + return self._SsrMotif + + def getSsrMotifNumber(self): + return self._SsrMotifNumber + + def getSsrStart(self): + return self._SsrStart + + def getSsrEnd(self): + return self._SsrEnd + + def getBesSize(self): + return self._BesSize + + def setAttributes(self, lResults, iCurrentLineNumber): + error = False + + if lResults[0] != '': + self.setBesName(lResults[0]) + else: + sys.stderr.write("WARNING: The field BES Name is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if lResults[1] != '': + self.setBesRedundancy(lResults[1]) + else: + sys.stderr.write("WARNING: The field BES Redundancy is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if lResults[2] != '': + self.setSsrNbNucleotides(lResults[2]) + else: + sys.stderr.write("WARNING: The field SSR Number Nucleotides is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if lResults[3] != '': + self.setSsrMotif(lResults[3]) + else: + sys.stderr.write("WARNING: The field SSR Motif is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if lResults[4] != '': + self.setSsrMotifNumber(lResults[4]) + else: + sys.stderr.write("WARNING: The field SSR Motif Number is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if lResults[5] != '': + self.setSsrStart(lResults[5]) + else: + sys.stderr.write("WARNING: The field SSR Start is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if lResults[6] != '': + self.setSsrEnd(lResults[6]) + else: + sys.stderr.write("WARNING: The field SSR End is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if lResults[7] != '': + self.setBesSize(lResults[7]) + else: + sys.stderr.write("WARNING: The field BES Size is empty in SSR results file in line %s\n" % iCurrentLineNumber) + error = True + + if error == True: + self._setAllToNull() + + def setAttributesFromString(self, ssrLine, iCurrentLineNumber ="", fieldSeparator ="\t"): + ssrLine = ssrLine.rstrip() + lSsrLineItem = ssrLine.split(fieldSeparator) + if len(lSsrLineItem) < 8: + sys.stderr.write("WARNING: The line %s is not a valid SSR Result line\n" % iCurrentLineNumber) + else: + self.setAttributes(lSsrLineItem, iCurrentLineNumber) + + def _setAllToNull(self): + self._BesName = '' + self._BesRedundancy = '' + self._SsrNbNucleotides = '' + self._SsrMotif = '' + self._SsrMotifNumber = '' + self._SsrStart = '' + self._SsrEnd = '' + self._BesSize = '' + \ No newline at end of file