Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/SsrParser.py @ 11:2da30502c2f1
Updated CompareOverlappingSmallQuery.xml
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:37:08 -0400 |
parents | 769e306b7933 |
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# 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 = ''