Пример #1
0
 def _getCoRegSeqs(self):
     # get gene list and related seqs
     geneList = map(lambda l: l.strip('\n'), open(self.mdapArgs[1]).readlines())
     coRegSeqs = MDAP_defs.seqSubSet(geneList,self.mdapArgs[0])
     
     # warn user if there are missing genes
     if coRegSeqs[1]:
         sys.stderr.write('Warning: %s seqs in your gene list were not found in the fasta file provided.\nA list of names follows:\n%s\n'\
                          % (len(coRegSeqs[1]),str(coRegSeqs[1])))
     return coRegSeqs
Пример #2
0
 def _getMaxSize(self):
     """Calculates the number of nucleotides in the set of co-regulated promoter regions."""
     
     # get gene list and related seqs
     geneList = map(lambda l: l.strip('\n'), open(self.mdapArgs[1]).readlines())
     self.coRegSeqs = MDAP_defs.seqSubSet(geneList,self.mdapArgs[0])
     
     # warn user if there are missing genes
     if self.coRegSeqs[1]:
         sys.stderr.write('Warning: %s seqs in your gene list were not found in the fasta file provided.\nA list of names follows:\n%s\n'\
                          % (len(self.coRegSeqs[1]),str(self.coRegSeqs[1])))
     
     # Concatonate, get and set self.maxsize
     return len(''.join(self.coRegSeqs[0].values()))