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
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()))