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()))
