def main(): try: pairs_file = sys.argv[1] except IndexError: print "Usage: python bin/masterControl.py /path/to/pairs_file" print "Defaulting to VapBC" pairs_file = 'bin/data/vapBC.gi' gs = getSequences.getSequences(pairs_file) gs.getAllSequences() al = gs.getAssociationList() excludeSeqs(al)
def main(): try: pairs_file = sys.argv[1] except IndexError: print "Usage: python bin/masterControl.py /path/to/pairs_file" print "Defaulting to VapBC" pairs_file = 'bin/data/vapBC.gi' reportProgress(0) gs = getSequences.getSequences(pairs_file) gs.getAllSequences() al = gs.getAssociationList() partnerAs = gs.getAList() partnerBs = gs.getBList() excludeList = assessSequences.excludeSeqs(al) excludeA = [] excludeB = [] for ex in excludeList: excludeA.append(ex[0]) excludeB.append(ex[1]) reportProgress(1) alignA = Alignment.Align(partnerAs) alignA.makeInfile('partner1ed.fa', excludeA) alignB = Alignment.Align(partnerBs) alignB.makeInfile('partner2ed.fa', excludeB) reportProgress(2) threads = [] thread1 = Alignment.AlignmentThread('partner1ed.fa', 'partner1ed.aln') thread2 = Alignment.AlignmentThread('partner2ed.fa', 'partner2ed.aln') threads.append(thread1) threads.append(thread2) for thread in threads: thread.start() for thread in threads: thread.join() reportProgress(3) catAlign = Alignment.ConcatenateAlignment('partner1ed.aln', 'partner2ed.aln', al) catAlign.padAlignment() catted = catAlign.concatenate() catAlign.writeResult('catteded.aln') reportProgress(4) formAlign = Alignment.FormatAlignment('catteded.aln', 'f_catteded.aln') formAlign.editBlankColumns() formAlign.format() reportProgress(5) sca = StatisticalCouplingAnalysis.StatisticalCouplingAnalysis('f_catteded.aln') sca.doSCA('edvapbc.sca') reportProgress(6) sca.editSCAOut('edvapbc.sca') reportProgress(7) sca.plotSCA()