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()
