def main():
print >>sys.stderr, "Print the result to screen"
if len(sys.argv) != 5:
print >>sys.stderr, 'Using python %s msapath/ hitpath/ \
identity[70] evalue[0.01]' % sys.argv[0]
sys.exit(0)
#------------------------------------------
msapath = sys.argv[1]
hitpath = sys.argv[2]
identity = float(sys.argv[3])
evalue = flaot(sys.argv[4])
psiD = readMsaPsiBatch(hitpath, identity, evalue)
def main():
print >> sys.stderr, "Print the result to file"
if len(sys.argv) < 8:
print >> sys.stderr, 'Using python %s psipath/ psiresult \
subjectlocus subjectSeq msaPath/ identity[70] evalue[10] \
deleteOverlap[0-nodelete, 1-delete(default)]{The last parameter is \
optional}' % sys.argv[0]
sys.exit(0)
#-------------------------------------------------------------
psipath = sys.argv[1]
psiresult = sys.argv[2]
subjL = sys.argv[3]
subjS = sys.argv[4]
msaPath = sys.argv[5]
identity = float(sys.argv[6])
evalue = float(sys.argv[7])
if len(sys.argv) == 9:
delete = int(sys.argv[8])
else:
delete = 1
psiD = readMsaPsiBatch(psipath, identity, evalue)
#output(psiD)
#------------------------------------------------
#pathced 20111006, add judgement of existing files
nolocus = 1
if os.path.isfile(subjL) and os.path.isfile(subjS):
nolocus = 0
nolocus = int(
raw_input("Do you want to recreate hitted locus\
file and seq file? Default no[0], 1 means yes. \n>>>"))
if nolocus:
getLocus(psiD, subjL)
getSeq(subjL, subjS)
#-----------------------------------------
#print subjS
subjSDict = readSubjS(subjS)
#print subjSDict
#sys.exit(1)
msaDict = readMsa(msaPath)
#print subjSDict
final(psiD, subjSDict, msaDict, psiresult, delete)
def main():
print >>sys.stderr, "Print the result to file"
if len(sys.argv) < 8:
print >>sys.stderr, 'Using python %s psipath/ psiresult \
subjectlocus subjectSeq msaPath/ identity[70] evalue[10] \
deleteOverlap[0-nodelete, 1-delete(default)]{The last parameter is \
optional}' % sys.argv[0]
sys.exit(0)
#-------------------------------------------------------------
psipath = sys.argv[1]
psiresult = sys.argv[2]
subjL = sys.argv[3]
subjS = sys.argv[4]
msaPath = sys.argv[5]
identity = float(sys.argv[6])
evalue = float(sys.argv[7])
if len(sys.argv) == 9:
delete = int(sys.argv[8])
else:
delete = 1
psiD = readMsaPsiBatch(psipath, identity, evalue)
#output(psiD)
#------------------------------------------------
#pathced 20111006, add judgement of existing files
nolocus = 1
if os.path.isfile(subjL) and os.path.isfile(subjS):
nolocus = 0
nolocus = int(raw_input("Do you want to recreate hitted locus\
file and seq file? Default no[0], 1 means yes. \n>>>"))
if nolocus:
getLocus(psiD, subjL)
getSeq(subjL, subjS)
#-----------------------------------------
#print subjS
subjSDict = readSubjS(subjS)
#print subjSDict
#sys.exit(1)
msaDict = readMsa(msaPath)
#print subjSDict
final(psiD, subjSDict, msaDict, psiresult, delete)
