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#!/usr/bin/python3
import sys
f = open(sys.argv[1], "rU")
bases = "ACGT"
aaInd = "ACDEFGHIKLMNPQRSTVWY"
def getCodonStr(n):
f = (n//16)
s = ((n&15)//4)
t = n&3
return "%s%s%s" %(bases[f], bases[s], bases[t])
for line in f:
enumName, aas = line.strip().split()
el = enumName.lower()
if False:
#sys.stdout.write("%s %d \n" % (aas, len(aas)))
sys.stdout.write("\tif(gCode == %s) {\n" % enumName)
sys.stdout.write("\t\tconst int ccitac%s[] = {" % el)
comCodedInt = 0
for allCodonsInd, aaLetter in enumerate(aas):
if aaLetter != "*":
if comCodedInt != 0:
sys.stdout.write(", ")
sys.stdout.write("%d" % allCodonsInd)
comCodedInt += 1
sys.stdout.write("};\n")
sys.stdout.write("\t\tn = %d;\n" % (comCodedInt))
sys.stdout.write("\t\tconst int caaind%s[] = {" % el)
comCodedInt = 0
for allCodonsInd, aaLetter in enumerate(aas):
if aaLetter != "*":
if comCodedInt != 0:
sys.stdout.write(", ")
sys.stdout.write("%d" % aaInd.index(aaLetter))
comCodedInt += 1
sys.stdout.write("};\n")
sys.stdout.write("\t\tconst char * ccodstr%s[] = {" % el)
comCodedInt = 0
for allCodonsInd, aaLetter in enumerate(aas):
if aaLetter != "*":
if comCodedInt != 0:
sys.stdout.write(", ")
sys.stdout.write('"%s"' % getCodonStr(allCodonsInd))
comCodedInt += 1
sys.stdout.write("};\n");
sys.stdout.write("\t\tstd::copy(ccitac%s, ccitac%s + n, back_inserter(c.compressedCodonIndToAllCodonsInd));\n" % (el, el))
sys.stdout.write("\t\tstd::copy(caaind%s, caaind%s + n, back_inserter(c.aaInd));\n"% (el, el))
sys.stdout.write("\t\tstd::copy(ccodstr%s, ccodstr%s + n, back_inserter(c.codonStrings));\n" % (el, el))
sys.stdout.write("\t\treturn c;\n\t}\n")
else:
#sys.stdout.write("%s %d \n" % (aas, len(aas)))
sys.stdout.write("\tif(gCode == %s) {\n" % enumName)
sys.stdout.write("\t\tconst int tr%s[] = {" % el)
comCodedInt = 0
for allCodonsInd, aaLetter in enumerate(aas):
if comCodedInt != 0:
sys.stdout.write(", ")
if aaLetter != "*":
sys.stdout.write("%d" % comCodedInt)
comCodedInt += 1
else:
sys.stdout.write("-1")
sys.stdout.write("};\n")
sys.stdout.write("\t\tstd::copy(tr%s, tr%s + 64, back_inserter(v));\n" % (el, el))
sys.stdout.write("\t\treturn v;\n\t}\n")
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