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import string
import sys
import random
import os
#RC
def invertSeq(sseq):
#print sseq
rseq = ""
count = 0
tseq = sseq
tseq = tseq.replace('\n','')
tseq = tseq[::-1]
for base in tseq:
base = string.upper(base)
if base == 'A':
base = 'T'
rseq+=base
elif base == 'T':
base = 'A'
rseq+=base
elif base == 'C':
base = 'G'
rseq+=base
elif base == 'G':
base = 'C'
rseq+=base
else:
#continue
rseq+=base
count+=1
if count == 60:
rseq+="\n"
count = 0
return rseq
if __name__ == "__main__":
random.seed()
infileName = ""
outfileName = ""
rsize = 0
rnumber = 0
shuffleperseq = 1
if len(sys.argv) < 6:
print "\nUsage: shuffleGenome <FastA input file> <output file> <Rearrangement size> <Number of rearrangements> <Shuffled sequences per seq>"
sys.exit(1)
else:
infileName = sys.argv[1]
outfileName = sys.argv[2]
rsize = int(sys.argv[3])
rnumber = int(sys.argv[4])
shuffleperseq = int(sys.argv[5])
filelist = []
if infileName == ".":
tempfiles = os.listdir(".")
for filen in tempfiles:
if filen.find("fna") != -1:
filelist.append(filen)
else:
filelist.append(infileName)
for seqfile in filelist:
infile = open(seqfile,'r')
header = infile.readline()
infiled = infile.read()
filelen = len(infiled)
print "\nInput sequence:%s"%seqfile
print "Input sequence length: %d\n"%filelen
#split genome into filelen/rsize parts
partlist = []
pos = 0
if rsize > filelen:
rsize = filelen
for part in xrange(0,filelen/rsize):
partlist.append(infiled[pos:(part+1)*rsize])
pos +=rsize
partlist.append(infiled[pos:])
for shuffleit in xrange(0,shuffleperseq):
count = 0
seq = ""
parttemp = ""
while count < rnumber:
#choose the 1st part
part1 = random.randint(0,len(partlist)-1)
#choose the 2nd
part2 = part1
while part2 == part1:
part2 = random.randint(0,len(partlist)-1)
#now choose:
#1)transposition,
#2)inversion,
operation = random.randint(1,2)
if operation == 1:
#transposition, translocation
parttemp = partlist[part1]
partlist[part1] = partlist[part2]
partlist[part2] = parttemp
print "Transposition"
print " Positions %d and %d swapped"%(part1,part2)
elif operation == 2:
#inversion
partlist[part1] = invertSeq(partlist[part1])
print "Inversion"
print " Position %d"%part1
count +=1
#create output
output = header
output = ">Shuffled-%d-"%(shuffleit+1) + header[1:]
partstring = string.upper(string.join(partlist))
partstring = partstring.replace(' ', '')
output += string.strip(partstring)
#write output to file
fname = seqfile[:-4]
fname+= "_Shuffled_%d.fna"%(shuffleit+1)
print "output: %s"%(fname)
fout = open(fname,'w')
fout.write(output)
fout.close()
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