def calcGC(targetDic, faPath):
tmpdic = {}
fa = Fasta.Parse(faPath)
for chrid in targetDic:
print chrid
tmpdic[chrid] = {}
for item in targetDic[chrid]:
seq = fa.seq[chrid][targetDic[chrid][item][0]:targetDic[chrid][item][1]].upper()
gc = (seq.count('G') + seq.count('C') ) / len(seq)
tmpdic[chrid][item] = gc
return tmpdic
def main():
try:
reffaPath = sys.argv[1]
refbedPath = sys.argv[2]
prefix = sys.argv[3]
except:
print sys.argv[0] + ' [ref fasta path] [ref bed path] [output prefix]'
sys.exit()
print 'Import fasta file.'
fa = Fasta.Parse(reffaPath)
print 'Import bed file.'
bedDic = importBed(refbedPath)
tdic, cdic = {}, {}
for n in range(1, 11):
tdic[n] = {'A': 0, 'T': 0, 'C': 0, 'G': 0}
cdic[n] = {'A': 0, 'T': 0, 'C': 0, 'G': 0}
tdic[-n] = {'A': 0, 'T': 0, 'C': 0, 'G': 0}
cdic[-n] = {'A': 0, 'T': 0, 'C': 0, 'G': 0}
print 'Calculate bases.'
for item in bedDic:
seq = fa.seq[bedDic[item][0]][bedDic[item][1]:bedDic[item][2]].upper()
seqlen = len(seq)
for pos in range(seqlen - 21):
k0 = seq[pos:pos + 21]
if k0[10] in 'CT':
k = k0
else:
k = revCom(k0)
for n in range(-10, 11):
if n == 0: continue
if k[10] == 'T':
tdic[n][k[n + 10]] += 1
elif k[10] == 'C':
cdic[n][k[n + 10]] += 1
print 'Write outputs.'
savefile = open(prefix + '.C10', 'w')
for b in 'TGCA':
savefile.write(b)
for n in range(-10, 11):
if n == 0:
if b == 'C':
savefile.write('\t1')
else:
savefile.write('\t0')
else:
savefile.write('\t%f' % (calcRatio(cdic[n], b)))
savefile.write('\n')
savefile.close()
savefile = open(prefix + '.T10', 'w')
for b in 'TGCA':
savefile.write(b)
for n in range(-10, 11):
if n == 0:
if b == 'T':
savefile.write('\t1')
else:
savefile.write('\t0')
else:
savefile.write('\t%f' % (calcRatio(tdic[n], b)))
savefile.write('\n')
savefile.close()