python23

#!/usr/bin/env python

import os
import sys

inputfile=sys.argv[1]
outputfile=sys.argv[2]

u=open(outputfile,'w')

with open(inputfile,'r') as s:
    si=s.readlines()
    for sil in si:
        sili=sil.strip()
        if str(sili[0]) == ">":
            u.write(sil)
            n=0
        else:
            for silib in sili:
#               bc=silib.lower()
                bc=silib.upper()
                n=n+1
                u.write(bc)
                if n%80 == 0:
                    u.write("\n")
            if n%80 != 0:
                u.write("\n")

#!/usr/bin/env python

u=open('3utr_mouse.fa','w')

with open('mouse_3utr.fa','r') as s:
    si=s.readlines()
    for sil in si:
        sili=sil.strip()
        if str(sili[0]) == ">":
            u.write(sil)
            n=0
        else:
            for silib in sili:
                bc=silib.lower()
                n=n+1
                u.write(bc)
                if n%50 == 0:
                    u.write("\n")
            if n%50 != 0:
                u.write("\n")