import sys
    import re
    t=open(sys.argv[1],'r').read()
    #reading the template sequences
    blocks=re.split(r'>.*.pdb',t)
    #Reading all the sequences
    blocks1=t.split(">")

    count=[]
    #Calculate the start gap from the template
    for fa in blocks[1:]:
        fasta=fa.split('\n')
        for i in range(len(fasta)):
            #modulate the gap size per line here
#but I want to remove one by one character not per line
            if fasta[i]=='-'*60:
                count.append(i)

    #Get the maximum lines of gap from start in all template sequences
    count=[i for i in count if count.count(i)>1]
    j=list(set(count))
    out=[]
    #Removing the lines form query+template sequence file
    for fa1 in blocks1[1:]:
        fasta1=fa1.split('\n',)
        for i in sorted(j, reverse=True): 
            del fasta1[i]
        #Remove comment for commandline output
        #print ">%s\n%s"%(fasta1[0],"\n".join(fasta1[1:]))
        out.append(">%s\n%s"%(fasta1[0],"\n".join(fasta1[1:])))
    #Output file operation
    f = open(sys.argv[1],'w')
    for k in out:
        f.write(k)
    f.close()
    print "DONE\nOutput name: "+sys.argv[1]

This script is removing line by line string. I want to remove (-) character wise from input files. Please guide how to split into string wise rather than line (\n)