>line1
ACCGAGCTACTAGXXXXX
>line2
ACGTAX

print """Input file must be named FILE.fasta"""
fasta_file = raw_input('Input file name:') # Input fasta file
char = raw_input('Which sequence should be stripped?:')
OutFileName = fasta_file.strip('.fasta') + '_stripped.fasta'
OutFile = open(OutFileName, 'w')
WriteOutFile = True
data = open(fasta_file, "r")
for line in data:
    if line.startswith('>'):
        OutPut = line
    else:
        OutPut = line.strip(char)
        print OutPut
    OutFile.write(OutPut)
print(char)
OutFile.close()
quit()