'''
Alan Garvey
filestuff.py

A program to demonstrate various operations you can do with text files.

'''
from readfasta import readfasta

def rnawrite():
    # read in the rna from disk
    # we assume there is exactly one sequence in the fasta file
    filename = input("Please enter the input filename: ")
    rnainfo = readfasta(filename)
    # Ignore all but the first sequence in the file and assume it is an RNA
    # sequence.
    rnasequence = rnainfo[0][2]

    # remove the start codon
    rnasequence = rnasequence[3:]


    # print the results
    print('The RNA sequence is:')
    print(rnasequence)

    # Save the result to an output file.
    outfilename = input("Please enter the output filename: ")
    handle = open(outfilename, mode="w")
    handle.write(rnasequence)
    handle.close()

def copyfile():
    filename = input("Please enter a filename: ")
    fobj_in = open(filename, mode="r")
    outname = filename.split(".")[0] + "-copy.txt"
    fobj_out = open(outname,"w")
    i = 1
    for line in fobj_in:
        print(line.rstrip())
        fobj_out.write(str(i) + ": " + line)
        i = i + 1
    fobj_in.close()
    fobj_out.close()