parser.py

import csv,re,textwrap,sys
inputFile = sys.argv
with open(inputFile[1], "rU") as csvfile:
    fastaname = csvfile.name.split(".")[0]
    filereader = csv.reader(csvfile, delimiter=',')
    rowcount = 0 
    output = open(fastaname + ".fasta", 'w')
    for row in filereader:
        if(rowcount == 0):
            header = ">" + ''.join(row[0].split())
            rowcount = 1
            print("Header initialized...")
        elif(rowcount == 1):
            if any("Start" in s for s in row):
                name = ''.join(row[0].split())
                print("Name initialized...")
                rowcount = 2
        elif(rowcount > 1):
            if (len(row[0]) != 0):
                rowHeader = header + "|" + row[1] + "|" + row[2] + "|" + name
                output.write(rowHeader + '\n')
                output.write('\n'.join(textwrap.wrap(row[0], 80)) + '\n')
    output.close()
csvfile.close()