#!/usr/bin/python

import string
import os
import sys
import re

# functions

def getSeq(file):
    infile = open(file, "r")
    seqlines = infile.readlines()
    seqlines = map(string.strip, seqlines)
    infile.close()
    if seqlines[0][0] == ">":
        seqlines = seqlines[1:]
    return string.join(seqlines, "")

# end of functions

lines = sys.stdin.readlines()
lines = map(string.strip, lines)

# check for no hit

if lines[0] == "No match found!":
    print "No match found!"
    sys.exit();

# check that the first line is a valid line and use this to determine whether the input is ok

data = lines[0].split(",")

if len(data) != 12:
    print "Input is not correct!"
    sys.exit();

# transform the data into a data structure

record = []

record.append(data[0]) # mRNA file
record.append(data[1]) # genomic file
record.append(data[2]) # strand
record.append([]) # exon info
for line in lines:
    data = line.split(",")
    record[3].append(data[3:12]) # each record is a array in a array, mStart, mEnd, gStart, gEnd, match, mismatch, gap, mseq, seq

# read command line parameters

format = "1"

for i in range(len(sys.argv)):
    if sys.argv[i] == "-o":
        if i+1 < len(sys.argv):
            if sys.argv[i+1].isdigit() and int(sys.argv[i+1]) >= 1 and int(sys.argv[i+1]) <= 3:
                format = sys.argv[i+1]
            else:
                print "Invalid output format type!"
                sys.exit();
        else:
            print "No output format specified!"
            sys.exit();

# print format 1, fasta formatted exons, each is a fasta sequence

if format == "1":

    num = 1
    for i in record[3]:
        if record[2] == "0":
            print ">Exon %s mRNA %s %s %s %s %s %s" % (num, record[0], i[0], i[1], i[4], i[5], i[6])
        else:
            print ">Exon %s Reverse_Complemented_mRNA %s %s %s %s %s %s" % (num, record[1], i[0], i[1], i[4], o[5], i[6])
        print i[7]
        print ">Exon %s Genomic %s %s %s %s %s %s" % (num, record[1], i[2], i[3], i[4], i[5], i[6])
        print i[8]
        num = num + 1
    
# print format 2, fasta formatted exons, as two fasta sequences, with '-' in the mseq for the introns

elif format == "2":
    # read in the seq file first
    seq = getSeq(record[1])
    # print out mRNA header
    if record[2] == "0":
        print ">mRNA %s %s %s" % (record[0], record[3][0][0], record[3][-1][1])
    else:
        print ">Reverse_Complemented_mRNA %s %s %s" % (record[0], record[3][0][0], record[3][-1][1])
    # print mRNA sequence
    outline = ""
    for i in range(len(record[3])):
        if i != len(record[3])-1:
            outline = outline + record[3][i][7] + "-" * (int(record[3][i+1][2])-int(record[3][i][3])-1)
        else:
            outline = outline + record[3][i][7]
    print outline
    # print out genomic header
    print ">Genomic %s %s %s" % (record[1], record[3][0][2], record[3][-1][3])
    # print out genomic sequence
    outline = ""
    for i in range(len(record[3])):
        if i != len(record[3])-1:
            outline = outline + record[3][i][8] + seq[int(record[3][i][3])+1:int(record[3][i+1][2])]
        else:
            outline = outline + record[3][i][8]
    print outline
    
# print format 3, fasta formatted introns, as individual fasta sequences    

elif format == "3":
    # read in the seq file first
    seq = getSeq(record[1])
    for i in range(len(record[3])-1): # iterate through each intron
        # print the header
        if record[2] == "0":
            print ">Intron %s sense file:%s start:%s end:%s length:%s" % (str(i+1), record[1], str(int(record[3][i][3])+1), str(int(record[3][i+1][2])-1), str(int(record[3][i+1][2])-int(record[3][i][3])-1))
        else:
            print ">Intron %s anti-sense file:%s start:%s end:%s length:%s" % (str(i+1), record[1], str(int(record[3][i][3])+1), str(int(record[3][i+1][2])-1), str(int(record[3][i+1][2])-int(record[3][i][3])-1))
        # print the intron sequence
        print seq[int(record[3][i][3])+1:int(record[3][i+1][2])]