#! /usr/bin/perl -w

#Command line usage: perl<space>ESTCombine.pl<space>input_file1<space>input_file2<space>output_file
#This script reads two Integration.pl output files;
#and appends the second one to the first one, which
#resutls into one file that is ready for Blast search with minor modification.

my $Line = 0;
my @ContgLineNum;
my @File1Data;
my @File2Data;

open FILE1, "$ARGV[0]"
    or die "Cannot open file1: $!";

while (<FILE1>) {
    if ($_ =~ /^Contig/) {
	push @ContigLineNum, $Line;
    }
    push @File1Data, $_;
    $Line += 1;
}

push @ContigLineNum, $Line;

close FILE1
    or die "Cannot close file1: $!";

open FILE2, "$ARGV[1]"
    or die "Cannot open file2: $!";

my $LineNum = 0;

while (<FILE2>) {
    chomp;
    if ($_ =~ /^Contig/) {
	my $temp = "";
	for (my $i = $ContigLineNum[$LineNum]; $i < ($ContigLineNum[$LineNum + 1] - 1); $i ++) {
	    $temp .= $File1Data[$i];
	}
	chomp ($_ = $temp);
	$LineNum += 1;
    }
    push @File2Data, $_;
}

close FILE2
    or die "Cannot close file2: $!";

open OUTPUT, ">$ARGV[2]"
    or die "Cannot open output file: $!";

foreach (@File2Data) {
    $_ =~ s/^Contig/>Contig/;
    $_ =~ s/^EST/>EST/;
    print OUTPUT "$_\n";
}

close OUTPUT
    or die "Cannot close output file: $!";