#! usr/bin/perl

#2009/1/2

sub usage { 
    print STDERR "usage: converts <extended fasta output plus gaps from SeqMan>\n\n"; 
    print STDERR "#program takes output from SeqMan alignment exported as single file, extended fasta including gaps\n";
    print STDERR "Creator: Laurie Stevison\n"; 
    exit; 
} #end sub 

if ($#ARGV  != 0) { # zero means one argument 
    &usage; 
} 
$efasta = $ARGV[0]; 

if($efasta =~ /\.fas/) {
    $fasta = $`;
    $output = $fasta . "_converted.fas"; 
} else {
	print "File not saved in fasta format. Please resave SeqMan output and try conversion again. Need \".fas\" extension.\n";
        exit;
} #end if

open(READFAS, $efasta); 
open(WRITEOUT, ">$output"); 

print STDERR "Reading input file...\n";

print STDOUT "Please indicate labeling for reverse sequences...\n";
chomp($reverse_seqs = (<STDIN>));

while (<READFAS>) {
    chomp;
    if (/>/) { 
	$seq_name = $'; #'
	push(@seq_names, $seq_name);
	if ($newseq==1) {
	    push(@sequences, $sequence);
	} #end if 
	$sequence = "";
	$newseq=0;
	next; 
    } else {
	$sequence .= $_;
	$newseq=1; 
    } #end else
} #end while
push(@sequences, $sequence);

print "done.\n\n";

print STDERR "Converting file...\n";

for ($i = 0; $i <= $#seq_names; $i++) {

    $seq_name = $seq_names[$i];
    @seq_name_array = split(/\;/ , $seq_name);
    $sequence = $sequences[$i];

    if($seq_name_array[0] =~ /$reverse_seqs/) {
	$revcom_sequence = reverse($sequence);
	$revcom_sequence =~ tr/ACGTacgt/TGCAtgca/;
    } else {
	$revcom_sequence = $sequence;
    } #end if

    if($seq_name_array[0] =~ /at offset/) {
	chomp($offset = $'); #'
	$dash_number = "-" x $offset;
    } else {
	print "File not saved in extended fasta format. Please resave SeqMan output and try conversion again.\n";
        exit;
    } #end if

    print WRITEOUT ">$seq_name_array[0]\n";
    print WRITEOUT "$dash_number" . "$revcom_sequence\n";
} #end for

print STDERR "done.\n\n";