#!/usr/bin/perl

# Copyright (c) 2011 Erik Aronesty (erik@q32.com)
# http://code.google.com/p/ea-utils/source/browse/trunk/clipper/gtf2bed
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ALSO, IT WOULD BE NICE IF YOU LET ME KNOW YOU USED IT.

use Data::Dumper;

$in = shift @ARGV;

open IN, ($in =~ /\.gz$/ ? "gunzip -c $in" : $in =~ /\.zip$/ ? "unzip -p $in" : "$in");
my $countExons=0;
while (<IN>) {
$gff = 2 if /^##gff-version 2/;
$gff = 3 if /^##gff-version 3/;
next if /^#/ && $gff;
s/\s+$//;
# 0-chr 1-src 2-feat 3-beg 4-end 5-scor 6-dir 7-fram 8-attr
my @f = split /\t/;
if ($gff) {
# most ver 2's stick gene names in the id field
($id) = $f[8]=~ /\bID="([^"]+)"/;
# most ver 3's stick unquoted names in the name field
($id) = $f[8]=~ /\bName=([^";]+)/ if !$id && $gff == 3;
} else {
($id) = $f[8]=~ /transcript_id "([^"]+)"/;
#print "before $id\n";
}
next unless (defined($id) && defined($f[0]));
if ($f[2] eq 'exon') {
	$countExons++;
die "no position at exon on line $." if ! $f[3];
# gff3 puts :\d in exons sometimes
#$id =~ s/:\d+$// if $gff == 3;
#print "after $id\n";

push @{$exons{$id}}, \@f;
# save lowest start
$trans{$id} = \@f if !$trans{$id};
} elsif ($f[2] eq 'start_codon') {
#optional, output codon start/stop as "thick" region in bed
$sc{$id}->[0] = $f[3];
} elsif ($f[2] eq 'CDS') {
#optional, output codon start/stop as "thick" region in bed
push @{$cds{$id}}, \@f;
# save lowest start
$cdx{$id} = \@f if !$cdx{$id};
} elsif ($f[2] eq 'stop_codon') {
$sc{$id}->[1] = $f[4];
} elsif ($f[2] eq 'miRNA' ) {
$trans{$id} = \@f if !$trans{$id};
push @{$exons{$id}}, \@f;
}
}
for $id (
# sort by chr then pos
sort {
$trans{$a}->[0] eq $trans{$b}->[0] ?
$trans{$a}->[3] <=> $trans{$b}->[3] :
$trans{$a}->[0] cmp $trans{$b}->[0]
} (keys(%trans)) ) {
my ($chr, undef, undef, undef, undef, undef, $dir, undef, $attr, undef, $cds, $cde) = @{$trans{$id}};
my ($cds, $cde);
($cds, $cde) = @{$sc{$id}} if $sc{$id};

# sort by pos
my @ex = sort {
$a->[3] <=> $b->[3]
} @{$exons{$id}};

my $beg = $ex[0][3];
my $end = $ex[-1][4];

if ($dir eq '-') {
# swap
$tmp=$cds;
$cds=$cde;
$cde=$tmp;
$cds -= 2 if $cds;
$cde += 2 if $cde;
}

# not specified, just use exons
$cds = $beg if !$cds;
$cde = $end if !$cde;

# adjust start for bed
--$beg; --$cds;

my $exn = @ex; # exon count
my $exst = join ",", map {$_->[3]-$beg-1} @ex; # exon start
my $exsz = join ",", map {$_->[4]-$_->[3]+1} @ex; # exon size

# added an extra comma to make it look exactly like ucsc's beds
print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,\n";
}
print STDERR "Found $countExons exons.\n";


close IN;
