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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/env perl | ||
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| # Copyright (c) 2011 Erik Aronesty ([email protected]) | ||
| # | ||
| # 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. | ||
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| use Getopt::Long; | ||
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| my $extended; | ||
| GetOptions("x"=>\$extended); | ||
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| $in = shift @ARGV; | ||
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| my $in_cmd =($in =~ /\.gz$/ ? "gunzip -c $in|" : $in =~ /\.zip$/ ? "unzip -p $in|" : "$in") || die "Can't open $in: $!\n"; | ||
| open IN, $in_cmd; | ||
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| while (<IN>) { | ||
| $gff = 2 if /^##gff-version 2/; | ||
| $gff = 3 if /^##gff-version 3/; | ||
| next if /^#/ && $gff; | ||
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| s/\s+$//; | ||
| # 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 "([^"]+)"/; | ||
| } | ||
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| next unless $id && $f[0]; | ||
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| if ($f[2] eq 'exon') { | ||
| die "no position at exon on line $." if ! $f[3]; | ||
| # gff3 puts :\d in exons sometimes | ||
| $id =~ s/:\d+$// if $gff == 3; | ||
| push @{$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 'stop_codon') { | ||
| $sc{$id}->[1] = $f[4]; | ||
| } elsif ($f[2] eq 'miRNA' ) { | ||
| $trans{$id} = \@f if !$trans{$id}; | ||
| push @{$exons{$id}}, \@f; | ||
| } | ||
| } | ||
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| 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}; | ||
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| # sort by pos | ||
| my @ex = sort { | ||
| $a->[3] <=> $b->[3] | ||
| } @{$exons{$id}}; | ||
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| my $beg = $ex[0][3]; | ||
| my $end = $ex[-1][4]; | ||
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| if ($dir eq '-') { | ||
| # swap | ||
| $tmp=$cds; | ||
| $cds=$cde; | ||
| $cde=$tmp; | ||
| $cds -= 2 if $cds; | ||
| $cde += 2 if $cde; | ||
| } | ||
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| # not specified, just use exons | ||
| $cds = $beg if !$cds; | ||
| $cde = $end if !$cde; | ||
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| # adjust start for bed | ||
| --$beg; --$cds; | ||
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| 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 | ||
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| my $gene_id; | ||
| my $extend = ""; | ||
| if ($extended) { | ||
| ($gene_id) = $attr =~ /gene_name "([^"]+)"/; | ||
| ($gene_id) = $attr =~ /gene_id "([^"]+)"/ unless $gene_id; | ||
| $extend="\t$gene_id"; | ||
| } | ||
| # 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,$extend\n"; | ||
| } | ||
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| close IN; |
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