126 lines
3.0 KiB
Perl
126 lines
3.0 KiB
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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use FindBin;
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use lib ("$FindBin::RealBin/../../PerlLib");
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use Gene_obj;
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use Fasta_reader;
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my $usage = "usage: $0 transcripts.gtf genome.fasta\n\n";
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my $gtf_file = $ARGV[0] or die $usage;
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my $genome_fasta_file = $ARGV[1] or die $usage;
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main: {
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my $fasta_reader = new Fasta_reader($genome_fasta_file);
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my %genome_seqs = $fasta_reader->retrieve_all_seqs_hash();
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my %genome_trans_to_coords;
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open (my $fh, $gtf_file) or die "Error, cannot open file $gtf_file";
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while (<$fh>) {
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chomp;
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unless (/\w/) { next; }
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my @x = split(/\t/);
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my $scaff = $x[0];
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my $type = $x[2];
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my $lend = $x[3];
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my $rend = $x[4];
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my $orient = $x[6];
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my $info = $x[8];
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unless ($type eq 'exon') { next; }
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my @parts = split(/;/, $info);
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my %atts;
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foreach my $part (@parts) {
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$part =~ s/^\s+|\s+$//;
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$part =~ s/\"//g;
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my ($att, $val) = split(/\s+/, $part);
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if (exists $atts{$att}) {
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die "Error, already defined attribute $att in $_";
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}
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$atts{$att} = $val;
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}
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my $gene_id = $atts{gene_id} or die "Error, no gene_id at $_";
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my $trans_id = $atts{transcript_id} or die "Error, no trans_id at $_";
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my ($end5, $end3) = ($orient eq '+') ? ($lend, $rend) : ($rend, $lend);
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$genome_trans_to_coords{$scaff}->{$gene_id}->{$trans_id}->{$end5} = $end3;
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}
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## Output genes in gff3 format:
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foreach my $scaff (sort keys %genome_trans_to_coords) {
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my $genes_href = $genome_trans_to_coords{$scaff};
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my $genome_seq = $genome_seqs{$scaff} or die "Error, cannot find genome sequence for acc: $scaff";
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foreach my $gene_id (keys %$genes_href) {
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my $trans_href = $genes_href->{$gene_id};
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my $intron_text = "";
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foreach my $trans_id (keys %$trans_href) {
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my $coords_href = $trans_href->{$trans_id};
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my $gene_obj = new Gene_obj();
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$gene_obj->{TU_feat_name} = $gene_id;
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$gene_obj->{Model_feat_name} = $trans_id;
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$gene_obj->{com_name} = "$gene_id $trans_id";
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$gene_obj->{asmbl_id} = $scaff;
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$gene_obj->populate_gene_object($coords_href, $coords_href);
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my $orientation = $gene_obj->get_orientation();
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#print $gene_obj->to_BED_format();
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my @intron_coords = $gene_obj->get_intron_coordinates();
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foreach my $intron (@intron_coords) {
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my ($end5, $end3) = @$intron;
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my ($lend, $rend) = sort {$a<=>$b} ($end5, $end3);
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my $left_splice_dinuc = substr($genome_seq, $lend-1, 2);
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my $right_splice_dinuc = substr($genome_seq, $rend-1-1, 2);
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$intron_text .= join("\t", $gene_id, $trans_id, $scaff, "$lend-$rend", $orientation, "$left_splice_dinuc..$right_splice_dinuc") . "\n";
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}
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}
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if ($intron_text) {
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print "$intron_text\n";
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}
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}
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}
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exit(0);
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}
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