20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,103 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+
+use lib ("$FindBin::RealBin/../../PerlLib");
+use Gene_obj;
+
+my $usage = "usage: $0 alignments.gff3\n\n";
+
+my $trans_gff3_file = $ARGV[0] or die $usage;
+
+
+main: {
+	
+	my %genome_trans_to_coords;
+	
+	open (my $fh, $trans_gff3_file) or die "Error, cannot open file $trans_gff3_file";
+	while (<$fh>) {
+		chomp;
+		
+		unless (/\w/) { next; }
+		
+		my @x = split(/\t/);
+
+		unless (scalar (@x) >= 8 && $x[8] =~ /ID=/) {
+			print STDERR "ignoring line: $_\n";
+			next;
+		}
+		
+		my $scaff = $x[0];
+		my $type = $x[2];
+		my $lend = $x[3];
+		my $rend = $x[4];
+
+		my $orient = $x[6];
+		
+		my $info = $x[8];
+		
+		my @parts = split(/;/, $info);
+		my %atts;
+		foreach my $part (@parts) {
+			$part =~ s/^\s+|\s+$//;
+			$part =~ s/\"//g;
+			my ($att, $val) = split(/=/, $part);
+			
+			if (exists $atts{$att}) {
+				die "Error, already defined attribute $att in $_";
+			}
+			
+			$atts{$att} = $val;
+		}
+
+		my $gene_id = $atts{ID} or die "Error, no gene_id at $_";
+		my $trans_id = $atts{Target} or die "Error, no trans_id at $_";
+		{
+			my @pieces = split(/\s+/, $trans_id);
+			$trans_id = shift @pieces;
+		}
+		
+		my ($end5, $end3) = ($orient eq '+') ? ($lend, $rend) : ($rend, $lend);
+
+		$genome_trans_to_coords{$scaff}->{$gene_id}->{$trans_id}->{$end5} = $end3;
+
+	}
+
+
+	## Output genes in gff3 format:
+
+	foreach my $scaff (sort keys %genome_trans_to_coords) {
+
+		my $genes_href = $genome_trans_to_coords{$scaff};
+
+		foreach my $gene_id (keys %$genes_href) {
+
+			my $trans_href = $genes_href->{$gene_id};
+
+			foreach my $trans_id (keys %$trans_href) {
+
+				my $coords_href = $trans_href->{$trans_id};
+
+				my $gene_obj = new Gene_obj();
+
+				$gene_obj->{TU_feat_name} = $gene_id;
+				$gene_obj->{Model_feat_name} = $trans_id;
+				$gene_obj->{com_name} = "$gene_id $trans_id";
+				
+				$gene_obj->{asmbl_id} = $scaff;
+				
+				$gene_obj->populate_gene_object($coords_href, $coords_href);
+			
+				print $gene_obj->to_BED_format();
+								
+			}
+		}
+	}
+
+
+	exit(0);
+}
+