20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,54 @@
+package BED_utils;
+
+use strict;
+use warnings;
+use Carp;
+use Gene_obj;
+
+sub index_BED_as_gene_objs {
+	my ($gff_filename, $gene_id_to_gene_obj_href) = @_;
+
+	my %contig_to_gene_list;
+
+	open (my $fh, $gff_filename) or die "Error, cannot open file $gff_filename";
+	while (<$fh>) {
+		if (/^\#/) { next; }
+        chomp;
+		unless (/\w/) { next; }
+		
+		my $bed_line = $_;
+		
+		my $gene_obj;
+
+		eval {
+			$gene_obj = &Gene_obj::BED_line_to_gene_obj($bed_line);
+			my @introns = $gene_obj->get_intron_coordinates(); # this method breaks if all exons are single bases.  Ignore these weird things.
+		};
+
+		if ($@) {
+			print STDERR "ERROR, cannot create gene for bed line:\n$bed_line\n$@\n";
+			next;
+		}
+		
+
+		my $gene_id = $gene_obj->{TU_feat_name};
+		
+		my $indexed_gene_obj = $gene_id_to_gene_obj_href->{$gene_id};
+	    if ($indexed_gene_obj) {
+			$indexed_gene_obj->add_isoform($gene_obj);
+		}
+		else {
+			$gene_id_to_gene_obj_href->{$gene_id} = $gene_obj;
+			my $contig = $gene_obj->{asmbl_id};
+			push (@{$contig_to_gene_list{$contig}}, $gene_id);
+		}
+	}
+	close $fh;
+
+	return(\%contig_to_gene_list);
+}
+
+
+
+1; #EOM
+