20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,186 @@
+#!/usr/bin/env perl
+
+package GFF3_alignment_utils;
+
+use strict;
+use warnings;
+use Carp;
+
+use Gene_obj;
+use Gene_obj_indexer;
+use CDNA::Alignment_segment;
+use CDNA::CDNA_alignment;
+use File::Basename;
+
+__run_test() unless caller;
+
+sub index_alignment_objs {
+    my ($gff3_alignment_file, $genome_alignment_indexer_href) = @_;
+    
+    unless ($gff3_alignment_file && -s $gff3_alignment_file) {
+        confess "Error, cannot find or open file $gff3_alignment_file";
+    }
+    unless (ref $genome_alignment_indexer_href) {
+        confess "Error, need genome indexer href as param ";
+    }
+    
+       	
+	my %genome_trans_to_alignment_segments;
+    my %trans_to_gene_id;
+
+	
+	open (my $fh, $gff3_alignment_file) or die "Error, cannot open file $gff3_alignment_file";
+	while (<$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 $per_id = $x[5];
+        if ($per_id eq ".") { $per_id = 100; } # making an assumption here.
+        
+		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);
+        
+        $info =~ /Target=\S+ (\d+) (\d+)/ or die "Error, cannot extract match coordinates from info: $info";
+        my $cdna_seg_lend = $1;
+        my $cdna_seg_rend = $2;
+        
+        ($cdna_seg_lend, $cdna_seg_rend) = sort {$a<=>$b} ($cdna_seg_lend, $cdna_seg_rend); # always + orient for transcript coords.
+        
+        
+        my $alignment_segment = new CDNA::Alignment_segment($end5, $end3, $cdna_seg_lend, $cdna_seg_rend, $per_id);
+        
+
+        push (@{$genome_trans_to_alignment_segments{$scaff}->{$trans_id}}, $alignment_segment);
+        
+		$trans_to_gene_id{$trans_id} = $gene_id;
+        
+	}
+    
+
+    my %scaff_to_align_list;
+    
+    
+	## Output genes in gff3 format:
+
+	foreach my $scaff (sort keys %genome_trans_to_alignment_segments) {
+        
+        my @alignment_accs = keys %{$genome_trans_to_alignment_segments{$scaff}};
+
+        foreach my $alignment_acc (@alignment_accs) {
+
+            my $segments_aref = $genome_trans_to_alignment_segments{$scaff}->{$alignment_acc};
+            
+            ## determine cdna length
+            my @cdna_coords;
+            foreach my $segment (@$segments_aref) {
+                push (@cdna_coords, $segment->get_mcoords());
+            }
+            @cdna_coords = sort {$a<=>$b} @cdna_coords;
+            my $max_coord = pop @cdna_coords;
+
+            my $cdna_alignment_obj = new CDNA::CDNA_alignment($max_coord, $segments_aref);
+            $cdna_alignment_obj->set_acc($alignment_acc);
+            $cdna_alignment_obj->{genome_acc} = $scaff;
+            
+            my $gene_id = $trans_to_gene_id{$alignment_acc} or confess "Error no gene_id for acc: $alignment_acc";
+
+            $cdna_alignment_obj->{gene_id} = $gene_id;
+            
+
+            $cdna_alignment_obj->{source} = basename($gff3_alignment_file);
+            
+            if (ref $genome_alignment_indexer_href eq "Gene_obj_indexer") {
+                $genome_alignment_indexer_href->store_gene($alignment_acc, $cdna_alignment_obj);
+                
+            }
+            else {
+                                
+                $genome_alignment_indexer_href->{$alignment_acc} = $cdna_alignment_obj;
+            }
+            push (@{$scaff_to_align_list{$scaff}}, $alignment_acc);
+        }
+    }
+
+    return(%scaff_to_align_list);
+}
+
+
+
+#################
+## Testing
+#################
+
+
+sub __run_test {
+    
+    my $usage = "usage: $0 file.alignment.gff3\n\n";
+
+    my $gff3_file = $ARGV[0] or die $usage;
+
+    my $indexer = {};
+    my %scaff_to_alignments = &index_alignment_objs($gff3_file, $indexer);
+    
+    
+    foreach my $scaffold (keys %scaff_to_alignments) {
+
+        my @align_ids = @{$scaff_to_alignments{$scaffold}};
+
+        foreach my $align_id (@align_ids) {
+            my $cdna_obj = $indexer->{$align_id};
+
+            print $cdna_obj->toString();
+        }
+    }
+    
+    
+    
+    exit(0);
+    
+
+
+}
+
+
+
+
+
+
+
+1; #EOM
+