20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,182 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use SAM_reader;
+use SAM_entry;
+use Carp;
+use List::Util qw(min max);
+
+my $usage = "usage: $0 file.sam [debug_flag=0]\n\n";
+
+my $sam_file = $ARGV[0] or die $usage;
+
+my $DEBUG = $ARGV[1];
+
+main: {
+
+    my %PATH_COUNTER;
+    
+	my $sam_reader = new SAM_reader($sam_file);
+
+	while ($sam_reader->has_next()) {
+
+		my $sam_entry = $sam_reader->get_next();
+        
+		if ($sam_entry->is_query_unmapped()) {
+			next;
+		}
+
+		my $read_name = $sam_entry->get_read_name();
+        if ($read_name =~ /\.p\d$/) {
+            # not the first path reported.
+            next;
+        }
+                
+        my $sequence = $sam_entry->get_sequence();
+        if ($sequence eq "*") {
+            next;
+        }
+        
+        my $sam_line = $sam_entry->get_original_line();
+
+        if ($DEBUG) {
+            print "$sam_line\n";
+        }
+
+
+        my $NM = 0; # full edit distance (includes mismatches and indels)
+                
+        if ($sam_line =~ /NM:i:(\d+)/) {
+            $NM = $1;
+        }
+        else {
+            die "Error, couldn't extract num mismatches from sam line: $sam_line";
+        }
+        my $cigar_align = $sam_entry->get_cigar_alignment();
+        my $num_indel_nts = 0;
+        while($cigar_align =~ /(\d+)[DI]/g) {
+            $num_indel_nts += $1;
+        }
+
+        my $num_mismatches = $NM - $num_indel_nts;
+
+        if ($num_mismatches < 0) {
+            confess "Error, calculated negative mismatch count from: NM:$NM, indel:$num_indel_nts, cigar: $cigar_align";
+        }
+
+        
+        
+
+		my $scaff_name = $sam_entry->get_scaffold_name();
+		
+		my $strand = $sam_entry->get_query_strand();
+
+        
+		my ($genome_coords_aref, $query_coords_aref) = $sam_entry->get_alignment_coords();
+
+        my $min_coord = 0 + 'inf';
+        my $max_coord = 0 - 'inf';
+
+        my $align_len = 0;
+        {
+            foreach my $coordset (@$genome_coords_aref) {
+                my $seglen = abs($coordset->[1] - $coordset->[0]) + 1;
+                $align_len += $seglen;
+
+                $min_coord = min($min_coord, $coordset->[0], $coordset->[1]);
+                $max_coord = max($max_coord, $coordset->[0], $coordset->[1]);
+
+                if ($DEBUG) {
+                    print STDERR join("\t", $coordset->[0], $coordset->[1], "seglen: $seglen") . "\n";
+                }
+            }
+        }
+
+
+        
+        if ($DEBUG) {
+            print STDERR "num_mismatches: $num_mismatches, align_length: $align_len\n";
+        }
+        
+        my $per_id = sprintf("%.1f", 100 - $num_mismatches/$align_len * 100); 
+
+        my $align_counter = "$read_name.p" . ++$PATH_COUNTER{$read_name};
+
+
+        my @genome_n_trans_coords;
+
+                
+        while (@$genome_coords_aref) {
+            my $genome_coordset_aref = shift @$genome_coords_aref;
+            my $trans_coordset_aref = shift @$query_coords_aref;
+
+            my ($genome_lend, $genome_rend) = @$genome_coordset_aref;
+            my ($trans_lend, $trans_rend) = sort {$a<=>$b} @$trans_coordset_aref;
+
+            push (@genome_n_trans_coords, [ $genome_lend, $genome_rend, $trans_lend, $trans_rend ] );
+
+        }
+
+        ## merge neighboring features if within a short distance unlikely to represent an intron.
+        my @merged_coords;
+        push (@merged_coords, shift @genome_n_trans_coords);
+
+        my $MERGE_DIST = 10;
+        while (@genome_n_trans_coords) {
+            my $coordset_ref = shift @genome_n_trans_coords;
+            my $last_coordset_ref = $merged_coords[$#merged_coords];
+            
+            if ($coordset_ref->[0] - $last_coordset_ref->[1] <= $MERGE_DIST) {
+                # merge it.
+                $last_coordset_ref->[1] = $coordset_ref->[1];
+
+                if ($strand eq "+") {
+                    $last_coordset_ref->[3] = $coordset_ref->[3];
+                } else {
+                    $last_coordset_ref->[2] = $coordset_ref->[2];
+                }
+            }
+            else {
+                # not merging.
+                push (@merged_coords, $coordset_ref);
+            }
+        }
+
+        #my $trans_align_len = 0;
+        #oreach my $coordset_ref (@merged_coords) {
+        #    my ($genome_lend, $genome_rend, $trans_lend, $trans_rend) = @$coordset_ref;
+        #    $trans_align_len += $trans_rend - $trans_lend + 1;
+        #}
+        #
+        #if ($DEBUG) {
+        #    print "interval-based alignment length: $trans_align_len\n";
+        #
+        
+        
+        
+        foreach my $coordset_ref (@merged_coords) {
+            my ($genome_lend, $genome_rend, $trans_lend, $trans_rend) = @$coordset_ref;
+            
+            print join("\t",
+                       $scaff_name,
+                       "minimap2",
+                       "cDNA_match",
+                       $genome_lend, $genome_rend,
+                       $per_id,
+                       $strand,
+                       ".",
+                       "ID=$align_counter;Parent=$align_counter.mrna;Target=$read_name $trans_lend $trans_rend") . "\n";
+        }
+        print "\n";
+        
+        
+        
+	}
+
+
+	exit(0);
+}