20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,130 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+
+use SAM_reader;
+use SAM_entry;
+use Fasta_reader;
+
+my $usage = "usage: $0 coord_sorted.sam genome.fa [SS_lib_type]\n\n";
+
+my $sam_file = $ARGV[0] or die $usage;
+my $genome_fa = $ARGV[1] or die $usage;
+my $SS_lib_type = $ARGV[2];
+
+main: {
+
+	my $sam_reader = new SAM_reader($sam_file);
+
+    my $fasta_reader = new Fasta_reader($genome_fa);
+    my %genome_seqs = $fasta_reader->retrieve_all_seqs_hash();
+
+
+	my $genome_acc = "";
+	my $genome_seq = "";
+
+
+	
+	while ($sam_reader->has_next()) {
+		
+		my $num_introns = 0;
+		
+		my $sam_entry = $sam_reader->get_next();
+
+        my $read_name = $sam_entry->reconstruct_full_read_name();
+        
+		my $cigar = $sam_entry->get_cigar_alignment();
+		my $scaffold = $sam_entry->get_scaffold_name();
+
+        if ($scaffold eq "*") { 
+            # unaligned read
+            next;
+        }
+
+
+		#print "$scaffold\t$cigar\n";
+		
+		unless ($genome_acc eq $scaffold) {
+			$genome_acc = $scaffold;
+			$genome_seq = $genome_seq = $genome_seqs{$genome_acc} or die "Error, no genome seq for acc: $genome_acc";
+		}
+        
+		my ($genome_coords_aref, $query_coords_aref) = $sam_entry->get_alignment_coords();
+		
+		my $strand = $sam_entry->get_query_strand();
+
+		my $transcribed_strand = "?";
+        if ($SS_lib_type) {
+            $transcribed_strand = $sam_entry->get_query_transcribed_strand($SS_lib_type);
+        }
+		
+		my $report_txt = "";
+
+		if (scalar @$genome_coords_aref > 1) {
+
+			my @genome_coords = @$genome_coords_aref;
+			## get the introns:
+			
+			for (my $i = 1; $i <= $#genome_coords; $i++) {
+				my $prev_coordset = $genome_coords[$i-1];	
+				my $curr_coordset = $genome_coords[$i];
+
+				my ($a_lend, $a_rend) = @$prev_coordset;
+				my ($b_lend, $b_rend) = @$curr_coordset;
+				
+                my $intron_lend = $a_rend + 1;
+                my $intron_rend = $b_lend - 1;
+				
+				my $intron_length = $b_lend - $a_rend - 1;
+				if ($intron_length < 0) {
+					die "Error, intron length invalid";
+				}
+				
+				if ($intron_length >= 20) {
+					my $intron_seq = substr($genome_seq, $a_rend +1 -1, $intron_length);
+					
+					my $left_intron = substr($intron_seq, 0, 2);
+					my $right_intron = substr($intron_seq, -2);
+					$num_introns++;
+					
+                    my $intron_dinucs = "$left_intron..$right_intron";
+                    if ($transcribed_strand eq "?") {
+
+                        ## make an educated guess
+                        if ($intron_dinucs eq "GT..AG"
+                            ||
+                            $intron_dinucs eq "GC..AG"
+                            ||
+                            $intron_dinucs eq "AT..AC") {
+                            $transcribed_strand = "+";
+                        }
+                        elsif ($intron_dinucs eq "CT..AC"
+                               ||
+                               $intron_dinucs eq "CT..GC"
+                               || 
+                               $intron_dinucs eq "GT..AT") {
+                            $transcribed_strand =  '-';
+                        }
+                    }
+
+                    
+                    $report_txt .= join("\t", $read_name,
+                                        "$scaffold",
+                                        "$intron_lend-$intron_rend",
+                                        "$transcribed_strand",
+                                        "$intron_dinucs") . "\n";
+				}
+			}
+			if ($num_introns >= 1) {
+				print "$report_txt\n"; # spacer between SAM entries
+			}
+		}
+	}
+
+
+	exit(0);
+}