20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,92 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin;
+use lib ("$FindBin::Bin/../../PerlLib");
+use SAM_reader;
+use SAM_entry;
+use Process_cmd;
+
+my $usage = "\n\n\tusage: $0 transcript_aligned.bam [out_prefix='ss_analysis']\n\n";
+
+my $bam_file = $ARGV[0] or die $usage;
+my $out_prefix = $ARGV[1] || "ss_analysis";
+
+main: {
+
+    my %transcript_to_orients;
+
+    my $sam_reader = new SAM_reader($bam_file);
+    print STDERR "-parsing file: $bam_file\n";
+    while (my $sam_entry = $sam_reader->get_next()) {
+
+        my $trans_name = $sam_entry->get_scaffold_name();
+        my $orient = $sam_entry->get_query_strand();
+
+
+        if ($sam_entry->is_paired()) {
+        
+            unless ($sam_entry->is_proper_pair() && $sam_entry->is_first_in_pair()) {
+                next;
+            }
+        }
+                    
+        $transcript_to_orients{$trans_name}->{$orient}++;
+        
+    }
+    print STDERR "-done parsing file, examining orientations of reads.\n";
+    
+    ## sum them up.
+    my @transcripts = keys %transcript_to_orients;
+    foreach my $transcript (@transcripts) {
+        
+        my $orient_plus = $transcript_to_orients{$transcript}->{'+'} || 0;
+        my $orient_minus = $transcript_to_orients{$transcript}->{'-'} || 0;
+        
+
+        my $total_reads = $orient_plus + $orient_minus;
+        
+        $transcript_to_orients{$transcript}->{'transcript'} = $transcript;
+        $transcript_to_orients{$transcript}->{'total_reads'} = $total_reads;
+    }
+
+    ####
+    my @structs = values %transcript_to_orients;
+    @structs = reverse sort {$a->{total_reads}<=>$b->{total_reads}} @structs; 
+    
+    # header
+    open (my $ofh, ">$out_prefix.dat") or die "Error, cannot write to $out_prefix.dat";
+    
+    print $ofh join("\t", "#transcript", "plus_strand_1stReads", "minus_strand_1stReads", "total_reads", "diff_ratio") . "\n";
+    
+    foreach my $struct (@structs) {
+        
+        my $struct = shift @structs;
+        
+
+        my ($plus, $minus, $total_reads, $transcript) = ($struct->{'+'},
+                                                         $struct->{'-'},
+                                                         $struct->{'total_reads'},
+                                                         $struct->{'transcript'});
+        unless ($plus) { $plus = 0; }
+        unless ($minus) { $minus = 0; }
+
+        my $diff_proportion = sprintf("%.3f", ($plus - $minus) / $total_reads);
+        
+        print $ofh join("\t", $transcript, $plus, $minus, $total_reads, $diff_proportion) . "\n";
+        
+    }
+    close $ofh;
+
+
+    ## plot it.
+    my $cmd  = "$FindBin::Bin/plot_strand_specificity_dist_by_quantile.Rscript $out_prefix.dat";
+    &process_cmd($cmd);
+    
+    
+    exit(0);
+}
+
+
+