20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,160 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../PerlLib");
+use Fasta_reader;
+use BHStats;
+
+my $usage = "\n\nusage: $0 transcripts.fasta\n\n";
+
+my $fasta_file = $ARGV[0] or die $usage;
+
+main: {
+
+    my $fasta_reader = new Fasta_reader($fasta_file);
+    
+    my @all_seq_lengths;
+
+    my $number_transcripts = 0;
+    
+    my $num_GC = 0;
+        
+    my %component_to_longest_isoform;
+    
+    my $tot_seq_len = 0;
+
+    my $missing_gene_ids_flag = 0;
+    
+    while (my $seq_obj = $fasta_reader->next()) {
+
+        my $acc = $seq_obj->get_accession();
+        
+        $number_transcripts++;
+         my $comp_id = $acc;
+
+
+        if (! $missing_gene_ids_flag) {
+            
+            if ($acc =~ /^(.*c\d+_g\d+)/) {
+                $comp_id = $1;
+            }
+            elsif ($acc =~ /^(.*comp\d+_c\d+)/) {
+                $comp_id = $1;
+            }
+            else {
+                print STDERR "Error, cannot decipher gene identifier from acc: $acc";
+                $missing_gene_ids_flag = 1;
+            }
+        }
+        
+        my $sequence = $seq_obj->get_sequence();
+
+        my $seq_len = length($sequence);
+
+        $tot_seq_len += $seq_len;
+
+        if ( (! exists $component_to_longest_isoform{$comp_id})
+             || 
+             $component_to_longest_isoform{$comp_id} < $seq_len) {
+            
+            $component_to_longest_isoform{$comp_id} = $seq_len;
+        }
+        
+        push (@all_seq_lengths, $seq_len);
+                
+        while ($sequence =~ /[gc]/ig) {
+            $num_GC++;
+        }
+
+    }
+
+    print "\n\n";
+    print "################################\n";
+    print "## Counts of transcripts, etc.\n";
+    print "################################\n";
+
+    print "Total trinity 'genes':\t" . scalar(keys %component_to_longest_isoform) . "\n";        
+    print "Total trinity transcripts:\t" . $number_transcripts . "\n";
+
+    
+    my $pct_gc = sprintf("%.2f", $num_GC / $tot_seq_len * 100);
+    
+
+    print "Percent GC: $pct_gc\n\n"; 
+    
+    print "########################################\n";
+    print "Stats based on ALL transcript contigs:\n";
+    print "########################################\n\n";
+
+    &report_stats(@all_seq_lengths);
+    print "\n\n";
+    
+    if ($missing_gene_ids_flag) {
+        print " - note: not reporting gene-based longest isoform info since couldn't parse Trinity accession info.\n";
+    }
+    else {
+        print "#####################################################\n";
+        print "## Stats based on ONLY LONGEST ISOFORM per 'GENE':\n";
+        print "#####################################################\n\n";
+        
+        &report_stats(values %component_to_longest_isoform);
+            
+        print "\n\n\n";
+    }
+    
+    
+    exit(0);
+}
+
+####
+sub report_stats {
+    my (@seq_lengths) = @_;
+
+    @seq_lengths = reverse sort {$a<=>$b} @seq_lengths;
+    
+    my $cum_seq_len = 0;
+    foreach my $len (@seq_lengths) {
+        $cum_seq_len += $len;
+    }
+    
+    for (my $i = 10; $i <= 50; $i += 10) {
+        my $cum_len_needed = $cum_seq_len * $i/100;
+        my $N_val = &get_contigNvalue($cum_len_needed, \@seq_lengths);
+        print "\tContig N$i: $N_val\n";
+    }
+    print "\n";
+    
+
+    my $median_len = &BHStats::median(@seq_lengths);
+    print "\tMedian contig length: $median_len\n";
+
+    my $avg_len = sprintf("%.2f", &BHStats::avg(@seq_lengths));
+    print "\tAverage contig: $avg_len\n";
+
+    
+        
+    print "\tTotal assembled bases: $cum_seq_len\n";
+
+    return;
+}
+
+
+
+sub get_contigNvalue {
+    my ($cum_len_needed, $seq_lengths_aref) = @_;
+    
+    my $partial_sum_len = 0;
+    foreach my $len (@$seq_lengths_aref) {
+        $partial_sum_len += $len;
+
+        if ($partial_sum_len >= $cum_len_needed) {
+            return($len);
+        }
+    }
+
+
+    return -1; # shouldn't happen.
+}