20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,180 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Statistics::Descriptive;
+
+my $usage = "usage: $0 bwasw.sam.align_stats [longest_contig_only] [no_require_100pct_align]\n\n";
+
+
+my $align_stats_file = $ARGV[0] or die $usage;
+my $longest_contig_only_flag = $ARGV[1] || 0;
+my $no_require_100pct_align = $ARGV[2] || 0;
+
+
+=format
+
+0       #
+1       scaff_name
+2       read_name
+3       read_length
+4       aligned_bases
+5       matches
+6       mismatches
+7       indel_bkpts
+8       sum_indel_lens
+9       pct_mismatches
+10      pct_indel_bkpts
+11      pct_indel_lens
+
+
+=cut
+
+
+    ;
+
+
+my @pct_mismatches;
+my @pct_indels;
+
+my $sum_length = 0;
+my $sum_mismatches = 0;
+my $sum_indels = 0;
+
+
+my @perfect_aligns;
+my @imperfect_aligns;
+
+open (my $fh, $align_stats_file) or die $!;
+
+
+
+my %core_acc_to_entries;
+
+
+my $prev_read_name = "";
+
+while (<$fh>) {
+    chomp;
+    my $line = $_;
+
+    my @x = split(/\t/);
+    if (scalar (@x) == 12 && $x[3] =~ /^\d+$/) {
+
+        my $read_name = $x[2];
+        if ($read_name eq $prev_read_name) { 
+            next; # only one alignment per read
+        }
+        $prev_read_name = $read_name;
+        
+
+
+        my $core_read_name = $read_name;
+        $core_read_name =~ s/_\d+$//;
+        $core_read_name =~ s/\.\d+\.PbioCR$//;
+        my $read_length = $x[3];
+        
+        push (@{$core_acc_to_entries{$core_read_name}}, { line => $line,
+                                                          read_len => $read_length,
+                                                      });
+    }
+}
+close $fh;
+
+
+foreach my $core_read_acc (keys %core_acc_to_entries) {
+
+    my @alignments = @{$core_acc_to_entries{$core_read_acc}};
+
+    if ($longest_contig_only_flag) {
+        @alignments = sort {$a->{read_len}<=>$b->{read_len}} @alignments;
+        my $longest_read = pop @alignments;
+        @alignments = ($longest_read);
+    }
+
+    foreach my $alignment (@alignments) {
+
+
+        my $line = $alignment->{line};
+        my @x = split(/\t/, $line);
+        
+
+        my $seq_length = $x[3];
+        my $aligned_bases = $x[4];
+        my $mismatches = $x[6];
+        my $indels = $x[8];
+        
+        my $pct_mism = $x[9];
+        my $pct_indl = $x[11];
+        
+        
+        push (@pct_mismatches, $pct_mism);
+        push (@pct_indels, $pct_indl);
+        
+        $sum_length += $aligned_bases;
+        $sum_mismatches += $mismatches;
+        $sum_indels += $indels;
+        
+        
+        if ($mismatches == 0 && $indels == 0 && ($no_require_100pct_align || $seq_length == $aligned_bases)) {
+            push (@perfect_aligns, $line);
+        }
+        else {
+            push (@imperfect_aligns, $line);
+        }
+        
+    }
+}
+
+
+my $avg_pct_mismatch = $sum_mismatches / $sum_length * 100;
+my $avg_pct_indel = $sum_indels / $sum_length * 100;
+
+print "// base stats:\n";
+print "Avg_pct_mismatch_all_bases: $avg_pct_mismatch\n";
+print "Avg_pct_indel_all_bases: $avg_pct_indel\n";
+
+
+print "\n// assembly stats:\n";
+my $stat = Statistics::Descriptive::Sparse->new();
+$stat->add_data(@pct_mismatches);
+print "Mean pct_mismatch of assembly: " . $stat->mean() . "\n";
+
+$stat->clear();
+$stat->add_data(@pct_indels);
+print "Mean pct_indel of assembly: " . $stat->mean() . "\n";
+print "\n\n";
+
+
+
+################################################
+#   write some files for downstream analysis
+################################################
+
+
+# write files for interrogation using R
+open (my $ofh, ">$align_stats_file.pct_mismatch.dat") or die $!;
+print $ofh join("\n", @pct_mismatches) . "\n";
+close $ofh;
+
+open ($ofh, ">$align_stats_file.pct_indel.dat") or die $!;
+print $ofh join("\n", @pct_indels) . "\n";
+close $ofh;
+
+open ($ofh, ">$align_stats_file.perfect_aligns.txt") or die $!;
+print $ofh join("\n", @perfect_aligns) . "\n" if @perfect_aligns;
+close $ofh;
+
+
+open ($ofh, ">$align_stats_file.imperfect_aligns.txt") or die $!;
+print $ofh join("\n", @imperfect_aligns) . "\n" if @imperfect_aligns;
+close $ofh;
+
+open ($ofh, ">$align_stats_file.all_aligns.txt") or die $!;
+print $ofh join("\n", @perfect_aligns, @imperfect_aligns) . "\n" if (@perfect_aligns || @imperfect_aligns);
+close $ofh;
+
+
+
+exit(0);
+