20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,68 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "\n\tusage: $0 cd-hit.clstr\n\n" .
+    "try running cd-hit first like so:\n" .
+    "\tcd-hit-est -o cdhit -c 0.98 -i Trinity.fasta -p 1 -d 0 -b 3 -T 10\n\n";
+
+my $cdhit_file = $ARGV[0] or die $usage;
+
+main: {
+
+    my $num_bad_clusters = 0;
+    
+    my $cluster;
+    my @trans;
+    
+    open(my $fh, $cdhit_file) or die $!;
+    while (<$fh>) {
+        chomp;
+        if (/^>/) {
+            if (@trans) {
+                $num_bad_clusters += &examine_cluster($cluster, \@trans);
+            }
+            $cluster = $_;
+            @trans = ();
+        }
+        else {
+            push (@trans, $_);
+        }
+    }
+    close $fh;
+
+    if (@trans) {
+        $num_bad_clusters += &examine_cluster($cluster, \@trans);
+    }
+
+    print "Num bad clusters: $num_bad_clusters\n";
+        
+    exit($num_bad_clusters);
+}
+
+####
+sub examine_cluster {
+    my ($cluster, $trans_aref) = @_;
+
+    my @trans = @$trans_aref;
+
+    my %cluster_ids;
+    foreach my $tran (@trans) {
+        $tran =~ /TRINITY_(DN\d+)_/;
+        $cluster_ids{$1}++;
+    }
+
+    my $num_clusters = scalar (keys %cluster_ids);
+    if ($num_clusters != 1) {
+        print STDERR "ERROR, got multiple clusters represented:\n"
+            . "$cluster\n" . join("\n", @trans) . "\n\n";
+        return(1);
+    }
+    else {
+        return(0);
+    }
+}
+
+           
+