20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,78 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib", "$FindBin::RealBin/../../PerlLib/KmerGraphLib");
+
+use Fasta_reader;
+use StringGraph;
+use StringNode;
+use ColorGradient;
+
+my $usage = "usage: $0 Butterfly.fasta\n\n";
+
+my $butterfly_fasta_file = $ARGV[0] or die $usage;
+
+
+main: {
+
+    my @seqs_n_paths;
+    
+    {
+        open (my $fh, $butterfly_fasta_file) or die $!;
+        while (<$fh>) {
+            if (/^>/) {
+                /^>(\S+) .* path=\[(.*)\]/ or die "Error, cannot parse header: $_";
+                
+                my $acc = $1;
+                my $path = $2;
+                push (@seqs_n_paths, [$acc, $path]);
+            }
+        }
+        close $fh;
+
+    }
+
+    my $graph = new StringGraph();
+    
+    my @colors = &ColorGradient::get_RGB_gradient(scalar(@seqs_n_paths));
+    @colors = &ColorGradient::convert_RGB_hex(@colors);
+    
+    foreach my $seq_n_path (@seqs_n_paths) {
+        my ($acc, $path_text) = @$seq_n_path;
+        
+        my @path_node_names = &get_path_node_names($path_text);
+        
+        my $color = shift @colors;
+
+        $graph->add_sequence_to_graph($acc, \@path_node_names, 1, $color);
+        
+    }
+    
+    print $graph->toGraphViz();
+    
+}
+
+####
+sub get_path_node_names {
+    my ($path_text) = @_;
+
+    my @node_names;
+    
+    my @parts = split(/\s+/, $path_text);
+    foreach my $part (@parts) {
+        my ($node_name, $coords) = split(/:/, $part);
+        
+        my ($lend, $rend) = split(/-/, $coords);
+        my $length = $rend-$lend + 1;
+        
+        $node_name = "${node_name}_len$length";
+        
+        push (@node_names, $node_name);
+    }
+    
+    return(@node_names);
+}
+