20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,153 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "\n\nusage: $0 chrysalis_dir/ component_no (WELDS|SCAFF|BOTH)\n\n";
+
+my $chrysalis_dir = $ARGV[0] or die $usage;
+my $component_no = $ARGV[1];
+my $draw_type = $ARGV[2] or die $usage;
+
+unless (defined $component_no) {
+    die $usage;
+}
+
+unless ($draw_type =~ /^(WELDS|SCAFF|BOTH)$/) {
+    die $usage;
+}
+
+main: {
+    
+    my $graph_from_iworm_file = "$chrysalis_dir/GraphFromIwormFasta.out";
+    
+    my %iworm_accs = &get_iworm_list_from_component($graph_from_iworm_file, $component_no);
+    
+    ## get the weld links:
+    my %welds = &parse_welds($graph_from_iworm_file, \%iworm_accs);
+    
+    ## get the scaffolding links:
+    my $scaffolding_file = "$chrysalis_dir/../iworm_scaffolds.txt";
+    my %scaffolds = &parse_scaffolded_pairs($scaffolding_file, \%iworm_accs);
+    
+    ## write dot file
+    print "digraph {\n";
+    
+    
+    my %iworm_to_id;
+    ## write node labels
+    my $counter = 0;
+    foreach my $iworm_acc (keys %iworm_accs) {
+        $counter++;
+        my $iworm_id = $iworm_to_id{$iworm_acc} = $counter;
+        print "\t$iworm_id [label=\"$iworm_acc\"];\n";
+    }
+ 
+    if ($draw_type =~ /WELDS|BOTH/) {
+        ## add weld links
+        foreach my $iworm_acc (keys %welds) {
+            my $iworm_id = $iworm_to_id{$iworm_acc};
+            foreach my $welded_iworm_acc (keys %{$welds{$iworm_acc}}) {
+                my $welded_id = $iworm_to_id{$welded_iworm_acc};
+                print "\t$iworm_id" . "->" . "$welded_id [color=\"blue\"];\n";
+            }
+        }
+    }
+    
+    if ($draw_type =~ /SCAFF|BOTH/) {
+        ## add scaffolding links
+        foreach my $iworm_acc (keys %scaffolds) {
+            my $iworm_id = $iworm_to_id{$iworm_acc};
+            unless (defined $iworm_id) { next; }
+            
+            foreach my $scaffolded_iworm_acc (keys %{$scaffolds{$iworm_acc}}) {
+                my $scaffolded_id = $iworm_to_id{$scaffolded_iworm_acc};
+                unless (defined $scaffolded_id) { next; }  # not all scaffolded entries were chosen for clustering if read support was insufficient
+                
+                print "\t$iworm_id" . "->" . "$scaffolded_id [color=\"green\"];\n";
+            }
+        }
+    }
+    
+    print "}\n";
+
+    exit(0);
+    
+
+}
+
+
+####
+sub parse_welds {
+    my ($graph_file, $iworm_accs_href) = @_;
+    
+    my %welds;
+
+    open (my $fh, $graph_file) or die "Error, cannot oepn file $graph_file";
+    while (<$fh>) {
+        chomp;
+        if (/^\#Welding: >(a\d+;\d+)_\S+ to >(a\d+;\d+)_/) {
+            my $iworm_acc_A = $1;
+            my $iworm_acc_B = $2;
+
+            ($iworm_acc_A, $iworm_acc_B) = sort ($iworm_acc_A, $iworm_acc_B);
+
+            if ($iworm_accs_href->{$iworm_acc_A} || $iworm_accs_href->{$iworm_acc_B}) { # really should only have situations where they're both included
+                
+                $welds{$iworm_acc_A}->{$iworm_acc_B} = 1;
+            }
+        }
+    }
+
+    close $fh;
+
+    return(%welds);
+}
+
+
+####
+sub get_iworm_list_from_component {
+    my ($graph_file, $component_no) = @_;
+
+    my %iworm_accs;
+    
+    open (my $fh, $graph_file) or die "Error, cannot open file $graph_file";
+    while (<$fh>) {
+        if (/^>Component_$component_no /) {
+            /\[iworm>(a\d+;\d+)_/ or die "Error, cannot parse iworm acc from $_ ";
+            my $iworm_acc = $1;
+            
+            $iworm_accs{$iworm_acc} = 1;
+        }
+    }
+    close $fh;
+
+
+    return(%iworm_accs);
+}
+
+
+####
+sub parse_scaffolded_pairs {
+    my ($scaffolding_file, $iworm_accs_href) = @_;
+
+    my %scaffolded_pairs;
+
+    open (my $fh, $scaffolding_file) or die "Error, cannot open file $scaffolding_file";
+    while (<$fh>) {
+        chomp;
+        my @x = split(/\t/);
+        my ($iworm_acc_A, $iworm_acc_B) = ($x[0], $x[2]);
+        
+        ($iworm_acc_A, $iworm_acc_B) = sort ($iworm_acc_A, $iworm_acc_B);
+
+        if ($iworm_accs_href->{$iworm_acc_A} || $iworm_accs_href->{$iworm_acc_B}) {
+            
+            $scaffolded_pairs{$iworm_acc_A}->{$iworm_acc_B} = 1;
+        }
+    }
+    close $fh;
+
+    return(%scaffolded_pairs);
+}
+