1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153
|
#!/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);
}
|