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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib", "$FindBin::RealBin/../../PerlLib/KmerGraphLib");
use Fasta_reader;
use ColorGradient;
use Data::Dumper;
my $usage = "usage: $0 graph.seqinfo refseqs.fa\n\n";
my $graph_seqinfo_file = $ARGV[0] or die $usage;
my $refseqs_fa_file = $ARGV[1] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($refseqs_fa_file);
my %refseq_fa = $fasta_reader->retrieve_all_seqs_hash();
my ($node_seq_to_node_id_href, $edges_aref) = &parse_seqinfo($graph_seqinfo_file);
my %refseq_to_nodes_list;
foreach my $refseq_acc (keys %refseq_fa) {
my $refseq_seq = $refseq_fa{$refseq_acc};
foreach my $node_seq (keys %$node_seq_to_node_id_href) {
my $node_id_info = $node_seq_to_node_id_href->{$node_seq};
my $idx = &get_node_start_pos($refseq_seq, $node_seq);
if ($idx >= 0) {
my ($node_id, @rest) = split(/\s+/, $node_id_info);
push (@{$refseq_to_nodes_list{$refseq_acc}}, { start_pos => $idx,
node_id => $node_id,
node_info => $node_id_info,
} );
}
}
}
my $dot_file = "$graph_seqinfo_file.dot";
open(my $ofh, ">$dot_file") or die "Error, cannot write to file: $dot_file";
# print Dumper(\%refseq_to_nodes_list);
## output graph:
print $ofh "digraph G {\n"
. " node [width=0.1,height=0.1,fontsize=10];\n"
. " edge [fontsize=12];\n"
. " margin=1.0;\n"
. " rankdir=LR;\n"
. " labeljust=l;\n";
foreach my $node_seq (keys %$node_seq_to_node_id_href) {
my $node_info_txt = $node_seq_to_node_id_href->{$node_seq};
print $ofh " $node_info_txt\n";
}
## get a different color for each refseq acc:
my @colors = &ColorGradient::convert_RGB_hex(&ColorGradient::get_RGB_gradient(scalar keys %refseq_fa));
foreach my $acc (keys %refseq_to_nodes_list) {
my @structs = @{$refseq_to_nodes_list{$acc}};
@structs = sort {$a->{start_pos}<=>$b->{start_pos}} @structs;
my $color = shift @colors;
## examine each edge
for (my $i = 0; $i < $#structs; $i++) {
my $node_id_begin = $structs[$i]->{node_id};
my $node_id_end = $structs[$i+1]->{node_id};
print $ofh " $node_id_begin->$node_id_end [label=\"$acc\", color=\"$color\"];\n";
}
}
foreach my $edge (@$edges_aref) {
print $ofh " $edge;\n";
}
print $ofh "}\n";
close $ofh;
exit(system("dot -Tpdf $dot_file > $dot_file.pdf"));
}
####
sub parse_seqinfo {
my ($seqinfo_file) = @_;
my %node_seq_to_node_id;
my @edges;
open(my $fh, $seqinfo_file) or die "Error, cannot open file: $seqinfo_file";
while(<$fh>) {
chomp;
my @x = split(/\t/);
if (scalar(@x) == 1) {
my $edge = $x[0];
if ($edge =~ /(\d+)->(\d+)/) {
push(@edges, $edge);
}
else {
die "Error, cannot identify $edge as an edge";
}
}
else {
my ($node_descr, $node_seq) = @x;
$node_seq_to_node_id{$node_seq} = $node_descr;
}
}
close $fh;
return(\%node_seq_to_node_id, \@edges);
}
####
sub get_node_start_pos {
my ($refseq_seq, $node_seq) = @_;
my $idx = index($refseq_seq, $node_seq);
if ($idx >= 0) {
return($idx);
}
else {
## try 1st kmer
my $first_kmer = substr($node_seq, 0, 25);
$idx = index($refseq_seq, $first_kmer);
if ($idx) {
return($idx);
}
else {
# try last kmer
my $last_kmer = substr($node_seq, -25);
$idx = index($refseq_seq, $last_kmer);
return($idx);
}
}
}
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