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Circos::Rule - routines for handling rules in Circos
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This module is not meant to be used directly.
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Circos is an application for the generation of publication-quality,
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circularly composited renditions of genomic data and related
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Circos is particularly suited for visualizing alignments, conservation
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and intra and inter-chromosomal relationships. However, Circos can be
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used to plot any kind of 2D data in a circular layout - its use is not
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limited to genomics. Circos' use of lines to relate position pairs
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(ribbons add a thickness parameter to each end) is effective to
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display relationships between objects or positions on one or more
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All documentation is in the form of tutorials at L<http://www.circos.ca>.
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# -------------------------------------------------------------------
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use Carp qw( carp confess croak );
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use Params::Validate qw(:all);
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use lib "$FindBin::RealBin";
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use lib "$FindBin::RealBin/../lib";
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use lib "$FindBin::RealBin/lib";
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use Circos::Configuration; # qw(%CONF $DIMS);
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use Circos::Constants;
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use Circos::Expression;
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my $conf_leaf = shift;
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my @rules = make_list( $conf_leaf );
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# first, grep out rules that have an importance value
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my @rules_ordered = sort { $b->{importance} <=> $a->{importance} } grep(defined $_->{importance}, @rules);
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# then add all remaining rules without importance
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push @rules_ordered, grep(! defined $_->{importance}, @rules);
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@rules = @rules_ordered;
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# - condition must exist
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# - assign tag automatically, if does not exist
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# - create a list of parameters that are being readjusted
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for my $i (0..@rules-1) {
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my $rule = $rules[$i];
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if(! defined $rule->{condition} && ! defined $rule->{flow}) {
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$Data::Dumper::Sortkeys = 1;
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$Data::Dumper::Terse = 1;
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fatal_error("rule","no_condition_no_flow",Dumper($rule));
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if(! defined $rule->{tag}) {
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printdebug_group("rule","assigning auto rule tag [$tag]");
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$rule->{__param} ||= {};
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for my $key (keys %$rule) {
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next if grep($key eq $_, qw(condition importance tag flow __param));
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$rule->{__param}{$key}++;
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sub apply_rules_to_track {
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my ($track, $rules, $param_path) = @_;
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for my $point ( @{ $track->{__data} } ) {
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for my $rule ( @$rules ) {
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if(defined $goto_rule_tag) {
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if($rule->{tag} ne $goto_rule_tag) {
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printdebug_group("rule","going to rule [$goto_rule_tag] and skipping rule [$rule->{tag}]");
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printdebug_group("rule","found rule [$goto_rule_tag]");
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$goto_rule_tag = undef;
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my $condition = $rule->{condition};
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my @flows = make_list(seek_parameter( "flow", $rule, $track->{rules} ));
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my $pass = test_rule( $point, $condition, [ $point, @$param_path ] ) if defined $condition;
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apply_rule_to_point($point,$rule,$param_path) if $pass;
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# if flow is not defined
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printdebug_group("rule","quitting rule chain");
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printdebug_group("rule","trying next rule");
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for my $flow (@flows) {
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my @flow_tok = split(" ",$flow);
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# if the flow string ends with "if true" or "if false" register
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# whether the flow command should be executed based on whether
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# the rule has passed
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printdebug_group("rule","parsing flow",$flow);
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if($flow =~ /\s+if\s+/) {
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if($flow =~ /\s+true\s*$/) {
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$toggle_flow = $pass ? 1 : 0;
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} elsif ($flow =~ /\s+false\s*$/) {
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$toggle_flow = !$pass ? 1 : 0;
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fatal_error("rules","flow_syntax_error",$flow);
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# by default the flow will trigger
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printdebug_group("rule","rule pass",$pass,"flow",$toggle_flow);
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if($flow =~ /^stop/) {
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} elsif ($flow =~ /^goto/) {
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my (undef,$tag,$if,$ifcond) = @flow_tok;
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$goto_rule_tag = $tag;
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printdebug_group("rule","goto to rule [$tag]");
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} elsif ($flow =~ /^restart/) {
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if(!$rule->{restart}) {
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$rule->{restart} = 1;
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printdebug_group("rule","restarting rule chain");
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printdebug_group("rule","cannot restart from rule more than once - quitting rule chain");
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} elsif ($flow =~ /^continue/) {
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printdebug_group("rule","continuing to next rule");
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fatal_error("rules","flow_syntax_error",$flow,$rule->{tag});
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if(defined $goto_rule_tag) {
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fatal_error("rule","bad_tag",$goto_rule_tag);
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# clear restart flags
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if($have_restarted) {
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map { delete $_->{restart} } @$rules;
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sub apply_rule_to_point {
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my ($point,$rule,$param_path) = @_;
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for my $param ( keys %{ $rule->{__param} } ) {
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my $value = $rule->{$param};
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printdebug_group("rule","applying rule var",$param,"value",$value);
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if ( $value =~ /^eval\(\s*(.*)\s*\)\s*$/ ) {
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$value = Circos::Expression::eval_expression( $point, $expr, [ $point, @$param_path ] );
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if ( $param eq "value" || $param eq "start" || $param eq "end" ) {
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if($value eq "undef") {
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delete $point->{data}[0]{ $param };
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$point->{data}[0]{ $param } = $value;
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if ( not_defined_or_one( $rule->{overwrite} ) ) {
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# overwrite is default
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if($value eq "undef") {
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delete $point->{param}{ $param };
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$point->{param}{ $param } = $value;
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} elsif ( ! exists $point->{param}{$param} ) {
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# overwrite only if parameter doesn't exist
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if($value ne "undef") {
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$point->{param}{$param} = $value;
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# -------------------------------------------------------------------
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my ( $point, $condition, $param_path ) = @_;
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for my $c (make_list($condition)) {
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my $cfmt = Circos::Expression::format_condition($c);
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my $pass = Circos::Expression::eval_expression($point,$cfmt,$param_path);
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printdebug_group("rule","condition [$condition] pass",$pass ? "PASS" : "FAIL");
added
removed
lib/Circos/Rule.pm
