Mercurial > repos > morinlab > oncocircos
changeset 0:b77ab858eac1 draft
Uploaded
| author | morinlab |
|---|---|
| date | Mon, 12 Sep 2016 16:23:26 -0400 |
| parents | |
| children | 916c60c717a6 |
| files | bin/make.circos.data bin/parse etc/bands.conf etc/breaks.conf etc/circos.conf etc/circos.conf~ etc/cnv.type.conf etc/cnv.type.conf~ etc/color.conf etc/color.conf~ etc/histogram.conf etc/ideogram.conf etc/ideogram.conf~ etc/ideogram.label.conf etc/ideogram.position.conf etc/ideogram.position.conf~ etc/library.conf etc/library.conf~ etc/r0r1.conf etc/r0r1.conf~ etc/rule.snp.conf etc/rule.type.conf etc/rule.type.conf~ etc/sv.type.conf etc/sv.type.conf~ etc/ticks.conf etc/ticks.conf~ etc/track.counter.conf etc/track.counter.conf~ etc/white.bin.conf etc/white.bin.conf~ oncocircos.xml parse.conf tool_dependencies.xml |
| diffstat | 34 files changed, 2142 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/make.circos.data Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,404 @@ +#!/bin/env perl + +=pod + +=head1 NAME + +make.circos.data - create Circos data files from summary tables of SV/CNV mutations + +=head1 SYNOPSIS + + bin/parse > table.txt + + # uses same config file as parse + cat table.txt | bin/make.circos.data + +=head1 DESCRIPTION + +=head1 OPTIONS + +=cut + +use strict; +use warnings FATAL=>"all"; + +use Carp; +use Config::General; +use Cwd qw(getcwd abs_path); +use Data::Dumper; +use File::Basename; +use FindBin; +use Getopt::Long; +use Math::Round qw(round nearest); +use Math::VecStat qw(sum min max average); +use Pod::Usage; +use Time::HiRes qw(gettimeofday tv_interval); +use Storable; +use lib "$FindBin::RealBin"; +use lib "$FindBin::RealBin/../lib"; +use lib "$FindBin::RealBin/lib"; + +our (%OPT,%CONF,$conf); +our @COMMAND_LINE = ("file=s", + "configfile=s", + "help", + "cdump", + "man", + "debug"); +our $VERSION = 0.02; + +# common and custom module imports below +#use Regexp::Common; +#use IO::File; +#use List::Util; +#use List::MoreUtils; +use Set::IntSpan; +#use Statistics::Descriptive; + +# read and parse configuration file +parse_config(); + +sub validateconfiguration { + +} + +################################################################ +# get files +my $table = read_file(); + +my $path = "$CONF{files}{root}/$CONF{files}{circos}"; +# karyotype +open(F,">$path/karyotype.txt"); +for my $chr (1..22,"X","Y") { + my $n = grep($_->{chr} eq $chr,@$table); + next unless $n; + printf F ("chr - hs%s %s 0 %d chr%s\n",$chr,$chr,$n,lc $chr); +} +close(F); + +# number of CNV +open(F,">$path/mutations.txt"); +open(FSV,">$path/mutations.stacked.sv.txt"); +open(FCNV,">$path/mutations.stacked.cnv.txt"); +for my $gene (@$table) { + my @sv; + my @sv_vals; + my @cnv; + my @cnv_vals; + # number of samples for each SV type + for my $type (sort { $CONF{sv}{types}{$b} <=> $CONF{sv}{types}{$a}} keys %{$CONF{sv}{types}}) { + push @sv, sprintf("sv_%s=%d",lc $type,$gene->{sv}{$type}||0); + push @sv_vals, $gene->{sv}{$type}||0; + } + # number of samples for each CNV type + for my $type (sort { $CONF{cnv}{types}{$b} <=> $CONF{cnv}{types}{$a}} keys %{$CONF{cnv}{types}}) { + next unless $CONF{cnv}{types}{$type}; + push @cnv, sprintf("cnv_%s=%d",lc $type,$gene->{cnv}{$type}{n}||0); + push @cnv_vals, $gene->{cnv}{$type}{n}||0; + } + my $cnv_plus = ($gene->{cnv}{amp}{n} ||0) + ($gene->{cnv}{gain}{n} ||0); + my $cnv_minus = ($gene->{cnv}{homd}{n}||0) + ($gene->{cnv}{hetd}{n} ||0); + printf F ("hs%s %d %d %s size=%d,sv_top_type=%s,sv_top_n=%d,sv_tot=%d,svaa_max_pos=%s,svaa_max_n=%d,cnv_top_type=%s,cnv_top_n=%d,cnv_top_avg=%f,cnv_top_med=%f,cnv_plus=%d,cnv_minus=%d,%s,%s\n", + $gene->{chr}, + $gene->{pos}, + $gene->{pos}+1, + $gene->{name}, + $gene->{size}, + keys %{$gene->{sv_top}}, + values %{$gene->{sv_top}}, + $gene->{sv}{"*"} || 0, + (keys %{$gene->{svaa_top}})||0, + (values %{$gene->{svaa_top}})||0, + $gene->{cnv_top}{class} || "-", + $gene->{cnv_top}{n} || 0, + $gene->{cnv_top}{avg} || 0, + $gene->{cnv_top}{med} || 0, + $cnv_plus||0, + $cnv_minus||0, + join(",",@sv), + join(",",@cnv)); + # stacked histograms of number of samples with each SV type + printf FSV ("hs%s %d %d %s name=%s,sv_top_type=%s,sv_top_n=%d\n", + $gene->{chr}, + $gene->{pos}, + $gene->{pos}+1, + join(",",@sv_vals), + $gene->{name}, + keys %{$gene->{sv_top}}, + values %{$gene->{sv_top}}, + ); + printf FCNV ("hs%s %d %d %s name=%s,cnv_top_type=%s,cnv_top_n=%d,cnv_top_avg=%f,cnv_top_med=%f\n", + $gene->{chr}, + $gene->{pos}, + $gene->{pos}+1, + join(",",@cnv_vals), + $gene->{name}, + $gene->{cnv_top}{class} || "-", + $gene->{cnv_top}{n} || 0, + $gene->{cnv_top}{avg} || 0, + $gene->{cnv_top}{med} || 0, + + ); +} +close(F); +close(FSV); +close(FCNV); + +sub read_file { + my $fh = get_handle(); + my @data; + my $chrpos; + while(<$fh>) { + chomp; + next if /^\#/; + my @tok = split; + my $gene = list2hash([qw(i id name chr start end size)], + [splice(@tok,0,7)]); + $gene->{pos} = $chrpos->{ $gene->{chr} }++; + # remaining tokens + for my $tok (@tok) { + my @subtok = split(":",$tok); + my $event = lc shift @subtok; + my $type = lc shift @subtok; + if($event =~ /sv/) { + $gene->{$event}{$type} = shift @subtok; + } elsif($event =~ /cnv/) { + my $h = { class=> $type, + n=> shift @subtok, + min=> shift @subtok, + avg=> shift @subtok, + med=> shift @subtok, + max=> shift @subtok}; + if($event =~ /top/) { + $gene->{$event} = $h; + } else { + $gene->{$event}{$type} = $h; + } + } + } + printdumper($gene); + push @data, $gene; + } + return \@data; +} + +sub list2hash { + my ($names,$list) = @_; + my $h; + my $i = 0; + for my $name (@$names) { + $h->{$name} = $list->[$i++]; + } + return $h; +} + +sub get_handle { + my $h; + if(my $file = $CONF{file}) { + die "No such file [$file]" unless -e $file; + open(FILE,$file); + $h = \*FILE; + } else { + $h = \*STDIN; + } + return $h; +} + +# HOUSEKEEPING ############################################################### + +sub dump_config { + printdumper(\%OPT,\%CONF); +} + +sub parse_config { + my $dump_debug_level = 3; + GetOptions(\%OPT,@COMMAND_LINE); + pod2usage() if $OPT{help}; + pod2usage(-verbose=>2) if $OPT{man}; + loadconfiguration($OPT{configfile}); + populateconfiguration(); # copy command line options to config hash + validateconfiguration(); + if ($CONF{cdump}) { + $Data::Dumper::Indent = 2; + $Data::Dumper::Quotekeys = 0; + $Data::Dumper::Terse = 0; + $Data::Dumper::Sortkeys = 1; + $Data::Dumper::Varname = "OPT"; + printdumper(\%OPT); + $Data::Dumper::Varname = "CONF"; + printdumper(\%CONF); + exit; + } +} + +sub populateconfiguration { + for my $var (keys %OPT) { + $CONF{$var} = $OPT{$var}; + } + repopulateconfiguration(\%CONF); +} + +sub repopulateconfiguration { + my ($node,$parent_node_name) = shift; + return unless ref($node) eq "HASH"; + for my $key (keys %$node) { + my $value = $node->{$key}; + if (ref($value) eq "HASH") { + repopulateconfiguration($value,$key); + } elsif (ref($value) eq "ARRAY") { + for my $item (@$value) { + repopulateconfiguration($item,$key); + } + } elsif (defined $value) { + my $new_value = parse_field($value,$key,$parent_node_name,$node); + $node->{$key} = $new_value; + } + } +} + +sub parse_field { + my ($str,$key,$parent_node_name,$node) = @_; + # replace configuration field + # conf(LEAF,LEAF,...) + while ( $str =~ /(conf\(\s*(.+?)\s*\))/g ) { + my ($template,$leaf) = ($1,$2); + if (defined $template && defined $leaf) { + my @leaf = split(/\s*,\s*/,$leaf); + my $new_template; + if (@leaf == 2 && $leaf[0] eq ".") { + $new_template = $node->{$leaf[1]}; + } else { + $new_template = fetch_conf(@leaf); + } + $str =~ s/\Q$template\E/$new_template/g; + } + } + if ($str =~ /\s*eval\s*\(\s*(.+)\s*\)/) { + my $fn = $1; + $str = eval $fn; + if ($@) { + die "could not parse configuration parameter [$@]"; + } + } + return $str; +} + +sub fetch_configuration { + my @config_path = @_; + my $node = \%CONF; + if(! @config_path) { + return \%CONF; + } + for my $path_element (@config_path) { + if (! exists $node->{$path_element}) { + return undef; + } else { + $node = $node->{$path_element}; + } + } + return $node; +} + +sub fetch_conf { + return fetch_configuration(@_); +} + +sub loadconfiguration { + my $file = shift; + if (defined $file) { + if (-e $file && -r _) { + # provided configuration file exists and can be read + $file = abs_path($file); + } else { + confess "The configuration file [$file] passed with -configfile does not exist or cannot be read."; + } + } else { + # otherwise, try to automatically find a configuration file + my ($scriptname,$path,$suffix) = fileparse($0); + my $cwd = getcwd(); + my $bindir = $FindBin::RealBin; + my $userdir = $ENV{HOME}; + my @candidate_files = ( + "$cwd/$scriptname.conf", + "$cwd/etc/$scriptname.conf", + "$cwd/../etc/$scriptname.conf", + "$bindir/$scriptname.conf", + "$bindir/etc/$scriptname.conf", + "$bindir/../etc/$scriptname.conf", + "$userdir/.$scriptname.conf", + ); + my @additional_files = (); + for my $candidate_file (@additional_files,@candidate_files) { + #printinfo("configsearch",$candidate_file); + if (-e $candidate_file && -r _) { + $file = $candidate_file; + #printinfo("configfound",$candidate_file); + last; + } + } + } + if (defined $file) { + $OPT{configfile} = $file; + $conf = new Config::General( + -ConfigFile=>$file, + -IncludeRelative=>1, + -IncludeAgain=>1, + -ExtendedAccess=>1, + -AllowMultiOptions=>"yes", + #-LowerCaseNames=>1, + -AutoTrue=>1 + ); + %CONF = $conf->getall; + } +} + +sub printdebug { + printinfo("debug",@_) if defined $CONF{debug}; +} + +sub printinfo { + print join(" ",map { defined $_ ? $_ : "_undef_" } @_),"\n"; +} + +sub printfinfo { + my ($fmt,@args) = @_; + @args = map { defined $_ ? $_ : "_undef_" } @args; + printf("$fmt\n",@args); +} + +sub printerr { + print STDERR join(" ",map { defined $_ ? $_ : "_undef_" } @_),"\n"; +} + +sub printdumper { + print Dumper(@_); +} + +=pod + +=head1 HISTORY + +=over + +=item * 30 Nov 2015 + +Started. + +=back + +=head1 AUTHOR + +Martin Krzywinski + +=head1 CONTACT + +Martin Krzywinski +Genome Sciences Center +BC Cancer Research Center +100-570 W 7th Ave +Vancouver BC V5Z 4S6 + +mkweb.bcgsc.ca +martink@bcgsc.ca + +=cut
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/parse Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,453 @@ +#!/bin/env perl + +=pod + +=head1 NAME + +parse - parse Ryan's MAF and CNV files and generate a summary table of all genes and their mutations and CNV status + +=head1 SYNOPSIS + + # automatically load etc/parse.conf + bin/parse + + # if config file is elsewhere + bin/parse -conf elsewhere/my.conf + +=head1 DESCRIPTION + +See etc/parse.conf for all settings. + +=head1 OPTIONS + +=cut + +use strict; +use warnings FATAL=>"all"; + +use Carp; +use Config::General; +use Cwd qw(getcwd abs_path); +use Data::Dumper; +use File::Basename; +use FindBin; +use Getopt::Long; +use Math::Round qw(round nearest); +use Math::VecStat qw(sum min max average); +use Pod::Usage; +use Time::HiRes qw(gettimeofday tv_interval); +use Statistics::Basic qw(median); +use Storable; +use lib "$FindBin::RealBin"; +use lib "$FindBin::RealBin/../lib"; +use lib "$FindBin::RealBin/lib"; + +our (%OPT,%CONF,$conf); +our @COMMAND_LINE = ("file=s", + "configfile=s", + "help", + "cdump", + "man", + "debug"); +our $VERSION = 0.02; + +# common and custom module imports below +#use Regexp::Common; +#use IO::File; +#use List::Util; +#use List::MoreUtils; +use Set::IntSpan; +#use Statistics::Descriptive; + +# read and parse configuration file +parse_config(); + +sub validateconfiguration { +} + +################################################################ +# get files +my $sv = read_file($CONF{files}{sv} ,"sv" ); +my $genes = read_file($CONF{files}{mart},"genes"); +my $cnv = read_file($CONF{files}{cnv} ,"cnv" ); + +################################################################ +# traverse all genes from biomart and determine number +# of SV and CNV events across samples +for my $chr (keys %$genes) { + next if $CONF{filter}{chr} && $chr ne $CONF{filter}{chr}; + printdebug("processing",$chr); + for my $gene (@{$genes->{$chr}}) { + my $id = $gene->{id}; + # filter out by presence and number of SV events + next if $CONF{filter}{sv} && ! $sv->{$id}; + # number of samples that have SV event + my @samples_sv = keys %{$sv->{$id}}; + next if $CONF{filter}{sv_num} && @samples_sv < $CONF{filter}{sv_num}; + + $gene->{affected} = 1; + + # register SV events + my $pos; + for my $sample (@samples_sv) { + for my $sv (sort {$b->{weight} <=> $a->{weight}} @{$sv->{$id}{$sample}}) { + $gene->{sv}{ $sv->{type} }++; + $gene->{sv}{ "*" }++; + $pos->{ $sv->{aa} }++; # register the protein position of the SV + next if $CONF{sv}{top_damage_only}; + } + } + # top SV event + if($gene->{sv}) { + my ($sv_top) = sort {$gene->{sv}{$b} <=> $gene->{sv}{$a}} grep($_ ne "*",keys %{$gene->{sv}}); + $gene->{sv_top}{$sv_top} = $gene->{sv}{$sv_top}; + } + for my $aa (sort {$pos->{$b} <=> $pos->{$a}} keys %$pos) { + #next unless $pos->{$aa} > 1; + my $n = $pos->{$aa}; + $gene->{svaa_top}{$aa} = $n if ! defined $gene->{svaa_top}; + $gene->{svaa}{"*"} += $n; + $gene->{svaa}{$aa} = $n; + } + # register CNV events + my @samples_cnv = keys %$cnv; + # lookup any CNV events -- this can take a bit of time + # we can bin the CNV hash later if needed + for my $sample (@samples_cnv) { + my $chr = $gene->{chr}; + next unless $cnv->{$sample}{$chr}; + for my $cnv (@{$cnv->{$sample}{$chr}}) { + my $int = $cnv->{set}->intersect($gene->{set})->cardinality; + next unless $int; + push @{$gene->{cnv}{$cnv->{category}}{$sample}}, $cnv->{avg}; + } + } + } +} + +################################################################ +# report +my $i = 0; +for my $chr (1..22,"X","Y") { + next unless $genes->{$chr}; + for my $gene (sort {$a->{start} <=> $b->{start}} @{$genes->{$chr}}) { + next unless $gene->{affected}; + my @report = ($i++,@{$gene}{qw(id name chr start end size)}); + if($gene->{sv}) { + push @report, sprintf("sv_top:%s:%d",keys %{$gene->{sv_top}},values %{$gene->{sv_top}}); + for my $type (sort keys %{$gene->{sv}}) { + push @report, sprintf("sv:%s:%d",$type,$gene->{sv}{$type}); + } + } + if($gene->{svaa}) { + push @report, sprintf("svaa_top:%s:%d",keys %{$gene->{svaa_top}},values %{$gene->{svaa_top}}); + for my $aa (sort {$gene->{svaa}{$b} <=> $gene->{svaa}{$a}} keys %{$gene->{svaa}}) { + push @report, sprintf("svaa:%s:%d",$aa,$gene->{svaa}{$aa}); + } + } + if($gene->{cnv}) { + my $type_count; + my $delins_count; + my $values_by_type; + for my $type (sort keys %{$gene->{cnv}}) { + my @sample_avg; + for my $sample (keys %{$gene->{cnv}{$type}}) { + # number of samples with this kind of CNV event + $type_count->{$type}++; + my @values = @{$gene->{cnv}{$type}{$sample}}; + push @sample_avg, average(@values); + push @{$values_by_type->{$type}}, @values; + } + push @report, sprintf("cnv:%s:%d:%f:%f:%f:%f", + $type, + int(@sample_avg), + scalar(min(@sample_avg)), + average(@sample_avg), + median(@sample_avg)->query, + scalar(max(@sample_avg))); + } + my ($top_type) = sort {$type_count->{$b} <=> $type_count->{$a}} keys %$type_count; + push @report, sprintf("cnv_top:%s:%d:%f:%f:%f:%f", + $top_type, + $type_count->{$top_type}, + scalar(min(@{$values_by_type->{$top_type}})), + average(@{$values_by_type->{$top_type}}), + median(@{$values_by_type->{$top_type}})->query, + scalar(max(@{$values_by_type->{$top_type}}))); + } + printinfo(@report); + } +} + +exit; + +sub read_file { + my ($file,$type) = @_; + open(F,$file) || die "Could not open file [$file] for reading"; + my $data; + + my @fields = grep(/\d/,keys %{$CONF{fields}{$type}}); + my @keys = split(",",$CONF{fields}{$type}{key}); + + my $i; + while(<F>) { + chomp; + next if /^\#/; + my @tok = split "\t"; + my $entry = {class=>$type}; + for my $col (@fields) { + my ($field_name,$field_transform) = split(":",$CONF{fields}{$type}{$col}); + my $value = $tok[$col]; + if($field_transform) { + $value = lc $value if $field_transform =~ /lc/; + } + $entry->{ $field_name } = $value; + } + # skip mutation types that are not important + next if $CONF{sv}{filter} && $type eq "sv" && exists $entry->{type} && ! $CONF{sv}{types}{$entry->{type}}; + next if $CONF{cnv}{filter} && $type eq "cnv" && exists $entry->{category} && ! $CONF{cnv}{types}{$entry->{category}}; + if($type eq "sv") { + $entry->{weight} = $CONF{sv}{types}{$entry->{type}}; + } + $entry->{chr} = "X" if $entry->{chr} eq 23; + $entry->{chr} = "Y" if $entry->{chr} eq 24; + next unless grep($entry->{chr} eq $_, (1..22,"X","Y")); + $entry->{set} = span(@{$entry}{qw(start end)}) if $entry->{start}; + $entry->{size} = $entry->{set}->cardinality; + #printdumper($entry); + $i++; + if(@keys == 1) { + push @{$data->{$entry->{$keys[0]}}}, $entry; + } elsif (@keys == 2) { + push @{$data->{$entry->{$keys[0]}}{$entry->{$keys[1]}}}, $entry; + } + } + printdebug("got",$i,$type); + return $data; +} + +sub list2hash { + my %h; + map {$h{$_}=1} @_; + return %h; +} + +sub span { + my ($x,$y) = @_; + if($x==$y) { + return Set::IntSpan->new($x); + } else { + return Set::IntSpan->new("$x-$y"); + } +} + +sub get_handle { + my $h; + if(my $file = $CONF{file}) { + die "No such file [$file]" unless -e $file; + open(FILE,$file); + $h = \*FILE; + } else { + $h = \*STDIN; + } + return $h; +} + +# HOUSEKEEPING ############################################################### + +sub dump_config { + printdumper(\%OPT,\%CONF); +} + +sub parse_config { + my $dump_debug_level = 3; + GetOptions(\%OPT,@COMMAND_LINE); + pod2usage() if $OPT{help}; + pod2usage(-verbose=>2) if $OPT{man}; + loadconfiguration($OPT{configfile}); + populateconfiguration(); # copy command line options to config hash + validateconfiguration(); + if ($CONF{cdump}) { + $Data::Dumper::Indent = 2; + $Data::Dumper::Quotekeys = 0; + $Data::Dumper::Terse = 0; + $Data::Dumper::Sortkeys = 1; + $Data::Dumper::Varname = "OPT"; + printdumper(\%OPT); + $Data::Dumper::Varname = "CONF"; + printdumper(\%CONF); + exit; + } +} + +sub populateconfiguration { + for my $var (keys %OPT) { + $CONF{$var} = $OPT{$var}; + } + repopulateconfiguration(\%CONF); +} + +sub repopulateconfiguration { + my ($node,$parent_node_name) = shift; + return unless ref($node) eq "HASH"; + for my $key (keys %$node) { + my $value = $node->{$key}; + if (ref($value) eq "HASH") { + repopulateconfiguration($value,$key); + } elsif (ref($value) eq "ARRAY") { + for my $item (@$value) { + repopulateconfiguration($item,$key); + } + } elsif (defined $value) { + my $new_value = parse_field($value,$key,$parent_node_name,$node); + $node->{$key} = $new_value; + } + } +} + +sub parse_field { + my ($str,$key,$parent_node_name,$node) = @_; + # replace configuration field + # conf(LEAF,LEAF,...) + while ( $str =~ /(conf\(\s*(.+?)\s*\))/g ) { + my ($template,$leaf) = ($1,$2); + if (defined $template && defined $leaf) { + my @leaf = split(/\s*,\s*/,$leaf); + my $new_template; + if (@leaf == 2 && $leaf[0] eq ".") { + $new_template = $node->{$leaf[1]}; + } else { + $new_template = fetch_conf(@leaf); + } + $str =~ s/\Q$template\E/$new_template/g; + } + } + if ($str =~ /\s*eval\s*\(\s*(.+)\s*\)/) { + my $fn = $1; + $str = eval $fn; + if ($@) { + die "could not parse configuration parameter [$@]"; + } + } + return $str; +} + +sub fetch_configuration { + my @config_path = @_; + my $node = \%CONF; + if(! @config_path) { + return \%CONF; + } + for my $path_element (@config_path) { + if (! exists $node->{$path_element}) { + return undef; + } else { + $node = $node->{$path_element}; + } + } + return $node; +} + +sub fetch_conf { + return fetch_configuration(@_); +} + +sub loadconfiguration { + my $file = shift; + if (defined $file) { + if (-e $file && -r _) { + # provided configuration file exists and can be read + $file = abs_path($file); + } else { + confess "The configuration file [$file] passed with -configfile does not exist or cannot be read."; + } + } else { + # otherwise, try to automatically find a configuration file + my ($scriptname,$path,$suffix) = fileparse($0); + my $cwd = getcwd(); + my $bindir = $FindBin::RealBin; + my $userdir = $ENV{HOME}; + my @candidate_files = ( + "$cwd/$scriptname.conf", + "$cwd/etc/$scriptname.conf", + "$cwd/../etc/$scriptname.conf", + "$bindir/$scriptname.conf", + "$bindir/etc/$scriptname.conf", + "$bindir/../etc/$scriptname.conf", + "$userdir/.$scriptname.conf", + ); + my @additional_files = (); + for my $candidate_file (@additional_files,@candidate_files) { + #printinfo("configsearch",$candidate_file); + if (-e $candidate_file && -r _) { + $file = $candidate_file; + #printinfo("configfound",$candidate_file); + last; + } + } + } + if (defined $file) { + $OPT{configfile} = $file; + $conf = new Config::General( + -ConfigFile=>$file, + -IncludeRelative=>1, + -IncludeAgain=>1, + -ExtendedAccess=>1, + -AllowMultiOptions=>"yes", + #-LowerCaseNames=>1, + -AutoTrue=>1 + ); + %CONF = $conf->getall; + } +} + +sub printdebug { + printinfo("debug",@_) if defined $CONF{debug}; +} + +sub printinfo { + print join(" ",map { defined $_ ? $_ : "_undef_" } @_),"\n"; +} + +sub printfinfo { + my ($fmt,@args) = @_; + @args = map { defined $_ ? $_ : "_undef_" } @args; + printf("$fmt\n",@args); +} + +sub printerr { + print STDERR join(" ",map { defined $_ ? $_ : "_undef_" } @_),"\n"; +} + +sub printdumper { + print Dumper(@_); +} + +=pod + +=head1 HISTORY + +=over + +=item * 30 Nov 2015 + +Started. + +=back + +=head1 AUTHOR + +Martin Krzywinski + +=head1 CONTACT + +Martin Krzywinski +Genome Sciences Center +BC Cancer Research Center +100-570 W 7th Ave +Vancouver BC V5Z 4S6 + +mkweb.bcgsc.ca +martink@bcgsc.ca + +=cut
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/bands.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,5 @@ +show_bands = yes +fill_bands = yes +band_stroke_thickness = 0 +band_stroke_color = white +band_transparency = 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/breaks.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,13 @@ +<break_style 1> +stroke_color = black +fill_color = blue +thickness = 0.25r +stroke_thickness = 2 +</break_style> + +<break_style 2> +stroke_color = white +stroke_thickness = 3 +thickness = 4r +</break_style> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/circos.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,312 @@ + +# You can control which tracks to show. +# +# These can be set at the command line using +# +# circos -param show_labels=no -param show_sv_total=no ... +# +# You can verify settings using -cdump +# +# circos -cdump | grep show_ + +show_labels = yes +show_sv_total = yes +show_svaa = yes +show_sv_stack = yes +show_sv_types = yes + +show_cnv_stack = yes +show_cnv_types = yes +show_cnv_plus_minus = yes +show_cnv_copy_number = yes + +sv_label_min = 5 + +################################################################ +# Colors are referenced using their name e.g. "amp" in +# parameters directly +# +# fill_color = amp + +<colors> +amp = vdred +gain = red +neut = dgrey +homd = blue +hetd = vdblue + +cnv-1 = amp +cnv-2 = gain +cnv-3 = hetd +cnv-4 = homd + +sv-1 = grey +sv-2 = vdblue +sv-3 = vdred +sv-4 = blue +sv-5 = red +sv-6 = lorange +sv-7 = vdorange +sv-8 = vlgrey + +# color lists, sorted numerically in increasing order +# using the text matched in capture brackets +sv = sv-(\d+) +cnv = cnv-(\d+) +</colors> + +chromosomes_units = 1 +chromosomes_display_default = yes +chromosomes = -hsY + +#chromosomes_display_default = no +#chromosomes = /hs[1234]$/ + +karyotype = data/karyotype.txt + +################################################################ +# For auto-spacing and positioning of tracks + +# Start, width and spacing of tracks +track_r0 = 0.99 +track_w = 0.1 +track_s = 0.025 + +# width and spacing of individual SV type tracks +sv_w = 0.0 # +sv_s = 0.015 # + +# Order in which SV and CNV tracks are shown +sv_types = nonsense_mutation,frame_shift_del,frame_shift_ins,in_frame_del,in_frame_ins,splice_site,nonstop_mutation,missense_mutation +cnv_types = amp,gain,hetd,homd + +<plots> + +# All plot blocks share data from the same file +file = data/mutations.txt +stroke_thickness = 0 + +################################################################ +# Gene labels, filtered by SNV total +<plot> +show = conf(show_labels) +type = text +r1 = dims(ideogram,radius_outer) + 500p +r0 = dims(ideogram,radius_outer) + 20p + conf(track_w)r + +label_size = 14 +label_snuggle = yes +max_snuggle_distance = 3r +snuggle_sampling = 1 +snuggle_tolerance = 0.25r + +show_links = yes +link_color = black +link_dims = 0p,5p,5p,5p,0p + +<rules> +<rule> +condition = var(sv_tot) < conf(sv_label_min) +show = no +</rule> +<rule> +condition = var(sv_tot) > 2*conf(sv_label_min) +label_font = bold +</rule> +</rules> +</plot> + +################################################################ +# SV total + +<plot> +show = conf(show_sv_total) +type = histogram +r1 = dims(ideogram,radius_outer) + 20p + conf(track_w)r +r0 = dims(ideogram,radius_outer) + 20p +min = 0 +#max = 20 +fill_color = black + +<<include white.bin.conf>> + +<axes> +<axis> +spacing = 0.1r +</axis> +</axes> + +<rules> +<rule> +condition = 1 +value = eval(var(sv_tot)) +flow = continue +</rule> +</rules> +</plot> + +################################################################ +# SV protein position recurrence + +<plot> +show = conf(show_svaa) +type = heatmap +r1 = dims(ideogram,radius_outer)+15p +r0 = dims(ideogram,radius_outer)+5p +min = 2 +max = 5 +color = grey,orange,red,dred +<rules> +<rule> +condition = 1 +value = eval(var(svaa_max_n)) +flow = continue +</rule> +<rule> +condition = var(value) == 1 +show = no +</rule> +</rules> +</plot> + + +################################################################ +# SV stacked barplot + +<plot> +show = conf(show_sv_stack) +file = data/mutations.stacked.sv.txt +orientation = in +type = histogram +r1 = eval(sprintf("%fr",conf(track_r0))) +r0 = eval(sprintf("%fr",conf(track_r0)-conf(track_w))) +min = 0 +max = 1 +fill_color = sv +normalize_bin_values = yes +<<include white.bin.conf>> +<<include track.counter.conf>> +</plot> + +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> + +############################################################### +# +/- CNV histograms + +<plot> +show = conf(show_cnv_plus_minus) +type = histogram +<<include r0r1.conf>> +max = 20 +min = -20 +fill_color = gain +<<include white.bin.conf>> +<axes> +<axis> +spacing = .1r +</axis> +<axis> +position = 0 +thickness = 2 +</axis> +</axes> +<backgrounds> +<background> +color = vvlgrey +</background> +</backgrounds> +<rules> +<rule> +condition = 1 +value = eval(var(cnv_plus)) +</rule> +</rules> +</plot> + +<plot> +show = conf(show_cnv_plus_minus) +type = histogram +<<include r0r1.conf>> +max = 20 +min = -20 +fill_color = homd +<<include white.bin.conf>> +<<include track.counter.conf>> +<rules> +<rule> +condition = 1 +value = eval(-var(cnv_minus)) +</rule> +</rules> +</plot> + +################################################################ +# CNV stacked bar plot + +<plot> +show = conf(show_cnv_stack) +file = data/mutations.stacked.cnv.txt +orientation = in +type = histogram +<<include r0r1.conf>> +min = 0 +max = 1 +fill_color = cnv +normalize_bin_values = yes +<<include white.bin.conf>> +<<include track.counter.conf>> +</plot> + +<plot> +show = conf(show_cnv_copy_number) +type = histogram +<<include r0r1.conf>> +min = -2 +max = 2 +<<include white.bin.conf>> +<<include track.counter.conf>> +<axes> +<axis> +position = 0 +color = black +</axis> +<axis> +spacing = 0.5 +y1 = 0 +color = lred +</axis> +<axis> +spacing = 0.5 +y0 = 0 +color = lblue +</axis> +</axes> +<rules> +<rule> +condition = !var(cnv_top_n) +show = no +</rule> +<rule> +condition = 1 +value = eval(var(cnv_top_avg)) +fill_color = eval(lc var(cnv_top_type)) +</rule> +</rules> +</plot> + +</plots> + +<image> +<<include etc/image.conf>> +</image> +<<include etc/housekeeping.conf>> +<<include etc/colors_fonts_patterns.conf>> +<<include ideogram.conf>> +#<<include ticks.conf>> +max_points_per_track* = 50000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/circos.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,309 @@ + +show_labels = yes +show_sv_total = yes +show_svaa = yes +show_sv_stack = yes +show_sv_types = yes + +show_cnv_stack = yes +show_cnv_types = yes +show_cnv_plus_minus = yes +show_cnv_copy_number = yes + +sv_label_min = 5 + +show_cnv = no # old + +<colors> +amp = dred +gain = red +neut = dgrey # not used +homd = blue +hetd = dblue + +cnv-1 = amp +cnv-2 = gain +cnv-3 = hetd +cnv-4 = homd + +sv-1 = black +sv-2 = dblue +sv-3 = dred +sv-4 = blue +sv-5 = red +sv-6 = lorange +sv-7 = orange +sv-8 = vlgrey + +sv = sv-(\d+) +cnv = cnv-(\d+) +</colors> + +chromosomes_units = 1 +chromosomes_display_default = yes +chromosomes = -hsY # hs1;hs2;hs3 + +karyotype = data/karyotype.txt + +# SV by type +sv_r0 = 0.90 # outer track radius +sv_w = 0.0 # track width +sv_s = 0.015 # track width for smaller tracks +# this is the order of the SV type tracks, from outside in +sv_types = nonsense_mutation,frame_shift_del,frame_shift_ins,in_frame_del,in_frame_ins,splice_site,nonstop_mutation,missense_mutation + +# CNV by type +cnv_r0 = 0.70 # outer track radius +cnv_w = 0.0 # track width +cnv_s = 0.015 # track width for smaller tracks +cnv_types = amp,gain,hetd,homd + +<plots> + +file = data/mutations.txt +stroke_thickness = 0 + +################################################################ +# SV total + +<plot> +show = conf(show_sv_total) +type = histogram +r1 = dims(ideogram,radius_outer) + 100p +r0 = dims(ideogram,radius_outer) + 20p +min = 0 +max = 20 +fill_color = black + +<axes> +<axis> +spacing = 4 +</axis> +</axes> + +<rules> +<rule> +condition = 1 +value = eval(var(sv_tot)) +flow = continue +</rule> +</rules> +</plot> + +################################################################ +# SV protein position recurrence + +<plot> +show = conf(show_svaa) +type = heatmap +r1 = dims(ideogram,radius_outer)+15p +r0 = dims(ideogram,radius_outer)+5p +min = 2 +max = 5 +color = grey,orange,red,dred +<rules> +<rule> +condition = 1 +value = eval(var(svaa_max_n)) +flow = continue +</rule> +<rule> +condition = var(value) == 1 +show = no +</rule> +</rules> +</plot> + +################################################################ +# Gene labels, filtered by SNV total +<plot> +show = conf(show_labels) +type = text +r1 = dims(ideogram,radius_outer) + 500p +r0 = dims(ideogram,radius_outer) + 100p + +label_snuggle = yes +show_links = yes + +label_size = 14 +link_color = black +link_dims = 0p,5p,5p,5p,0p + +<rules> +<rule> +condition = var(sv_tot) < conf(sv_label_min) +show = no +</rule> +</rules> +</plot> + +################################################################ +# SV stacked barplot + +<plot> +show = conf(show_sv_stack) +file = data/mutations.stacked.sv.txt +orientation = in +type = histogram +r1 = 0.995r +r0 = 0.925r +min = 0 +max = 1 +fill_color = sv +normalize_bin_values = yes +</plot> + +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> +<<include sv.type.conf>> + +################################################################ +# CNV stacked bar plot + +<plot> +show = conf(show_cnv_stack) +file = data/mutations.stacked.cnv.txt +orientation = in +type = histogram +r1 = 0.775r +r0 = 0.725r +min = 0 +max = 1 +fill_color = cnv +normalize_bin_values = yes +</plot> + +################################################################ +# CNV in samples, by event type + +<<include cnv.type.conf>> +<<include cnv.type.conf>> +<<include cnv.type.conf>> +<<include cnv.type.conf>> + +############################################################### +# +/- CNV histograms + +<plot> +show = conf(show_cnv_plus_minus) +type = histogram +r1 = 0.625r +r0 = 0.55r +max = 20 +min = -20 +fill_color = blue +<axes> +<axis> +spacing = 5 +</axis> +<axis> +position = 0 +thickness = 2 +</axis> +</axes> +<backgrounds> +<background> +color = vvlgrey +</background> +</backgrounds> +<rules> +<rule> +condition = 1 +value = eval(var(cnv_plus)) +</rule> +</rules> +</plot> + +<plot> +show = conf(show_cnv_plus_minus) +type = histogram +r1 = 0.625r +r0 = 0.55r +max = 20 +min = -20 +fill_color = red +<rules> +<rule> +condition = 1 +value = eval(-var(cnv_minus)) +</rule> +</rules> +</plot> + +<plot> +show = conf(show_cnv) +type = histogram +r1 = 0.775r +r0 = 0.725r +min = 0 + +<axes> +<axis> +spacing = 10 +</axis> +</axes> + +<rules> +<rule> +condition = !var(cnv_tot) +show = no +</rule> +<rule> +condition = 1 +value = eval(var(cnv_tot)) +fill_color = eval(lc var(cnv_type)) +</rule> +</rules> + +</plot> + +<plot> +show = conf(show_cnv_copy_number) +type = histogram +r1 = 0.525r +r0 = 0.40r +min = -2 +max = 2 +<axes> +<axis> +position = 0 +color = black +</axis> +<axis> +spacing = 0.5 +y1 = 0 +color = lred +</axis> +<axis> +spacing = 0.5 +y0 = 0 +color = lblue +</axis> +</axes> +<rules> +<rule> +condition = !var(cnv_top_n) +show = no +</rule> +<rule> +condition = 1 +value = eval(var(cnv_top_avg)) +fill_color = eval(lc var(cnv_top_type)) +</rule> +</rules> +</plot> + +</plots> + +<image> +<<include etc/image.conf>> +</image> +<<include etc/housekeeping.conf>> +<<include etc/colors_fonts_patterns.conf>> +<<include ideogram.conf>> +#<<include ticks.conf>> +max_points_per_track* = 50000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/cnv.type.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,32 @@ +<plot> +show = conf(show_cnv_types) +init_counter = cnv:0 +post_increment_counter = cnv:1 +type = scatter +r1 = eval(sprintf("%fr",conf(cnv_r0) - counter(cnv)*(conf(cnv_w)+conf(cnv_s)))) +r0 = eval(sprintf("%fr",conf(cnv_r0) - counter(cnv)*(conf(cnv_w)+conf(cnv_s)) - conf(cnv_w))) +min = 0 +max = 0 +color = eval(sprintf("cnv-%d",1+counter(cnv))) +<axes> +<axis> +position = 0 +</axis> +</axes> +<rules> +<rule> +condition = 1 +type = eval(sprintf("cnv_%s",(split(",",qq{conf(cnv_types)}))[counter(cnv)])) +flow = continue +</rule> +<rule> +condition = !var(var(type)) +show = no +</rule> +<rule> +condition = 1 +value = 0 +glyph_size = eval(remap_int(var(var(type)),1,10,10,30)) +</rule> +</rules> +</plot>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/cnv.type.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,32 @@ +<plot> +show = conf(show_sv_types) +init_counter = sv:0 +post_increment_counter = sv:1 +type = scatter +r1 = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s)))) +r0 = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s)) - conf(sv_w))) +min = 0 +max = 0 +color = eval(sprintf("dark2-8-qual-%d",1+counter(sv))) +<axes> +<axis> +position = 0 +</axis> +</axes> +<rules> +<rule> +condition = 1 +type = eval(sprintf("sv_%s",(split(",",qq{conf(sv_types)}))[counter(sv)])) +flow = continue +</rule> +<rule> +condition = !var(var(type)) +show = no +</rule> +<rule> +condition = 1 +value = 0 +glyph_size = eval(remap_int(var(var(type)),1,10,10,30)) +</rule> +</rules> +</plot>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/color.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,1 @@ +color = eval((counter(plot)%3) == 0 ? "blue" : (counter(plot)%3) == 1 ? "orange,red,dred" : "black")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/color.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,1 @@ +color = eval((counter(plot)%3) == 0 ? "blue" : (counter(plot)%3) == 1 ? "orange,red,dred" : "red")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/histogram.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,86 @@ +# this file defines the histograms about system inputs and outputs + +<plots> + +<plot> +type = histogram +<axes> +<axis> +# grey axis every 100 units +color = grey_a3 +spacing = 100 +thickness = 2p +</axis> +<axis> +# black axis every 100 units +color = black_a2 +spacing = 500 +thickness = 2p +</axis> +</axes> +z=0 +</plot> + + + +# datatrack type +type = histogram +thickness = 0p +color = black + +# radial position of the histogram +r0 = 1r+150p +r1 = 1.3r + +# value start and end of the drawn histogram +min = 0 +# the maximum should be the maximum of all primary inputs or final outputs +# i.e. max_value(max_value(total primary inputs), max_value(total finalgoods),max_value(total emission_X)) +max = 1246.0 + +<plot> +# Normal histogram for resources +file = ../data/histogram_data_resources.txt +fill_color = col_resources_a1 +z=100 +</plot> + +<plot> +# Normal histogram for final_goods +file = ../data/histogram_data_final_goods.txt +fill_color = col_final_goods_a1 +z=100 +</plot> + +<plot> +# Normal histogram for emission_0 +file = ../data/histogram_data_emission_0.txt +fill_color = col_emission_0_a1 +z=100 +</plot> + +<plot> +# text labels plot for normal or stacked histograms for resources, fd and emissions +type = text +color = black +file = ../data/histogram_labels.txt +#note: if label do not fit in the space r1-r0, they will not be drawn +r0 = 1.32r +r1 = 1.5r +label_parallel = yes +#show_links = no +#link_dims = 0p,2p,6p,2p,5p +#link_thickness = 2p +#link_color = black +#label_snuggle = yes +#max_snuggle_distance = 1r +#snuggle_tolerance = 0.25r +#snuggle_sampling = 2 +#snuggle_refine = yes +label_size = 20p +label_font = default +padding = 0p +rpadding = 0p +</plot> + +</plots>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/ideogram.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,14 @@ + +<ideogram> + +<spacing> + +default = 0.001r + +</spacing> + +<<include ideogram.position.conf>> +<<include ideogram.label.conf>> + +</ideogram> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/ideogram.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,21 @@ + +<ideogram> + +<spacing> + +default = 0.002r +break = 0.25r + +axis_break = yes +axis_break_style = 2 +axis_break_at_edge = yes + +<<include breaks.conf>> + +</spacing> + +<<include ideogram.position.conf>> +<<include ideogram.label.conf>> + +</ideogram> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/ideogram.label.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,19 @@ + +show_label = yes +label_font = default +label_radius = dims(image,radius)-35p +label_with_tag = yes +label_size = 24 +label_parallel = no +label_case = lower + +# you can format the label by using properties +# of the ideogram, accessible with var(PROPERTY): +# +# chr, chr_with_tag, chrlength, display_idx, end, idx, +# label, length, reverse, scale, size, start, tag + +label_format = eval(sprintf("%s%s",var(chr) =~ /hs[234]$/ ? " " : "",var(label))) +#label_format = eval(sprintf("chr%s",var(label))) +#label_format = eval(my $x = var(label); $x = "" if $x =~ /1/; $x ? sprintf("chr%s",$x) : "") +#label_format = eval(my $x = var(label); my ($num) = $x =~ /(\d+)/g; $num < 10 ? $x : "")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/ideogram.position.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,6 @@ +radius = 0.8r +thickness = 10p +fill = yes +fill_color = black +stroke_thickness = 1 +stroke_color = black
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/ideogram.position.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,6 @@ +radius = 0.85r +thickness = 10p +fill = yes +fill_color = black +stroke_thickness = 1 +stroke_color = black
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/library.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,31 @@ +<plot> +minsize = 5e6 +file = data/lib.eval(counter(library)).txt +<<include color.conf>> +<<include r0r1.conf>> +<rules> +<<include rule.type.conf>> +</rules> +</plot> + +<plot> +file = data/lib.eval(counter(library)).txt +<<include color.conf>> +<<include r0r1.conf>> +<rules> +<<include rule.type.conf>> +</rules> +</plot> + +<plot> +minsize = 5e6 +file = data/lib.eval(counter(library)).txt +<<include color.conf>> +<<include r0r1.conf>> +<rules> +<<include rule.type.conf>> +</rules> + +post_increment_counter = library:1 + +</plot>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/library.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,29 @@ +<plot> +file = data/lib.eval(counter(library)).txt +<<include color.conf>> +<<include r0r1.conf>> +<rules> +<<include rule.type.conf>> +</rules> +</plot> + +<plot> +file = data/lib.eval(counter(library)).txt +<<include color.conf>> +<<include r0r1.conf>> +<rules> +<<include rule.type.conf>> +</rules> +</plot> + +<plot> +file = data/lib.eval(counter(library)).txt +<<include color.conf>> +<<include r0r1.conf>> +<rules> +<<include rule.type.conf>> +</rules> + +post_increment_counter = library:1 + +</plot>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/r0r1.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,2 @@ +r1 = eval(sprintf("%fr",conf(track_r0)-7*conf(sv_w)-6*conf(sv_s)-conf(track_s)-counter(x)*(conf(track_w)+conf(track_s)))) +r0 = eval(sprintf("%fr",conf(track_r0)-7*conf(sv_w)-6*conf(sv_s)-conf(track_s)-counter(x)*(conf(track_w)+conf(track_s))-conf(track_w)))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/r0r1.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,2 @@ +r1 = eval(sprintf("%fr",((counter(plot)%3==2)?-conf(tw):0) + ((counter(plot)%3==0)?conf(tws):0) + conf(t0) - counter(library)*(conf(tw)+conf(ts)))) +r0 = eval(sprintf("%fr",((counter(plot)%3==2)?-conf(tws):0) + ((counter(plot)%3==0)?+conf(tw):0) + conf(t0) - counter(library)*(conf(tw)+conf(ts)) - conf(tw)))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/rule.snp.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,4 @@ +<rule> +condition = var(type) ne "snp" +show = no +</rule>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/rule.type.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,26 @@ +<rule> +condition = (counter(plot)%3) == 0 && var(type) eq "ins" +show = yes +</rule> + +<rule> +condition = (counter(plot)%3) == 1 && var(type) eq "snp" && var(class) eq "missense_mutation" +z = 10 +show = yes +</rule> + +<rule> +condition = (counter(plot)%3) == 1 && var(type) eq "snp" && var(class) eq "all" +color = grey +show = yes +</rule> + +<rule> +condition = (counter(plot)%3) == 2 && var(type) eq "del" +show = yes +</rule> +<rule> +condition = 1 +show = no +</rule> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/rule.type.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,21 @@ +<rule> +condition = var(class) ne "all" +show = no +</rule> +<rule> +condition = (counter(plot)%3) == 0 && var(type) eq "ins" +show = yes +</rule> +<rule> +condition = (counter(plot)%3) == 1 && var(type) eq "snp" +show = yes +</rule> +<rule> +condition = (counter(plot)%3) == 2 && var(type) eq "del" +show = yes +</rule> +<rule> +condition = 1 +show = no +</rule> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/sv.type.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,32 @@ +<plot> +show = conf(show_sv_types) +init_counter = sv:0 +post_increment_counter = sv:1 +type = scatter +r1 = eval(sprintf("%fr",conf(track_r0) - counter(x)*(conf(track_w)+conf(track_s)) - counter(sv)*(conf(sv_w)+conf(sv_s)))) +r0 = eval(sprintf("%fr",conf(track_r0) - counter(x)*(conf(track_w)+conf(track_s)) - counter(sv)*(conf(sv_w)+conf(sv_s)) - conf(sv_w))) +min = 0 +max = 0 +color = eval(sprintf("sv-%d",1+counter(sv))) +<axes> +<axis> +position = 0 +</axis> +</axes> +<rules> +<rule> +condition = 1 +type = eval(sprintf("sv_%s",(split(",",qq{conf(sv_types)}))[counter(sv)])) +flow = continue +</rule> +<rule> +condition = !var(var(type)) +show = no +</rule> +<rule> +condition = 1 +value = 0 +glyph_size = eval(remap_int(var(var(type)),1,10,10,30)) +</rule> +</rules> +</plot>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/sv.type.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,32 @@ +<plot> +show = conf(show_sv_types) +init_counter = sv:0 +post_increment_counter = sv:1 +type = scatter +r1 = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s)))) +r0 = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s)) - conf(sv_w))) +min = 0 +max = 0 +color = eval(sprintf("sv-%d",1+counter(sv))) +<axes> +<axis> +position = 0 +</axis> +</axes> +<rules> +<rule> +condition = 1 +type = eval(sprintf("sv_%s",(split(",",qq{conf(sv_types)}))[counter(sv)])) +flow = continue +</rule> +<rule> +condition = !var(var(type)) +show = no +</rule> +<rule> +condition = 1 +value = 0 +glyph_size = eval(remap_int(var(var(type)),1,10,10,30)) +</rule> +</rules> +</plot>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/ticks.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,40 @@ + +show_ticks = yes +show_tick_labels = yes +#show_grid = yes + +<ticks> +radius = dims(ideogram,radius_outer) +color = black +thickness = 2p + +grid_start = 0.2r +grid_end = 0.999r +grid_color = lgrey +grid_thickness = 1p + +<tick> +spacing = 1u +size = 6p +</tick> + +<tick> +show = no +spacing = 10u +size = 10p +grid = yes +grid_color = vlgrey +</tick> + +<tick> +show = no +grid = yes +spacing = 20u +size = 15p +show_label = yes +label_size = 20p +label_offset = 10p +format = %d +</tick> + +</ticks>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/ticks.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,39 @@ + +show_ticks = yes +show_tick_labels = yes +show_grid = yes + +<ticks> +radius = dims(ideogram,radius_outer) +multiplier = 1e-6 +color = black +thickness = 2p + +grid_start = 0.2r +grid_end = 0.999r +grid_color = lgrey +grid_thickness = 1p + +<tick> +spacing = 5u +size = 6p +</tick> + +<tick> +spacing = 10u +size = 10p +grid = yes +grid_color = vlgrey +</tick> + +<tick> +grid = yes +spacing = 20u +size = 15p +show_label = yes +label_size = 20p +label_offset = 10p +format = %d +</tick> + +</ticks>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/track.counter.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,2 @@ +init_counter = x:0 +post_increment_counter = x:1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/track.counter.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,2 @@ +init_counter = track:1 +post_increment_counter = track:1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/white.bin.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,4 @@ +extend_bin = no +color = white_a4 +stroke_thickness = 1 +stroke_type = bin
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/etc/white.bin.conf~ Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,4 @@ +extend_bin = no +color = white +stroke_thickness = 1 +stroke_type = bin
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oncocircos.xml Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,77 @@ +<tool id="oncocircos" name="Oncocircos" version="0.69"> + + <description> + creates a genome-centric visualization of SNV and CNV Data + </description> + + <requirements> + <requirement type="package" version="0.69">circos_perl_environment</requirement> + <requirement type="package" version="0.69">circos</requirement> + </requirements> + + + <command error_checking="aggressive"> + + mkdir data; + mkdir circos; + mkdir circos/data; + mkdir circos/etc; + + cp $__tool_directory__/etc/* circos/etc/; + + mkdir etc; + + ln -s $input_maf data/snv.txt; + ln -s $input_seg data/cnv.txt; + cat $__tool_directory__/parse.conf + + #if $advancedOptions.filter_snvs != 1: + | sed 's/^SNV_FILTER$/sv = yes/g' + | sed 's/^SNV_FILTER_NUM$/sv_num = $advancedOptions.filter_snvs/g' + #else: + | sed 's/^SNV_FILTER$/sv = no/g' + | sed 's/^SNV_FILTER_NUM$//g' + #end if + + #if $advancedOptions.chromosome != "": + | sed 's/^CHR$/chr = $advancedOptions.chromosome/g' + #else: + | sed 's/^CHR$//g' + #end if + + | sed "s#^ROOT#root = \$(pwd)#g" + | sed 's#^CNV$#cnv = data/cnv.txt#g' + | sed 's#^SNV$#sv = data/snv.txt#g' + | sed 's#^MART#mart = $biomart#g' + | sed 's#^CIRCOS#circos = circos/data#g' + + > ./etc/parse.conf; + + perl $__tool_directory__/bin/parse --conf ./etc/parse.conf | perl $__tool_directory__/bin/make.circos.data --conf ./etc/parse.conf; + + circos --conf ./circos/etc/circos.conf; + + cp circos.png $png; + cp circos.svg $svg; + cp ./etc/parse.conf $tmp; + + </command> + + <inputs> + <param type="data" format="maf" name="input_maf" label="Cohort Wide MAF File"/> + <param type="data" format="segs" name="input_seg" label="Cohort Wide SEGS File"/> + <param type="data" format="" name="biomart" label="Biomart File"/> + <section name="advancedOptions"> + <param type="integer" name="filter_snvs" + min="1" value="1" max="100" + label="Filter genes with a cohort wide snv tally below this value"/> + <param type="text" name="chromosome" value="" + label="Restrict plot to the following chromosome"/> + </section> + </inputs> + <outputs> + <data format="png" name="png" /> + <data format="svg" name="svg" /> + <data format="txt" name="tmp" /> + </outputs> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parse.conf Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,72 @@ +<filter> +SNV_FILTER +SNV_FILTER_NUM +CHR +</filter> + +<files> +ROOT +CNV +SNV +MART +CIRCOS +</files> + +<fields> +<cnv> +key = sample,chr +0 = sample +1 = chr +2 = start +3 = end +5 = avg +6 = category:lc +</cnv> + +<sv> +key = id,sample +4 = chr +5 = start +6 = end +8 = type:lc +15 = sample +47 = id +53 = aa +</sv> + +<genes> +key = chr +0 = id +2 = end +3 = start +4 = chr +5 = name +</genes> +</fields> + +<cnv> +filter = yes +<types> +amp = 20 +gain = 15 +neut = 0 +hetd = 10 +homd = 5 +hlamp = 0 +</types> +</cnv> + +<sv> +filter = yes +top_damage_only = yes +<types> +nonsense_mutation = 35 +frame_shift_del = 30 +frame_shift_ins = 25 +in_frame_del = 20 +in_frame_ins = 15 +splice_site = 10 +nonstop_mutation = 5 +missense_mutation = 1 +</types> +</sv> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Sep 12 16:23:26 2016 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="circos_perl_environment" version="0.69"> + <repository changeset_revision="a6a59681930e" name="package_circos_0_69" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="circos" version="0.69"> + <repository changeset_revision="a6a59681930e" name="package_circos_0_69" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>