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createIdeogramFromBED-1.pl
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createIdeogramFromBED-1.pl
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#!/usr/bin/perl
#
# INGLÊS/ENGLISH
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# http://www.gnu.org/copyleft/gpl.html
#
#
# PORTUGUÊS/PORTUGUESE
# Este programa é distribuído na expectativa de ser útil aos seus
# usuários, porém NÃO TEM NENHUMA GARANTIA, EXPLÍCITAS OU IMPLÍCITAS,
# COMERCIAIS OU DE ATENDIMENTO A UMA DETERMINADA FINALIDADE. Consulte
# a Licença Pública Geral GNU para maiores detalhes.
# http://www.gnu.org/copyleft/gpl.html
#
# Copyright (C) 2012 Universidade de São Paulo
#
# Universidade de São Paulo
# Laboratório de Biologia do Desenvolvimento de Abelhas
# Núcleo de Bioinformática (LBDA-BioInfo)
#
# Daniel Guariz Pinheiro
# dgpinheiro@gmail.com
# http://zulu.fmrp.usp.br/bioinfo
#
# $Id$
=head1 NAME
=head1 SYNOPSIS
=head1 ABSTRACT
=head1 DESCRIPTION
Arguments:
-h/--help Help
-l/--level Log level [Default: FATAL]
OFF
FATAL
ERROR
WARN
INFO
DEBUG
TRACE
ALL
=head1 AUTHOR
Daniel Guariz Pinheiro E<lt>dgpinheiro@gmail.comE<gt>
Copyright (c) 2012 Universidade de São Paulo
=head1 LICENSE
GNU General Public License
http://www.gnu.org/copyleft/gpl.html
=cut
use strict;
use warnings;
use Readonly;
use Getopt::Long;
use File::Basename;
use vars qw/$LOGGER/;
INIT {
use Log::Log4perl qw/:easy/;
Log::Log4perl->easy_init($FATAL);
$LOGGER = Log::Log4perl->get_logger($0);
}
my ($level, $gfile, $infile, $outbase, $title);
Usage("Too few arguments") if $#ARGV < 0;
GetOptions( "h|?|help" => sub { &Usage(); },
"l|level=s"=> \$level,
"g|genome=s"=>\$gfile,
"i|infile=s"=>\$infile,
"o|outbase=s"=>\$outbase,
"t|title=s"=>\$title
) or &Usage();
use File::Basename;
$title||=basename($infile);
if ($level) {
my %LEVEL = (
'OFF' =>$OFF,
'FATAL' =>$FATAL,
'ERROR' =>$ERROR,
'WARN' =>$WARN,
'INFO' =>$INFO,
'DEBUG' =>$DEBUG,
'TRACE' =>$TRACE,
'ALL' =>$ALL);
$LOGGER->logdie("Wrong log level ($level). Choose one of: ".join(', ', keys %LEVEL)) unless (exists $LEVEL{$level});
Log::Log4perl->easy_init($LEVEL{$level});
}
$outbase||="./ideogram";
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-file=>$gfile, -format=>'FASTA');
use R;
use Cwd;
&R::initR("--silent");
&R::library("RSPerl");
&R::eval('suppressMessages(library(package="GenomicRanges"))');
&R::eval('suppressMessages(library(package="ggbio"))');
&R::eval('suppressMessages(library(package="scales"))');
unless (-e "$gfile.RData") {
my %glength;
while (my $seq = $in->next_seq()) {
$glength{$seq->display_id()} = $seq->length();
}
# foreach my $s (keys %glength) {
# print $s,"\t",$glength{$s},"\n";
# }
my @kglength = sort { &compn($a, $b) } keys %glength;
#print STDERR join(";",@kglength),"\n";
&R::eval(
'gr <<- GRanges(seqnames = Rle(c('.join(', ', map { '"'.$_.'"' } @kglength ).')),
ranges = IRanges(1, end = c('.join(', ', @glength{@kglength}).'),names=c('.join(', ', map { '"'.$_.'"' } @kglength ).'))
)'
);
&R::eval('seqlengths(gr)[c('.join(', ', map { '"'.$_.'"' } @kglength ).')] <<- c('.join(', ', @glength{@kglength}).')');
&R::eval('save(list = ls(all=TRUE,envir=globalenv()), file = "'."$gfile.RData".'")');
}
else {
&R::eval('load(file="'."$gfile.RData".'",envir = globalenv())');
}
#&R::eval('print(head(gr))');
my %input;
my %ref;
#open(IN, "<", $infile) or $LOGGER->logdie($!);
#while(<IN>) {
# chomp;
# my ($chr, $start, $end, $peakname, $score, $strand) = split(/\t/, $_);
# my ($region) = $peakname=~/^([^\/]+)/;
# $LOGGER->logdie("Missing region ($peakname)") unless ($region);
# if ($region ne 'promoter') {
# $region= 'other';
# }
# $input{ $chr }->{basename($peakname)} = {'start' => $start, 'end'=> $end, 'score'=>$score, 'strand'=>(($strand eq ".") ? "*" : $strand), 'region'=>$region};
# $ref{$chr} = undef;
#}
#close(IN);
#foreach my $k (sort { &compn($a, $b) } keys %ref) {
# print STDERR $k,"\n";
#}
#my @refs = sort { &compn($a, $b) } keys %ref;
#&R::eval(
# 'grref <<- GRanges(seqnames = Rle(as.character(seqnames(gr[c('.join(', ', map { '"'.$_.'"' } @refs).')]))),
# ranges = ranges( gr[c('.join(', ', map { '"'.$_.'"' } @refs).')] ),
# '.((scalar(@refs)) ? 'chrnames = as.factor(c('.join(', ', map { '"'.$_.'"' } @refs).'))' : 'chrnames = as.factor(as.character(seqnames(gr[c('.join(', ', map { '"'.$_.'"' } @refs).')])))' ).'
# )'
# );
&R::eval(
'grref <<- GRanges(seqnames = Rle( names(gr[grep("^GroupUn", names(gr),invert=TRUE)]) ),
ranges = ranges(gr[grep("^GroupUn", names(gr),invert=TRUE)])
)');
&R::eval('isCircular(grref) <- rep(FALSE, length(names(grref)))');
&R::eval('isCircular(grref)[which(names(isCircular(grref))=="MT")] <- TRUE');
&R::eval('seqlengths(grref)[names(seqlengths(grref))] <<- seqlengths(gr)[names(seqlengths(grref))]');
my %result;
#foreach my $chr (@refs) {
# foreach my $peakname (keys %{ $input{$chr} }) {
# push(@{ $result{'seq_id'} }, $chr );
# push(@{ $result{'start'} }, $input{$chr}->{$peakname}->{'start'} );
# push(@{ $result{'end'} }, $input{$chr}->{$peakname}->{'end'} );
# push(@{ $result{'strand'} }, $input{$chr}->{$peakname}->{'strand'} );
# push(@{ $result{'score'} }, $input{$chr}->{$peakname}->{'score'} );
# push(@{ $result{'region'} }, $input{$chr}->{$peakname}->{'region'} );
# push(@{ $result{'ID'} }, $peakname);
## print ">>>>".$input{$chr}->{$peakname}->{'score'}."\n";
## print ">>>>".$input{$chr}->{$peakname}->{'strand'}."\n";
# }
#}
#
#close(IN);
#
#
#&R::eval(
# 'grmap <<- GRanges(seqnames = Rle(c('.join(', ', map { '"'.$_.'"' } @{ $result{'seq_id'} } ).')),
# ranges = IRanges(c('.join(', ', @{ $result{'start'} }).'), end = c('.join(', ', @{ $result{'end'} }).')),
# strand =Rle(strand(c('.join(', ', map { '"'.$_.'"' } @{ $result{'strand'} } ).'))),
# score =Rle(c('.join(', ', @{ $result{'score'} } ).')),
# Region =Rle(c('.join(', ', map { '"'.$_.'"' } @{ $result{'region'} } ).')),
# ID=Rle(c('.join(', ', map { '"'.$_.'"' } @{ $result{'ID'} } ).')),
# seqinfo=seqinfo(grref)
# )'
# );
&R::eval('inbed <<- read.delim(file="'.$infile.'", header=FALSE, stringsAsFactors=FALSE)');
#&R::eval('inbed <<- rbind(inbed,cbind(names(grref),1,1,"other/REF",500,"."))');
#&R::eval('inbed <<- rbind(inbed,cbind(c("Group1"),9893408,29893400,"other/REF",250,"."))');
&R::eval('inbed$V2 <<- as.numeric(inbed$V2)');
&R::eval('inbed$V3 <<- as.numeric(inbed$V3)');
&R::eval('inbed$V5 <<- as.numeric(inbed$V5)');
&R::eval('region <<- gsub("/.*$", "", inbed$V4) ');
&R::eval('region[ grep("promoter", region) ] <<- "promoter" ');
&R::eval('region[ grep("promoter", region, invert=TRUE) ] <<- "other" ');
&R::eval('grmap <<- GRanges(seqnames = Rle(inbed$V1),
ranges = IRanges(start = inbed$V2, end = inbed$V3),
strand =Rle(strand( gsub(".", "*", inbed$V6) )),
score =Rle(inbed$V5),
Region =Rle(region),
ID=Rle( gsub("^.[^/]+/", "", inbed$V4) ),
seqinfo=seqinfo(grref)
)'
);
my $pwd = getcwd();
my $pngfile1 = $outbase.'_karyogram.png';
my $pngfile2 = $outbase.'_circle1.png';
my $pngfile3 = $outbase.'_circle2.png';
&R::eval('seqlengths(grmap)[names(seqlengths(grmap))] <<- seqlengths(gr)[names(seqlengths(grmap))]');
&R::eval('setwd("'.$pwd.'")');
&R::eval('seqlevels(grref, force=TRUE) <<- seqlevels(grref)[order(as.numeric(gsub("Group|MT","",seqlevels(grref))))]');
&R::eval('seqlevels(grmap, force=TRUE) <<- seqlevels(grmap)[order(as.numeric(gsub("Group|MT","",seqlevels(grmap))))]');
&R::eval('png(filename="'.$pngfile1.'", bg="white", res=300, width=3000, height=3000)
p<<- autoplot(seqinfo(grmap)) + layout_karyogram(grmap, geom="rect", ylim=c(10,NULL), aes(ymin=0, ymax=score, xmin=start, xmax=end, fill=Region, colour=Region))+ggtitle("'.$title.'")+scale_color_discrete(na.value = "brown")+xlab("Chromosome Size (bp)")+ylab("ChIP-Seq Peak Signal")+theme_classic()+theme_tracks_sunset()+theme(strip.text.y = element_text(angle = 360), axis.ticks = element_line(colour = "grey40", size = 0.25), axis.text.y = element_text(size=5,angle=0,hjust=1,vjust=0,face="plain") )+scale_fill_manual( values = c("promoter" = "blue", "other"= "gray40"))+scale_colour_manual( values = c("promoter" = "blue", "other"= "gray40"))+scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x)))
plot(p)
dev.off()');
#+theme_classic()+theme_tracks_sunset()+theme(strip.text.y = element_text(angle = 360), axis.ticks = element_line(colour = "grey40", size = 0.25), axis.text.y = element_text(size=5,angle=0,hjust=1,vjust=0,face="plain") )+scale_fill_manual( values = c("promoter" = "blue", "other"= "gray40"))+scale_colour_manual( values = c("promoter" = "blue", "other"= "gray40"))
#+scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x)))
#+scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x)), limits=c(0,500))
&R::eval("grmapplus <<- grmap[which(as.character(strand(grmap))=='+')]");
&R::eval("grmapminus <<- grmap[which(as.character(strand(grmap))=='-')]");
&R::eval("grmapnone <<- grmap[which(as.character(strand(grmap))=='*')]");
&R::eval('grmapnonepromo <<- grmapnone[which(as.character(elementMetadata(grmapnone)$Region)=="promoter")]');
&R::eval('grmapnoneother <<- grmapnone[which(as.character(elementMetadata(grmapnone)$Region)=="other")]');
&R::eval('save(list = ls(all=TRUE,envir=globalenv()), file = "'."test.RData".'")');
#&R::eval('
#png(filename="'.$pngfile2.'", bg="white", res=300, width=3000, height=3000)
#p <<- ggplot() + layout_circle(grref, geom = "text", aes(label = seqnames), vjust = 0, radius = 40, trackWidth = 2) + layout_circle(grref, geom = "ideo", fill = "azure2", radius = 30,trackWidth = 4)
#p <<- p + layout_circle(grref, geom = "scale", size = 2, radius = 35, trackWidth = 2)
#if ( dim(elementMetadata(grmapplus))[1] > 0 ) {
# p <<- p + layout_circle(grmapplus, geom = "rect", color = "steelblue", radius = 26, trackWidth = 3)
#}
#if ( dim(elementMetadata(grmapminus))[1] > 0 ) {
# p <<- p + layout_circle(grmapminus, geom = "rect", color = "gold", radius = 23, trackWidth = 3)
#}
#if ( dim(elementMetadata(grmapnone))[1] > 0 ) {
# p <<- p + layout_circle(grmapnone, geom = "rect", color = "seagreen", radius = 23, trackWidth = 3)
#}
#
#p <<- p+ggtitle("'.$title.'")
#plot(p)
#dev.off()');
&R::eval('
png(filename="'.$pngfile3.'", bg="white", res=300, width=3000, height=3000)
p <<- ggplot() + layout_circle(grref, geom = "ideo", fill = "azure2", radius = 30,trackWidth = 4)+layout_circle(grref, geom = "text", aes(label = seqnames), vjust = 0, radius = 40, trackWidth = 2)
p <<- p + layout_circle(grref, geom = "scale", size = 2, radius = 35, trackWidth = 2)
if ( dim(elementMetadata(grmapnoneother))[1] > 0 ) {
p <<- p + layout_circle(grmapnoneother, geom = "bar", aes(y=score,fill=Region,colour=Region), colour="gray40", fill="gray40", radius = 30, trackWidth = -10)
}
if ( dim(elementMetadata(grmapnonepromo))[1] > 0 ) {
p <<- p + layout_circle(grmapnonepromo, geom = "bar", aes(y=score,fill=Region,colour=Region), colour="blue", fill="blue", radius = 30, trackWidth = -10)
}
p <<- p + ggtitle("'.$title.'")+scale_fill_manual( values = c("promoter" = "blue", "other"= "gray40") )
plot(p)
dev.off()');
# Subroutines
sub compn {
my ($x, $y) = @_;
my ($xn,$yn);
if ($x=~/^Group/) {
($xn)=$x=~/(\d+)$/;
if ($x=~/^GroupUn/) {
$xn+=1000;
}
} elsif ($x=~/^MT/) {
$xn=0;
} else {
$LOGGER->logdie("Error: $x");
}
if ($y=~/Group/) {
($yn)=$y=~/(\d+)$/;
if ($y=~/^GroupUn/) {
$yn+=1000;
}
} elsif ($y=~/^MT/) {
$yn=0;
} else {
$LOGGER->logdie("Error: $y");
}
return ($xn <=> $yn);
}
sub Usage {
my ($msg) = @_;
Readonly my $USAGE => <<"END_USAGE";
Daniel Guariz Pinheiro (dgpinheiro\@gmail.com)
(c)2012 Universidade de São Paulo
Usage
$0 [-h/--help] [-l/--level <LEVEL>]
Argument(s)
-h --help Help
-l --level Log level [Default: FATAL]
-g --genome Genome multi-fasta file
-i --infile Input file (bed coordinates)
-o --outbase Output base filenames
-t --title Plot title [Default: <Input file basename>]
END_USAGE
print STDERR "\nERR: $msg\n\n" if $msg;
print STDERR qq[$0 ] . q[$Revision$] . qq[\n];
print STDERR $USAGE;
exit(1);
}