run_multicorrelate_bed.pl

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

my $dir;
my $debug; my $verbose; my $simulate;
my $cmd; my $ret;
my $self = bless {};
use File::Basename;
# ($name,$path,$suffix) = fileparse($inputfile,@suffixlist);
# $name = fileparse($fullname,@suffixlist);
# $basename = basename($fullname,@suffixlist);
# $dirname  = dirname($fullname);
my $tag = 'multicorrelate_bed';
my $no_stats;
my $no_plots;
my $suffix = '.bed.gz';
my $bedtools = 'bedtools2';
my $sep = 'versus';

# See copy of make-matrix.py at the bottom of this script
my $make_matrix = "$ENV{HOME}/bin/make-matrix.py";
my $datamash = "$ENV{HOME}/datamash/bin/datamash";


GetOptions(
           'i|d|dir:s'            => \$dir,
           'tag:s'                => \$tag,
           'suffix:s'             => \$suffix,
           'bedtools:s'           => \$bedtools,
           'datamash:s'           => \$datamash,
           'no_plots'             => \$no_plots,
           'debug'                => \$debug,
           'no_stats'             => \$no_stats,
           'verbose'              => \$verbose,
           'simulate'             => \$simulate,
          );

$cmd = "find -L $dir -name \"*$suffix\"";
print STDERR "# $cmd\n";
$ret = `$cmd`; chomp $ret;
my @beds = split("\n",$ret);
my $num_samples = scalar(@beds);
foreach my $inputfile1 (@beds) {
  foreach my $inputfile2 (@beds) {
    $self->bedtools_jaccard($inputfile1,$inputfile2);
  }
}
my $basename = basename($dir);
my $outpairwise = "$dir/$basename.$tag.samples.$num_samples.txt";
# Pairwise Jaccard
$cmd = "find $dir -name \"*$sep*.jaccard.txt\" " . q{ | grep jaccard | xargs grep "" | perl -lne 's|}.$dir."/".q{||g; print' | perl -pi -e "s/\.}.$sep.q{\./\t/" | perl -pi -e "s/.jaccard.txt:/\t/" } . " > $outpairwise";
print STDERR "# $cmd\n";
$ret = `$cmd`; chomp $ret;

# Matrix of Jaccard Statistics
my $outmatrix = "$dir/$basename.$tag.samples.$num_samples.mat";
# . q{ | awk '$1 ~ /^f/ && $2 ~ /^f/' } . " 
$cmd = "awk 'NF==3' $outpairwise | python $make_matrix > $outmatrix";
print STDERR "# $cmd\n";
$ret = `$cmd`; chomp $ret;

my $outlabels = "$dir/$basename.$tag.samples.$num_samples.labels.txt";
$cmd = "cut -f 1 $outmatrix > $outlabels";
print STDERR "# $cmd\n";
$ret = `$cmd`; chomp $ret;

exit(0) if ($no_plots);

use Statistics::R;
my $R = Statistics::R->new();
$R->startR;

# matrixfile="basename.multicorrelate_bed.samples.14.mat"
# labelsfile="basename.multicorrelate_bed.samples.14.labels.txt"

$cmd = "matrixfile=\"$outmatrix\""; $R->send($cmd);
$cmd = "labelsfile=\"$outlabels\""; $R->send($cmd);
my $pcafile = "$dir/$basename.$tag.samples.$num_samples.pca.pdf";
$cmd = "pdf(\"$pcafile\",width=10,height=5)"; $R->send($cmd); print $R->read . "\n";

$cmd = <<EOF;
x <- read.table(matrixfile)
labels <- read.table(labelsfile)

library(ggplot2)
library(RColorBrewer)
blues <- colorRampPalette(c('dark blue', 'light blue'))
greens <- colorRampPalette(c('dark green', 'light green'))
reds <- colorRampPalette(c('pink', 'dark red'))
  
ngroups <- length(unique(labels))
pca <- princomp(x)

qplot(pca\$scores[,1], pca\$scores[,2], color=labels[,1],     geom="point", size=1) + scale_color_manual(values = c(blues(4), greens(5), reds(5)))

dev.off()

EOF
$R->send($cmd);

print STDERR "pcafile:\n";
print "$pcafile\n";

$cmd = "matrixfile=\"$outmatrix\""; $R->send($cmd);

my $heatmapfile = "$dir/$basename.$tag.samples.$num_samples.heatmap.pdf";
$cmd = "pdf(\"$heatmapfile\",width=10,height=10)"; $R->send($cmd); print $R->read . "\n";

$cmd = <<EOF;

x <- read.table(matrixfile)

library(gplots)
library(RColorBrewer)
jaccard_table <- x[, -1]
jaccard_matrix <- as.matrix(jaccard_table)

heatmap.2(jaccard_matrix, col = brewer.pal(9,"Blues"), margins = c(14, 14), density.info = "none", lhei=c(2, 8), trace= "none")
dev.off()

EOF
$R->send($cmd);

$R->stopR();

print STDERR "heatmapfile:\n";
print "$heatmapfile\n";


$DB::single=1;1;

########################################

sub bedtools_jaccard {
  my $self       = shift;
  my $inputfile1 = shift;
  my $inputfile2 = shift;
  my ($name1,$path1,$suffix1) = fileparse($inputfile1,$suffix);
  my $root1 = $name1; $root1 =~ s/_S\d+_L00[1-8]_R[12]_001//;
  my ($name2,$path2,$suffix2) = fileparse($inputfile2,$suffix);
  my $root2 = $name2; $root2 =~ s/_S\d+_L00[1-8]_R[12]_001//;

  my $outpref = "$dir/$root1.$sep.$root2";
  my $outfile = "$outpref.jaccard.tsv";
  $cmd = "$bedtools jaccard -a $inputfile1 -b $inputfile2 > $outfile";
  print STDERR "# $cmd\n";
  $ret = `$cmd`; chomp $ret;
  $cmd = "cat $outfile | awk 'NR>1' | cut -f 3 > $outpref.jaccard.txt";
  print STDERR "# $cmd\n";
  $ret = `$cmd`; chomp $ret;

  return undef;
}

my $outfile = $path . $name . ".$tag.bed.gz";
$cmd = "bedtools2 genomecov -ibam $inputfile -bga | grep -w " . q{ '0$' } . " | gzip -c > $outfile";
print STDERR "# $cmd\n";
$ret = `$cmd`;

print STDERR "outfile\n";
print "$outfile\n";

unless ($no_stats) {
  my $statsfile = $path . $name . ".$tag.stats.txt";

  $cmd = "gunzip -c $outfile | " . q{ awk '{$5 = $3-$2; print $5}' }. " | $datamash --header-out count 1 sum 1 mean 1 median 1 min 1 max 1 sstdev 1 q1 1 q3 1 iqr 1 pskew 1 sskew 1 pkurt 1 skurt 1 dpo 1 jarque 1 ". q{ | perl -lne 's/field-1/} . $root . q{/g; print' } . "| $datamash transpose";
  print STDERR "# $cmd\n";
  $ret = `$cmd`;
  open STATS, ">$statsfile" or die $!;
  print STATS $ret;
  close STATS;
  print STDERR "statsfile\n";
  print "$statsfile\n";
}

$DB::single=1;1;
$DB::single=1;1;

# run_multicorrelate_bed.pl
#
# Cared for by Albert Vilella <[email protected]>
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

run_multicorrelate_bed.pl - DESCRIPTION 

=head1 SYNOPSIS

See Description

=head1 DESCRIPTION

Look for bed files in a directory and run bedtools jaccard
all-against-all. Produce a matrix for PCA and heatmap plotting

Dependencies:

bedtools version 2.+ - https://github.com/arq5x/bedtools2 [required]

datamash - https://www.gnu.org/software/datamash/download [optional]

R + library(ggplot2) +  library(gplots) + library(RColorBrewer) [optional]

Perl Options:

GetOptions(
           'i|d|dir:s'            => \$dir,
           'tag:s'                => \$tag,
           'suffix:s'             => \$suffix,
           'datamash:s'           => \$datamash,
           'debug'                => \$debug,
           'no_stats'             => \$no_stats,
           'verbose'              => \$verbose,
           'simulate'             => \$simulate,
          );


=head1 AUTHOR - Albert Vilella

Email [email protected]

Describe contact details here

=head1 CONTRIBUTORS

Additional contributors names and emails here

=cut

__DATA__
# make-matrix.py
#!/usr/bin/python env
import sys
import collections 

matrix = collections.defaultdict(dict)
for line in sys.stdin:
        fields = line.strip().split()
        matrix[fields[0]][fields[1]] = float(fields[2])

keys = sorted(matrix.keys())
sys.stdout.write("\t" + "\t".join(keys) + '\n')
for k in keys:
        sys.stdout.write(k)
        for j in keys:
                sys.stdout.write('\t' + str(matrix[k][j]))
        sys.stdout.write('\n')