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#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE__;
####################################################################
#
# Required:
#
# --GO_annots <string> GO assignments to genes.
#
# --gene_factors_file <string> gene factors file
#
# --factor <string> the gene factor defining the genes of interest.
#
# --GO_id <string> GO ID to examine.
#
# --fpkm_matrix <string> FPKM matrix file.
#
# Optional:
#
# --output_prefix <string> output prefix (default: 'factor,GO_id')
#
# --samples <string> samples description file (for heatmaps)
#
####################################################################
__EOUSAGE__
;
my $GO_annots_file;
my $gene_factors_file;
my $factor;
my $GO_id;
my $fpkm_matrix;
my $output_prefix;
my $samples_file;
&GetOptions ( 'h' => \$help_flag,
'GO_annots=s' => \$GO_annots_file,
'gene_factors_file=s' => \$gene_factors_file,
'factor=s' => \$factor,
'GO_id=s' => \$GO_id,
'fpkm_matrix=s' => \$fpkm_matrix,
'output_prefix=s' => \$output_prefix,
'samples=s' => \$samples_file,
);
if ($help_flag) {
die $usage;
}
unless ($GO_annots_file && $gene_factors_file && $factor && $GO_id && $fpkm_matrix) {
die $usage;
}
unless ($output_prefix) {
$output_prefix = join(",", $factor, $GO_id);
}
main: {
my %genes = &get_genes_assigned_to_factor($gene_factors_file, $factor);
my %genes_with_GO = &get_subset_of_genes_with_GO_id($GO_annots_file, $GO_id, \%genes);
my $fpkm_outfile = "$output_prefix.fpkm";
open (my $ofh, ">$fpkm_outfile") or die "Error, cannot write to $fpkm_outfile";
open (my $fh, $fpkm_matrix) or die "Error, cannot open file $fpkm_matrix";
my $header = <$fh>;
print $ofh $header;
my %genes_want = %genes_with_GO;
while (<$fh>) {
my $line = $_;
my @x = split(/\t/);
my $acc = $x[0];
if ($genes_with_GO{$acc}) {
print $ofh $line;
delete $genes_want{$acc};
}
}
close $ofh;
if (%genes_want) {
use Data::Dumper;
die "Error, didn't find fpkm matrix rows for genes: " . Dumper(\%genes_want);
}
## generate a heatmap
my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m $fpkm_outfile --log2 --heatmap --gene_dist euclidean --sample_dist euclidean";
if ($samples_file) {
$cmd .= " -s $samples_file ";
}
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, CMD: $cmd died with ret $ret";
}
exit(0);
}
####
sub get_genes_assigned_to_factor {
my ($gene_factors_file, $factor_want) = @_;
my %genes;
open (my $fh, $gene_factors_file) or die $!;
while (<$fh>) {
chomp;
my ($gene, $factor) = split(/\t/);
if ($factor eq $factor_want) {
$genes{$gene} = 1;
}
}
close $fh;
unless (%genes) {
confess "Error, no genes found assigned to factor [$factor_want] in file $gene_factors_file";
}
return(%genes);
}
####
sub get_subset_of_genes_with_GO_id {
my ($GO_annots_file, $GO_id, $genes_href) = @_;
my %genes_with_GO;
open (my $fh, $GO_annots_file) or die $!;
while (<$fh>) {
chomp;
my ($gene, $go_annots) = split(/\t/);
if ($genes_href->{$gene} && $go_annots =~ /$GO_id/) {
$genes_with_GO{$gene} = 1;
}
}
close $fh;
unless (%genes_with_GO) {
confess "Error, no genes found with GO: [$GO_id] in file: $GO_annots_file for genes: " . Dumper($genes_href);
}
return(%genes_with_GO);
}
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