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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);
use POSIX qw (ceil);
my $help_flag;
my $rsem_expr_file;
my $num_quintiles = 10;
my $feature_list_file;
my $min_fpkm = 0.5;
my $usage = <<_EOUSAGE_;
##############################################################################
#
# Required:
#
# --rsem_expr_file <string> gene or isoform.results file generated by RSEM
#
# --feature_list_file <string> file containing list of features (transcript or gene identifiers, corresponding to rsem_expr_file above
#
# Optional:
#
# --num_quintiles <int> default: 10
#
# --min_fpkm <float> default: 0.5 (features with lower expression estimates are not included in the expr quantiles)
#
##############################################################################
_EOUSAGE_
;
&GetOptions ( 'h' => \$help_flag,
'rsem_expr_file=s' => \$rsem_expr_file,
'num_quintiles=i' => \$num_quintiles,
'feature_list_file=s' => \$feature_list_file,
'min_fpkm=f' => \$min_fpkm,
);
if ($help_flag) {
die $usage;
}
unless($rsem_expr_file && $feature_list_file) {
die $usage;
}
main: {
my %feature_to_quintile = &compute_expression_quintile($rsem_expr_file, $num_quintiles);
my %seen;
my %quintile_to_count;
open (my $fh, $feature_list_file) or die "Error, cannot open file $feature_list_file";
while (<$fh>) {
chomp;
my $acc = $_;
if ($seen{$acc}) {
#print STDERR "WARNING: $acc already counted from list. Ignoring.\n";
next;
}
$seen{$acc} = 1;
my $quintile = $feature_to_quintile{$acc};
unless (defined $quintile) {
print STDERR "WARNING: $acc not assigned to expr quintile.\n";
next;
}
$quintile_to_count{$quintile}++;
}
close $fh;
foreach my $quintile (sort {$a<=>$b} keys %quintile_to_count) {
my $count = $quintile_to_count{$quintile};
print join("\t", $quintile, $count) . "\n";
}
exit(0);
}
####
sub compute_expression_quintile {
my ($rsem_expr_file, $num_quintiles) = @_;
my @entries;
open (my $fh, $rsem_expr_file) or die $!;
my $header = <$fh>;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $acc = $x[0];
my $fpkm = $x[6];
if ($fpkm >= $min_fpkm) {
push (@entries, { acc => $acc,
fpkm => $fpkm,
});
}
}
close $fh;
@entries = sort {$a->{fpkm}<=>$b->{fpkm}} @entries;
my $num_entries = scalar(@entries);
my %acc_to_quintile;
my $quintile_size = sprintf("%.1f", 100/$num_quintiles);
my $num_entries_per_quintile = $num_entries/$num_quintiles;
for (my $i = 0; $i <= $#entries; $i++) {
my $entry = $entries[$i];
my $quintile_num = ceil( ($i+1) / $num_entries_per_quintile);
my $acc = $entry->{acc};
$acc_to_quintile{$acc} = $quintile_num;
}
return(%acc_to_quintile);
}
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