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|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#####################################################
#
# --DE_results <string> DE_results file
#
# --gene_trans_map <string> gene-trans-map file
#
#####################################################
__EOUSAGE__
;
my $help_flag;
my $DE_results_file;
my $gene_trans_map_file;
&GetOptions ( 'h' => \$help_flag,
'DE_results=s' => \$DE_results_file,
'gene_trans_map=s' => \$gene_trans_map_file,
);
if ($help_flag) {
die $usage;
}
unless ($DE_results_file && $gene_trans_map_file) {
die $usage;
}
main: {
my %trans_to_gene = &parse_gene_trans_map($gene_trans_map_file);
my %gene_to_up_down_trans;
open(my $fh, $DE_results_file) or die "Error, cannot open file $DE_results_file";
my $header = <$fh>;
chomp $header;
my @header_fields = split(/\t/, $header);
my %header_col_index;
while (<$fh>) {
chomp;
my @fields = split(/\t/);
unless (%header_col_index) {
if (scalar(@fields) == scalar(@header_fields) + 1) {
unshift(@header_fields, "");
}
}
my $trans_name = $fields[0];
my $gene_name = $trans_to_gene{$trans_name} or die "Error, cannot find gene_id corresponding to trans [$trans_name] ";
my $struct = { name => $trans_name };
for (my $i = 1; $i <= $#fields; $i++) {
my $col_header = $header_fields[$i];
my $val = $fields[$i];
$struct->{$col_header} = $val;
}
my $fdr = $struct->{FDR};
unless (defined $fdr) {
die "Error, no FDR set for @fields";
}
unless ($fdr <= 0.05) { next; }
my $logFC = $struct->{logFC};
unless (defined $logFC) {
die "Error, no logFC set for @fields";
}
unless (abs($logFC) >= 1) { # 2-fold min
next;
}
if ($logFC > 0) {
push (@{$gene_to_up_down_trans{$gene_name}->{UP}}, $struct);
}
else {
push(@{$gene_to_up_down_trans{$gene_name}->{DOWN}}, $struct);
}
}
close $fh;
foreach my $gene_name (keys %gene_to_up_down_trans) {
my @up;
if (exists $gene_to_up_down_trans{$gene_name}->{UP}) {
@up = @{$gene_to_up_down_trans{$gene_name}->{UP}};
}
my @down;
if (exists $gene_to_up_down_trans{$gene_name}->{DOWN}) {
@down = @{$gene_to_up_down_trans{$gene_name}->{DOWN}};
}
if (@up && @down) {
## got DTU candidate:
print "# $gene_name\n";
foreach my $up_entry (@up) {
print join("\t", "UP", &struct_to_string($up_entry)) . "\n";
}
foreach my $down_entry (@down) {
print join("\t", "DOWN", &struct_to_string($down_entry)) . "\n";
}
print "\n"; # spacer
}
}
exit(0);
}
####
sub parse_gene_trans_map {
my ($gene_trans_map_file) = @_;
my %trans_to_gene;
open(my $fh, $gene_trans_map_file) or die "Error, cannot open file $gene_trans_map_file";
while (<$fh>) {
chomp;
unless (/\w/) { next; }
if (/^\#/) { next; }
my ($gene, $trans) = split(/\t/);
$trans_to_gene{$trans} = $gene;
}
return(%trans_to_gene);
}
####
sub struct_to_string {
my ($struct) = @_;
my $ret_text = join("\t", $struct->{name}, $struct->{sampleA}, $struct->{sampleB},
$struct->{logFC}, $struct->{FDR});
return($ret_text);
}
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