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|
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my $usage = "\n\nusage: $0 quant.sf gene_to_trans_map_file.txt\n\n\n";
my $quant_sf = $ARGV[0] or die $usage;
my $gene_to_trans_map_file = $ARGV[1] or die $usage;
main: {
my %trans_to_gene_info;
{
open (my $fh, $gene_to_trans_map_file) or die "Error, cannot open file $gene_to_trans_map_file";
while (<$fh>) {
unless (/\w/) { next; }
chomp;
my ($gene, $trans, @rest) = split(/\s+/);
unless ($gene && $trans) {
die "Error, cannot extract gene & trans relationship from line $_ of file $gene_to_trans_map_file";
}
$trans_to_gene_info{$trans} = $gene;
}
close $fh;
}
open (my $fh, $quant_sf) or die "Error, cannot open file $quant_sf";
my $header = <$fh>;
chomp $header;
my %field_index;
my @fields = split(/\t/, $header);
{
for (my $i = 0; $i <= $#fields; $i++) {
my $field = $fields[$i];
$field_index{$field} = $i;
}
}
my %gene_data;
while (<$fh>) {
chomp;
# quant.sf format:
#
#Name Length EffectiveLength TPM NumReads
#TRINITY_DN10_c0_g1_i1 334 67.2849 3125.31 7
#TRINITY_DN11_c0_g1_i1 319 55.1277 0 0
#TRINITY_DN12_c0_g1_i1 244 244 1231.18 10
#TRINITY_DN17_c0_g1_i1 229 229 393.549 3
#TRINITY_DN18_c0_g1_i1 633 360.371 593.619 7.12107
my @x = split(/\t/);
my $trans_id = $x[ $field_index{Name} ];
my $tpm = $x[ $field_index{TPM} ];
my $length = $x[ $field_index{Length} ];
my $eff_length = $x[ $field_index{EffectiveLength} ];
my $est_counts = $x[ $field_index{NumReads} ];
my $gene = $trans_to_gene_info{$trans_id} or die "Error, cannot find gene identifier for transcript [$trans_id] ";
push (@{$gene_data{$gene}}, { Name => $trans_id,
TPM => $tpm,
Length => $length,
EffectiveLength => $eff_length,
NumReads => $est_counts,
});
}
close $fh;
## Output gene summaries:
print $header . "\n";
foreach my $gene (keys %gene_data) {
my @trans_structs = @{$gene_data{$gene}};
my @trans_ids;
my $sum_counts = 0;
my $sum_tpm = 0;
my $counts_per_len_sum = 0;
my $counts_per_eff_len_sum = 0;
my $sum_lengths = 0;
my $sum_eff_lengths = 0;
my $num_trans = scalar(@trans_structs);
foreach my $struct (@trans_structs) {
#print Dumper($struct);
my $trans_id = $struct->{Name};
my $tpm = $struct->{TPM};
my $length = $struct->{Length};
my $eff_length = $struct->{EffectiveLength};
my $est_counts = $struct->{NumReads};
unless ($eff_length > 0) {
$eff_length = 1; # cannot have zero length feature!
}
unless ($length > 0 && $eff_length > 0) {
die "Error, length: $length, eff_length: $eff_length" . Dumper($struct);
}
$sum_lengths += $length;
$sum_eff_lengths += $eff_length;
$counts_per_len_sum += $est_counts/$length;
$counts_per_eff_len_sum += $est_counts/$eff_length;
$sum_counts += $est_counts;
$sum_tpm += $tpm;
}
my $gene_length = $sum_lengths / $num_trans;
my $gene_eff_length = $sum_eff_lengths / $num_trans;
if ($sum_counts) {
# set lengths as weighted by expression of isoforms.
eval {
$gene_length = $sum_counts / $counts_per_len_sum;
$gene_eff_length = $sum_counts / $counts_per_eff_len_sum;
};
if ($@) {
print STDERR "$@\n" . Dumper(\@trans_structs);
die;
}
}
my %gene_info = ( Name => $gene,
TPM => sprintf("%.2f", $sum_tpm),
Length => sprintf("%.2f", $gene_length),
EffectiveLength => sprintf("%.2f", $gene_eff_length),
NumReads => sprintf("%.2f", $sum_counts),
);
my @vals;
foreach my $field (@fields) {
my $result = $gene_info{$field};
unless (defined $result) {
$result = "NA";
}
push (@vals, $result);
}
print join("\t", @vals) . "\n";
}
exit(0);
}
|
