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|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 EXPR.matrix Trinity.fasta\n\n";
my $matrix_file = $ARGV[0] or die $usage;
my $fasta_file = $ARGV[1] or die $usage;
my %trans_lengths;
{
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $sequence = $seq_obj->get_sequence();
my $seq_len = length($sequence);
$trans_lengths{$acc} = $seq_len;
}
}
open (my $fh, $matrix_file) or die $!;
my $header = <$fh>;
my @trans;
my $sum_expr = 0;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $acc = shift @x; # gene accession
my $max_expr = 0;
my $trans_sum_expr = 0;
while (@x) {
my $expr = shift @x;
$trans_sum_expr += $expr;
$sum_expr += $expr;
if ($expr > $max_expr) {
$max_expr = $expr;
}
}
my $seq_len = $trans_lengths{$acc} or die "Error, no seq length for acc: $acc";
push (@trans, { acc => $acc,
len => $seq_len,
sum_expr => $trans_sum_expr,
max_expr => $max_expr,
});
}
@trans = reverse sort { $a->{sum_expr} <=> $b->{sum_expr}
||
$a->{len} <=> $b->{len} } @trans;
## write output table
{
open (my $ofh, ">$matrix_file.E-inputs") or die $!;
print $ofh join("\t", "#acc", "length", "max_expr_over_samples", "sum_expr_over_samples") . "\n";
foreach my $t (@trans) {
print $ofh join("\t", $t->{acc}, $t->{len}, $t->{max_expr}, $t->{sum_expr}) . "\n";
}
close $ofh;
}
my %Estats_wanted = map { $_ => 1 } (1..100);
print "#E\tmin_expr\tE-N50\tnum_transcripts\n";
my $sum = 0;
my @captured;
while (@trans) {
my $t = shift @trans;
push (@captured, $t);
$sum += $t->{sum_expr};
my $pct = int($sum/$sum_expr * 100);
if ($Estats_wanted{$pct}) {
my $min_max_expr = &get_min_max(@captured);
delete($Estats_wanted{$pct});
my $N50 = &calc_N50(@captured);
my $num_trans = scalar(@captured);
print "E$pct\t$min_max_expr\t$N50\t$num_trans\n";
}
}
# ensure that we do E100
if (%Estats_wanted) {
if (exists $Estats_wanted{"100"}) {
my $min_max_expr = &get_min_max(@captured);
my $N50 = &calc_N50(@captured);
my $num_trans = scalar(@captured);
print "E100\t$min_max_expr\t$N50\t$num_trans\n";
}
}
exit(0);
####
sub get_min_max {
my @entries = @_;
my $min = $entries[0]->{max_expr};
foreach my $entry (@entries) {
if ($entry->{max_expr} < $min) {
$min = $entry->{max_expr};
}
}
return($min);
}
####
sub calc_N50 {
my @entries = @_;
@entries = reverse sort {$a->{len}<=>$b->{len}} @entries;
my $sum_len = 0;
foreach my $entry (@entries) {
$sum_len += $entry->{len};
}
my $loc_sum = 0;
foreach my $entry (@entries) {
$loc_sum += $entry->{len};
if ($loc_sum / $sum_len * 100 >= 50) {
return($entry->{len});
}
}
return(-1); # error
}
|
