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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
use BHStats;
my $usage = "\n\nusage: $0 transcripts.fasta\n\n";
my $fasta_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($fasta_file);
my @all_seq_lengths;
my $number_transcripts = 0;
my $num_GC = 0;
my %component_to_longest_isoform;
my $tot_seq_len = 0;
my $missing_gene_ids_flag = 0;
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
$number_transcripts++;
my $comp_id = $acc;
if (! $missing_gene_ids_flag) {
if ($acc =~ /^(.*c\d+_g\d+)/) {
$comp_id = $1;
}
elsif ($acc =~ /^(.*comp\d+_c\d+)/) {
$comp_id = $1;
}
else {
print STDERR "Error, cannot decipher gene identifier from acc: $acc";
$missing_gene_ids_flag = 1;
}
}
my $sequence = $seq_obj->get_sequence();
my $seq_len = length($sequence);
$tot_seq_len += $seq_len;
if ( (! exists $component_to_longest_isoform{$comp_id})
||
$component_to_longest_isoform{$comp_id} < $seq_len) {
$component_to_longest_isoform{$comp_id} = $seq_len;
}
push (@all_seq_lengths, $seq_len);
while ($sequence =~ /[gc]/ig) {
$num_GC++;
}
}
print "\n\n";
print "################################\n";
print "## Counts of transcripts, etc.\n";
print "################################\n";
print "Total trinity 'genes':\t" . scalar(keys %component_to_longest_isoform) . "\n";
print "Total trinity transcripts:\t" . $number_transcripts . "\n";
my $pct_gc = sprintf("%.2f", $num_GC / $tot_seq_len * 100);
print "Percent GC: $pct_gc\n\n";
print "########################################\n";
print "Stats based on ALL transcript contigs:\n";
print "########################################\n\n";
&report_stats(@all_seq_lengths);
print "\n\n";
if ($missing_gene_ids_flag) {
print " - note: not reporting gene-based longest isoform info since couldn't parse Trinity accession info.\n";
}
else {
print "#####################################################\n";
print "## Stats based on ONLY LONGEST ISOFORM per 'GENE':\n";
print "#####################################################\n\n";
&report_stats(values %component_to_longest_isoform);
print "\n\n\n";
}
exit(0);
}
####
sub report_stats {
my (@seq_lengths) = @_;
@seq_lengths = reverse sort {$a<=>$b} @seq_lengths;
my $cum_seq_len = 0;
foreach my $len (@seq_lengths) {
$cum_seq_len += $len;
}
for (my $i = 10; $i <= 50; $i += 10) {
my $cum_len_needed = $cum_seq_len * $i/100;
my $N_val = &get_contigNvalue($cum_len_needed, \@seq_lengths);
print "\tContig N$i: $N_val\n";
}
print "\n";
my $median_len = &BHStats::median(@seq_lengths);
print "\tMedian contig length: $median_len\n";
my $avg_len = sprintf("%.2f", &BHStats::avg(@seq_lengths));
print "\tAverage contig: $avg_len\n";
print "\tTotal assembled bases: $cum_seq_len\n";
return;
}
sub get_contigNvalue {
my ($cum_len_needed, $seq_lengths_aref) = @_;
my $partial_sum_len = 0;
foreach my $len (@$seq_lengths_aref) {
$partial_sum_len += $len;
if ($partial_sum_len >= $cum_len_needed) {
return($len);
}
}
return -1; # shouldn't happen.
}
|
