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#!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "\n\n\tusage: $0 < list of audit.txt files from stdin \n\n\n";
my $MIN_SEQ_LEN = 1000;
my $total_genes = 0;
my $total_genes_reco = 0;
my $total_refseq_trans = 0;
my $total_iso_reco_count = 0;
my $total_extra = 0;
print join("\t", "gene_id", "reco_gene_flag", "num_refseqs", "num_FL_trin", "num_extra_trin") . "\n";
my $counter = 0;
while (<>) {
chomp;
my $dir = dirname($_);
$counter++;
my $gene_id = basename($dir);
my $trin_fasta_file = "$dir/trinity_out_dir.Trinity.fasta";
if (! -e $trin_fasta_file) {
print STDERR "ERROR: Cannot locate file: $trin_fasta_file\n";
next;
}
my $fasta_reader = new Fasta_reader($trin_fasta_file);
my %trin_seqs = $fasta_reader->retrieve_all_seqs_hash();
my %trin_lens = &get_seq_lens(%trin_seqs);
my $FL_reco_file = "$dir/FL.test.pslx.maps";
my %reco_refseq;
my %reco_trin_to_refseq = &parse_reco($FL_reco_file, \%reco_refseq);
my $num_FL_trin = scalar(keys %reco_trin_to_refseq);
my $refseqs_fa = "$dir/refseqs.fa";
my @refseq_accs = &get_accs($refseqs_fa);
my $num_refseqs = scalar(@refseq_accs);
my @failed_reco_refseqs;
foreach my $acc (@refseq_accs) {
unless ($reco_refseq{$acc}) {
push (@failed_reco_refseqs, $acc);
}
}
my $num_failed_reco_refseqs = scalar(@failed_reco_refseqs);
my @extra_trin_accs;
foreach my $trin_acc (keys %trin_seqs) {
if (! exists $reco_trin_to_refseq{$trin_acc}) {
if ($trin_lens{$trin_acc} >= $MIN_SEQ_LEN) {
push (@extra_trin_accs, $trin_acc);
}
}
}
my $num_extra_trin = scalar(@extra_trin_accs);
my $reco_gene_flag = ($num_failed_reco_refseqs == 0) ? "YES" : "NO";
print join("\t", $gene_id, $reco_gene_flag, $num_refseqs, $num_FL_trin, $num_extra_trin) . "\n";
$total_genes++;
if ($reco_gene_flag eq "YES") {
$total_genes_reco++;
}
$total_refseq_trans += $num_refseqs;
$total_iso_reco_count += $num_FL_trin;
$total_extra += $num_extra_trin;
}
if ($counter > 1) {
print "\n\n";
print join("\t", "Total_Genes", "Total_Genes_Reco", "Total_RefTrans", "Total_RefTransReco", "Total_extra_trans") . "\n";
print join("\t", $total_genes, $total_genes_reco, $total_refseq_trans, $total_iso_reco_count, $total_extra) . "\n";
}
exit(0);
####
sub get_accs {
my ($fasta_file) = @_;
my @accs;
open (my $fh, $fasta_file) or die $!;
while (<$fh>) {
if (/^>(\S+)/) {
push (@accs, $1);
}
}
return(@accs);
}
####
sub parse_reco {
my ($reco_file, $reco_refseq_href) = @_;
my %trin_to_reco_acc;
open (my $fh, $reco_file) or die $!;
while (<$fh>) {
chomp;
my ($trans_acc, $trinity_contigs) = split(/\t/);
my @trin_contigs = split(/,/, $trinity_contigs);
foreach my $trin (@trin_contigs) {
$trin_to_reco_acc{$trin}->{$trans_acc} = 1;
$reco_refseq_href->{$trans_acc} = 1;
}
}
close $fh;
return(%trin_to_reco_acc);
}
####
sub get_seq_lens {
my (%trin_seqs) = @_;
my %lens;
foreach my $acc (keys %trin_seqs) {
my $seq = $trin_seqs{$acc};
my $seqlen = length($seq);
$lens{$acc} = $seqlen;
}
return(%lens);
}
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