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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
my $usage = "usage: $0 seqs.fasta\n\n";
my $file = $ARGV[0] or die $usage;
my %seq_to_header;
my $fasta_reader = new Fasta_reader($file);
while (my $seq_obj = $fasta_reader->next()) {
my $sequence = $seq_obj->get_sequence();
my $header = $seq_obj->get_header();
if (exists $seq_to_header{$sequence}) {
push (@{$seq_to_header{$sequence}}, $header);
}
else {
$seq_to_header{$sequence} = [$header];
}
}
my $found_dups_flag = 0;
foreach my $sequence (keys %seq_to_header) {
my @dups = @{$seq_to_header{$sequence}};
if (scalar(@dups) > 1) {
print "# Repeated seqs found:\n";
print join("\n", @dups) . "\n";
print "$sequence\n\n";
$found_dups_flag = 1;
}
}
exit($found_dups_flag);
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