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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
my $usage = "\n\n\tusage: $0 all_long_orfs.pep\n\n";
my $pep_file = $ARGV[0] or die $usage;
main: {
my %contig_to_longest_prot;
my $fasta_reader = new Fasta_reader($pep_file);
while (my $seq_obj = $fasta_reader->next()) {
my $header = $seq_obj->get_header();
my $sequence = $seq_obj->get_sequence();
my $len = length($sequence);
if ($header =~ / (\S+):\d+-\d+\([+-]\)/) {
my $contig = $1;
&store_entry(\%contig_to_longest_prot, $seq_obj, $len, $contig);
}
else {
die "Error, cannot parse header info: $header ";
}
}
foreach my $struct (values %contig_to_longest_prot) {
my $fa = $struct->{seq_obj}->get_FASTA_format();
print $fa;
}
exit(0);
}
####
sub store_entry {
my ($contig_to_longest_prot_href, $seq_obj, $len, $contig) = @_;
my $struct = $contig_to_longest_prot_href->{$contig};
if ( (! $struct) || $struct->{length} < $len) {
$struct = { seq_obj => $seq_obj,
length => $len,
};
$contig_to_longest_prot_href->{$contig} = $struct;
}
return;
}
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