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lib/Bio/BPWrapper/SeqManipulations.pm  view on Meta::CPAN

	    $seqobj->id($names{$id});
	    warn "$id replaced by $names{$id}\n";
	} else {
	    warn "$id not changed\n";
	}
	$out->write_seq($seqobj);
    }
}


sub update_longest_orf {
    while( my $seqobj  = $in->next_seq() ) {
	my $pep_string = $seqobj->translate( undef, undef, 0 )->seq();
	unless ($pep_string =~ /\*[A-Z]/) { # no internal stop; don't proceed
	    my $id = $seqobj->id();
	    $seqobj->id($id . "|+1");
	    $seqobj = &_trim_end_to_frame($seqobj);
	    $out->write_seq($seqobj);
#	    warn $seqobj->id, ": +1 ok\n";
	    next;
	}