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Revision 1.1 - (download) (as text) (annotate)
Mon Jan 17 01:27:44 2005 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2, Root-bobdev_news, merge-bobdev_news-1, caBIG-dataload-0, merge-trunktag-bobdev_news-1, merge-bodev_news-3, efrank-preMakefileToStandardMk, caBIG-00-00-00, merge-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
add start prediction code

# usage: extract_DNA_sequence_from_object_for_start_predictions < stream_of_ORF_objects > fasta_for_sims

$/ = "///\n";
while (defined($obj = <STDIN>))
{
    chomp $obj;
    if ($obj =~ /^(.*?)\/\//s)
    {
	$obj = $1;
    }

    foreach $kv (split(/\n/,$obj))
    {
	if ($kv =~ /^([^=]+)=(.*)$/)
	{
	    $key_value_pairs{$1} = $2;
	}
    }

    ($seq = $key_value_pairs{"SEQ"})   || die "missing SEQ";
    ($id  = $key_value_pairs{"ID"})   || die "missing ID";
    $seq =~ s/(TAA|TAG|TGA)$//;
    print ">$id\n$seq\n";
}

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