Provided by: libbio-featureio-perl_1.6.905-2_all bug


       Bio::FeatureIO::ptt - read/write features in PTT format


        # read features
        my $fin = Bio::FeatureIO->new(-file=>'genes.ptt', -format=>'ptt');
        my @cds;
        while (my $f = $fin->next_feature) {
          push @cds, $f if $f->strand > 0;

        # write features (NOT IMPLEMENTED)
        my $fout = Bio::FeatureIO->new(-fh=>\*STDOUT, -format=>'ptt');
        for my $f (@cds) {


       The PTT file format is a table of protein features.  It is used mainly by NCBI who produce
       PTT files for all their published genomes found in <>.  It
       has the following format:

       Line 1
           Description of sequence to which the features belong
            eg. "Leptospira interrogans chromosome II, complete sequence - 0..358943"

           It is usually equivalent to the DEFINITION line of a Genbank file, with the length of
           the sequence appended. It is unclear why "0" is used as a starting range, it should be

       Line 2
           Number of feature lines in the table
            eg. "367 proteins"

       Line 3
           Column headers, tab separated
            eg. "Location  Strand  Length  PID Gene  Synonym Code  COG Product"

            Location : "begin..end" span of feature
            Strand   : "+" or "-"
            Length   : number of amino acids excluding the stop codon
            PID      : analogous to Genbank /db_xref="GI:xxxxxxxxx"
            Gene     : analogous to Genbank /gene="xxxx"
            Synonym  : analogous to Genbank /locus_tag="xxxx"
            Synonym  : analogous to Genbank /locus_tag="xxxx"
            COG      : CDD COG code with COG letter categories appended
            Product  : analogous to Genbank /product="xxxx"

       Line 4 onwards
           Feature lines, nine columns, tab separated, "-" used for empty fields
            eg. "2491..3423  + 310 24217063  metF  LB002 - COG0685E
           5,10-methylenetetrahydrofolate reductase"


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AUTHOR - Torsten Seemann

       Email torsten.seemann AT


       Based on and by Allen Day.


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : _initialize
        Function: Reading? parses the header of the input

        Title   : next_feature
        Usage   : $io->next_feature()
        Function: read the next feature from the PTT file
        Example :
        Args    :
        Returns : Bio::SeqFeatureI object

   write_feature (NOT IMPLEMENTED)
        Title   : write_feature
        Usage   : $io->write_feature($feature)
        Function: write a Bio::SeqFeatureI object in PTT format
        Example :
        Args    : Bio::SeqFeatureI object
        Returns :

        Title   : description
        Usage   : $obj->description($newval)
        Function: set/get the PTT file description for/from line one
        Example :
        Returns : value of description (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

        Title   : protein_count
        Usage   : $obj->protein_count($newval)
        Function: set/get the PTT protein count for/from line two
        Example :
        Args    : on set, new value (a scalar or undef, optional)
        Returns : value of protein_count (a scalar)