NAME

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

SYNOPSIS

        # 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) {
          $fout->write_feature($f);
        }

DESCRIPTION

       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 <ftp://ftp.ncbi.nih.gov/genomes/>.  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
           "1".

       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"

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         http://bugzilla.open-bio.org/

AUTHOR - Torsten Seemann

       Email torsten.seemann AT infotech.monash.edu.au

CONTRIBUTORS

       Based on bed.pm and gff.pm by Allen Day.

APPENDIX

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

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

   next_feature
        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 :

   description
        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)

   protein_count
        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)