Bio::FeatureIO::ptt(3pm)				User Contributed Perl Documentation				  Bio::FeatureIO::ptt(3pm)

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:

	 https://redmine.open-bio.org/projects/bioperl/

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)

perl v5.14.2							    2012-03-02						  Bio::FeatureIO::ptt(3pm)