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Bio::FeatureIO::ptt(3)User Contributed Perl DocumentatioBio::FeatureIO::ptt(3)

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)

perl v5.32.0			  2014-09-05		Bio::FeatureIO::ptt(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Torsten Seemann | CONTRIBUTORS | APPENDIX

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