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

       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 -

	   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

	    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
	    eg.	"2491..3423  + 310 24217063  metF  LB002 - COG0685E
	   5,10-methylenetetrahydrofolate reductase"

   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.			- General discussion	- About	the mailing lists

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

       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

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)

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


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