Christopher Fields > BioPerl-1.6.901 > Bio::FeatureIO::ptt



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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 "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"


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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.

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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)
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