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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:

   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)