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Summary

Bio::FeatureIO::ptt - read/write features in PTT format

Package variables

Included modules

Inherit

Bio::FeatureIO

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:
    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".
    Number of feature lines in the table
eg. "367 proteins"
    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"

    Feature lines, nine columns, tab separated, "-" used for empty fields
eg. "2491..3423 + 310 24217063 metF LB002 - COG0685E 5,10-methylenetetrahydrofolate reductase"

Methods

Methods description

 Title   : _initialize
 Function: Reading? parses the header of the input
           Writing?

 Title   : next_feature
 Usage   : $io->next_feature()
 Function: read the next feature from the PTT file
 Example : 
 Args    : 
 Returns : Bio::SeqFeatureI object

 Title   : write_feature
 Usage   : $io->write_feature($feature)
 Function: write a Bio::SeqFeature object in PTT format with no header
 Example : 
 Args    : Bio::SeqFeature 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)

Methods code

sub _initialize {

  my($self,%arg) = @_;

  $self->SUPER::_initialize(%arg);

  if ($self->mode eq 'r') {
    # Line 1
    my $desc = $self->_readline();
    chomp $desc;
    $self->description($desc);
    # Line 2
    my $line = $self->_readline();
    $line =~ m/^(\d+) proteins/ or $self->throw("Invalid protein count");
    $self->protein_count($1);
    # Line 3
    $self->_readline();
  }

}

sub next_feature {

  my $self = shift;
  $self->mode eq 'r' || return; # returns if can't read next_feature when we're in write mode
  
  my $line = $self->_readline() or return; # returns if end of file, no more features?
  chomp $line;
  my @col = split m/\t/, $line;
  @col==$NUM_COL or $self->throw("Too many columns for PTT line");

  $col[0] =~ m/(\d+)\.\.(\d+)/ or $self->throw("Invalid location (column 1)");
  my $feat = Bio::SeqFeature::Generic->new(-start=>$1, -end=>$2, -primary=>'CDS');
  $col[1] =~ m/^([+-])$/ or $self->throw("Invalid strand (column 2)");
  $feat->strand($1 eq '+' ? +1 : -1);
  for my $i (2 .. $NUM_COL-1) {
    $feat->add_tag_value($NAME_OF{$i}, $col[$i]) if $col[$i] ne '-';
  }
  return $feat;

}

sub write_feature {

  my($self,$feat) = @_;

  # Example, with header:
  # Location  Strand  Length  PID Gene  Synonym Code  COG Product
  # 190..255  + 21  16763391  thrL  STM0001 - - thr operon leader peptide

  $self->throw("Only Bio::SeqFeature::Generic or Bio::SeqFeature::Annotated objects are writeable") 
  unless ( $feat->isa('Bio::SeqFeature::Generic') || $feat->isa('Bio::SeqFeature::Annotated') );

  # Default
  my ($len,$pid,$gene,$synonym,$code,$cog,$product) = qw(- - - - - - -);

  my $start = $feat->start;
  my $end   = $feat->end;
  my $loc   = "$start..$end";

  my $strand = $feat->strand == 1 ? '+' : '-';

  $len = int(($end - $start)/3);

  $product = join ' ',$feat->get_tag_values("product")     if ($feat->has_tag("product"));
  $pid     = join ' ',$feat->get_tag_values("protein_id")  if ($feat->has_tag("protein_id"));
  $code    = join ' ',$feat->get_tag_values("codon_start") if ($feat->has_tag("codon_start"));

  $self->_print(join("\t",($loc,$strand,$len,$pid,$gene,$synonym,$code,$cog,$product)) . "\n");

  $self->write_feature($_) foreach $feat->get_SeqFeatures();

}

sub description {

  my $self = shift;
  return $self->{'description'} = shift if @_;
  return $self->{'description'};

}

sub protein_count {

  my $self = shift;
  return $self->{'protein_count'} = shift if @_;
  return $self->{'protein_count'};
}

1;

}

General documentation

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
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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.

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/

Email torsten.seemann AT infotech.monash.edu.au

Based on bed.pm and gff.pm by Allen Day.

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _