Bio::FeatureIO ptt
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Summary
Bio::FeatureIO::ptt - read/write features in PTT format
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::Generic
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:
    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"
Methods
_initializeDescriptionCode
next_featureDescriptionCode
write_featureDescriptionCode
descriptionDescriptionCode
protein_countDescriptionCode
Methods description
_initializecode    nextTop
 Title   : _initialize
Function: Reading? parses the header of the input
Writing?
next_featurecodeprevnextTop
 Title   : next_feature
Usage : $io->next_feature()
Function: read the next feature from the PTT file
Example :
Args :
Returns : Bio::SeqFeatureI object
write_featurecodeprevnextTop
 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 :
descriptioncodeprevnextTop
 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_countcodeprevnextTop
 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
_initializedescriptionprevnextTop
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(); }
}
next_featuredescriptionprevnextTop
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 $feat;
}
write_featuredescriptionprevnextTop
sub write_feature {
  my($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();
}
descriptiondescriptionprevnextTop
sub description {
  my $self = shift;
  return $self->{'description'} = shift if @_;
  return $self->{'description'};
}
protein_countdescriptionprevnextTop
sub protein_count {
  my $self = shift;
  return $self->{'protein_count'} = shift if @_;
  return $self->{'protein_count'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHOR - Torsten SeemannTop
Email torsten.seemann AT infotech.monash.edu.au
CONTRIBUTORSTop
Based on bed.pm and gff.pm by Allen Day.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _