=pod =head1 NAME Bio::FeatureIO::ptt - read/write features in PTT format =head1 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); } =head1 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 L. It has the following format: =over 4 =item 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". =item Line 2 Number of feature lines in the table eg. "367 proteins" =item 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" =item 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" =back =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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: https://redmine.open-bio.org/projects/bioperl/ =head1 AUTHOR - Torsten Seemann Email torsten.seemann AT infotech.monash.edu.au =head1 CONTRIBUTORS Based on bed.pm and gff.pm by Allen Day. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::FeatureIO::ptt; use strict; use base qw(Bio::FeatureIO); use Bio::SeqFeature::Generic; # map tab-separated column number to field name our %NAME_OF = ( 0 => 'Location', 1 => 'Strand', 2 => 'Length', 3 => 'PID', 4 => 'Gene', 5 => 'Synonym', 6 => 'Code', 7 => 'COG', 8 => 'Product', ); our $NUM_COL = 9; =head2 _initialize Title : _initialize Function: Reading? parses the header of the input Writing? =cut sub _initialize { my($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(); } } =head2 next_feature Title : next_feature Usage : $io->next_feature() Function: read the next feature from the PTT file Example : Args : Returns : Bio::SeqFeatureI object =cut 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; } =head2 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 : =cut sub write_feature { shift->throw_not_implemented; } =head2 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) =cut sub description { my $self = shift; return $self->{'description'} = shift if @_; return $self->{'description'}; } =head2 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) =cut sub protein_count { my $self = shift; return $self->{'protein_count'} = shift if @_; return $self->{'protein_count'}; } 1;