Raw content of Bio::Tools::GFF
<![CDATA[# $Id: GFF.pm,v 1.26 2002/11/24 21:35:40 jason Exp $
#
# BioPerl module for Bio::Tools::GFF
#
# Cared for by the Bioperl core team
#
# Copyright Matthew Pocock
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser
=head1 SYNOPSIS
use Bio::Tools::GFF;
# specify input via -fh or -file
my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);
my $feature;
# loop over the input stream
while($feature = $gffio->next_feature()) {
# do something with feature
}
$gffio->close();
# you can also obtain a GFF parser as a SeqAnalasisParserI in
# HT analysis pipelines (see Bio::SeqAnalysisParserI and
# Bio::Factory::SeqAnalysisParserFactory)
my $factory = Bio::Factory::SeqAnalysisParserFactory->new();
my $parser = $factory->get_parser(-input => \*STDIN, -method => "gff");
while($feature = $parser->next_feature()) {
# do something with feature
}
=head1 DESCRIPTION
This class provides a simple GFF parser and writer. In the sense of a
SeqAnalysisParser, it parses an input file or stream into SeqFeatureI
objects, but is not in any way specific to a particular analysis
program and the output that program produces.
That is, if you can get your analysis program spit out GFF, here is
your result parser.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Matthew Pocock
Email mrp@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::GFF;
use vars qw(@ISA);
use strict;
use Bio::Root::IO;
use Bio::SeqAnalysisParserI;
use Bio::SeqFeature::Generic;
@ISA = qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
=head2 new
Title : new
Usage :
Function: Creates a new instance. Recognized named parameters are -file, -fh,
and -gff_version.
Returns : a new object
Args : names parameters
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($gff_version) = $self->_rearrange([qw(GFF_VERSION)],@args);
# initialize IO
$self->_initialize_io(@args);
$gff_version ||= 2;
if(($gff_version != 1) && ($gff_version != 2)) {
$self->throw("Can't build a GFF object with the unknown version ".
$gff_version);
}
$self->gff_version($gff_version);
return $self;
}
=head2 next_feature
Title : next_feature
Usage : $seqfeature = $gffio->next_feature();
Function: Returns the next feature available in the input file or stream, or
undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
Args : none
=cut
sub next_feature {
my ($self) = @_;
my $gff_string;
# be graceful about empty lines or comments, and make sure we return undef
# if the input's consumed
while(($gff_string = $self->_readline()) && defined($gff_string)) {
next if($gff_string =~ /^\#/ || $gff_string =~ /^\s*$/ ||
$gff_string =~ /^\/\//);
last;
}
return undef unless $gff_string;
my $feat = Bio::SeqFeature::Generic->new();
$self->from_gff_string($feat, $gff_string);
return $feat;
}
=head2 from_gff_string
Title : from_gff_string
Usage : $gff->from_gff_string($feature, $gff_string);
Function: Sets properties of a SeqFeatureI object from a GFF-formatted
string. Interpretation of the string depends on the version
that has been specified at initialization.
This method is used by next_feature(). It actually dispatches to
one of the version-specific (private) methods.
Example :
Returns : void
Args : A Bio::SeqFeatureI implementing object to be initialized
The GFF-formatted string to initialize it from
=cut
sub from_gff_string {
my ($self, $feat, $gff_string) = @_;
if($self->gff_version() == 1) {
$self->_from_gff1_string($feat, $gff_string);
} else {
$self->_from_gff2_string($feat, $gff_string);
}
}
=head2 _from_gff1_string
Title : _from_gff1_string
Usage :
Function:
Example :
Returns : void
Args : A Bio::SeqFeatureI implementing object to be initialized
The GFF-formatted string to initialize it from
=cut
sub _from_gff1_string {
my ($gff, $feat, $string) = @_;
chomp $string;
my ($seqname, $source, $primary, $start, $end, $score, $strand, $frame, @group) = split(/\t/, $string);
if ( !defined $frame ) {
$feat->throw("[$string] does not look like GFF to me");
}
$frame = 0 unless( $frame =~ /^\d+$/);
$feat->seq_id($seqname);
$feat->source_tag($source);
$feat->primary_tag($primary);
$feat->start($start);
$feat->end($end);
$feat->frame($frame);
if ( $score eq '.' ) {
#$feat->score(undef);
} else {
$feat->score($score);
}
if ( $strand eq '-' ) { $feat->strand(-1); }
if ( $strand eq '+' ) { $feat->strand(1); }
if ( $strand eq '.' ) { $feat->strand(0); }
foreach my $g ( @group ) {
if ( $g =~ /(\S+)=(\S+)/ ) {
my $tag = $1;
my $value = $2;
$feat->add_tag_value($1, $2);
} else {
$feat->add_tag_value('group', $g);
}
}
}
=head2 _from_gff2_string
Title : _from_gff2_string
Usage :
Function:
Example :
Returns : void
Args : A Bio::SeqFeatureI implementing object to be initialized
The GFF2-formatted string to initialize it from
=cut
sub _from_gff2_string {
my ($gff, $feat, $string) = @_;
chomp($string);
# according to the Sanger website, GFF2 should be single-tab separated elements, and the
# free-text at the end should contain text-translated tab symbols but no "real" tabs,
# so splitting on \t is safe, and $attribs gets the entire attributes field to be parsed later
my ($seqname, $source, $primary, $start, $end, $score, $strand, $frame, @attribs) = split(/\t+/, $string);
my $attribs = join '', @attribs; # just in case the rule against tab characters has been broken
if ( !defined $frame ) {
$feat->throw("[$string] does not look like GFF2 to me");
}
$feat->seq_id($seqname);
$feat->source_tag($source);
$feat->primary_tag($primary);
$feat->start($start);
$feat->end($end);
$feat->frame($frame);
if ( $score eq '.' ) {
#$feat->score(undef);
} else {
$feat->score($score);
}
if ( $strand eq '-' ) { $feat->strand(-1); }
if ( $strand eq '+' ) { $feat->strand(1); }
if ( $strand eq '.' ) { $feat->strand(0); }
# <Begin Inefficient Code from Mark Wilkinson>
# this routine is necessay to allow the presence of semicolons in
# quoted text Semicolons are the delimiting character for new
# tag/value attributes. it is more or less a "state" machine, with
# the "quoted" flag going up and down as we pass thorugh quotes to
# distinguish free-text semicolon and hash symbols from GFF control
# characters
my $flag = 0; # this could be changed to a bit and just be twiddled
my @parsed;
# run through each character one at a time and check it
# NOTE: changed to foreach loop which is more efficient in perl
# --jasons
foreach my $a ( split //, $attribs ) {
# flag up on entering quoted text, down on leaving it
if( $a eq '"') { $flag = ( $flag == 0 ) ? 1:0 }
elsif( $a eq ';' && $flag ) { $a = "INSERT_SEMICOLON_HERE"}
elsif( $a eq '#' && ! $flag ) { last }
push @parsed, $a;
}
$attribs = join "", @parsed; # rejoin into a single string
# <End Inefficient Code>
# Please feel free to fix this and make it more "perlish"
my @key_vals = split /;/, $attribs; # attributes are semicolon-delimited
foreach my $pair ( @key_vals ) {
# replace semicolons that were removed from free-text above.
$pair =~ s/INSERT_SEMICOLON_HERE/;/g;
# separate the key from the value
my ($blank, $key, $values) = split /^\s*([\w\d]+)\s/, $pair;
if( defined $values ) {
my @values;
# free text is quoted, so match each free-text block
# and remove it from the $values string
while ($values =~ s/"(.*?)"//){
# and push it on to the list of values (tags may have
# more than one value... and the value may be undef)
push @values, $1;
}
# and what is left over should be space-separated
# non-free-text values
my @othervals = split /\s+/, $values;
foreach my $othervalue(@othervals){
# get rid of any empty strings which might
# result from the split
if (CORE::length($othervalue) > 0) {push @values, $othervalue}
}
foreach my $value(@values){
$feat->add_tag_value($key, $value);
}
}
}
}
=head2 write_feature
Title : write_feature
Usage : $gffio->write_feature($feature);
Function: Writes the specified SeqFeatureI object in GFF format to the stream
associated with this instance.
Returns : none
Args : An array of Bio::SeqFeatureI implementing objects to be serialized
=cut
sub write_feature {
my ($self, @features) = @_;
foreach my $feature ( @features ) {
$self->_print($self->gff_string($feature)."\n");
}
}
=head2 gff_string
Title : gff_string
Usage : $gffstr = $gffio->gff_string($feature);
Function: Obtain the GFF-formatted representation of a SeqFeatureI object.
The formatting depends on the version specified at initialization.
This method is used by write_feature(). It actually dispatches to
one of the version-specific (private) methods.
Example :
Returns : A GFF-formatted string representation of the SeqFeature
Args : A Bio::SeqFeatureI implementing object to be GFF-stringified
=cut
sub gff_string{
my ($self, $feature) = @_;
if($self->gff_version() == 1) {
return $self->_gff1_string($feature);
} else {
return $self->_gff2_string($feature);
}
}
=head2 _gff1_string
Title : _gff1_string
Usage : $gffstr = $gffio->_gff1_string
Function:
Example :
Returns : A GFF1-formatted string representation of the SeqFeature
Args : A Bio::SeqFeatureI implementing object to be GFF-stringified
=cut
sub _gff1_string{
my ($gff, $feat) = @_;
my ($str,$score,$frame,$name,$strand);
if( $feat->can('score') ) {
$score = $feat->score();
}
$score = '.' unless defined $score;
if( $feat->can('frame') ) {
$frame = $feat->frame();
}
$frame = '.' unless defined $frame;
$strand = $feat->strand();
if(! $strand) {
$strand = ".";
} elsif( $strand == 1 ) {
$strand = '+';
} elsif ( $feat->strand == -1 ) {
$strand = '-';
}
if( $feat->can('seqname') ) {
$name = $feat->seq_id();
$name ||= 'SEQ';
} else {
$name = 'SEQ';
}
$str = join("\t",
$name,
$feat->source_tag(),
$feat->primary_tag(),
$feat->start(),
$feat->end(),
$score,
$strand,
$frame);
foreach my $tag ( $feat->all_tags ) {
foreach my $value ( $feat->each_tag_value($tag) ) {
$str .= " $tag=$value";
}
}
return $str;
}
=head2 _gff2_string
Title : _gff2_string
Usage : $gffstr = $gffio->_gff2_string
Function:
Example :
Returns : A GFF2-formatted string representation of the SeqFeature
Args : A Bio::SeqFeatureI implementing object to be GFF2-stringified
=cut
sub _gff2_string{
my ($gff, $feat) = @_;
my ($str,$score,$frame,$name,$strand);
if( $feat->can('score') ) {
$score = $feat->score();
}
$score = '.' unless defined $score;
if( $feat->can('frame') ) {
$frame = $feat->frame();
}
$frame = '.' unless defined $frame;
$strand = $feat->strand();
if(! $strand) {
$strand = ".";
} elsif( $strand == 1 ) {
$strand = '+';
} elsif ( $feat->strand == -1 ) {
$strand = '-';
}
if( $feat->can('seqname') ) {
$name = $feat->seq_id();
$name ||= 'SEQ';
} else {
$name = 'SEQ';
}
$str = join("\t",
$name,
$feat->source_tag(),
$feat->primary_tag(),
$feat->start(),
$feat->end(),
$score,
$strand,
$frame);
# the routine below is the only modification I made to the original
# ->gff_string routine (above) as on November 17th, 2000, the
# Sanger webpage describing GFF2 format reads: "From version 2
# onwards, the attribute field must have a tag value structure
# following the syntax used within objects in a .ace file,
# flattened onto one line by semicolon separators. Tags must be
# standard identifiers ([A-Za-z][A-Za-z0-9_]*). Free text values
# must be quoted with double quotes".
# MW
my $valuestr;
my @all_tags = $feat->all_tags;
if (@all_tags) { # only play this game if it is worth playing...
$str .= "\t"; # my interpretation of the GFF2
# specification suggests the need
# for this additional TAB character...??
foreach my $tag ( @all_tags ) {
my $valuestr; # a string which will hold one or more values
# for this tag, with quoted free text and
# space-separated individual values.
foreach my $value ( $feat->each_tag_value($tag) ) {
if ($value =~ /[^A-Za-z0-9_]/){
$value =~ s/\t/\\t/g; # substitute tab and newline
# characters
$value =~ s/\n/\\n/g; # to their UNIX equivalents
$value = '"' . $value . '" '} # if the value contains
# anything other than valid
# tag/value characters, then
# quote it
$value = "\"\"" unless defined $value;
# if it is completely empty,
# then just make empty double
# quotes
$valuestr .= $value . " "; # with a trailing space in case
# there are multiple values
# for this tag (allowed in GFF2 and .ace format)
}
$str .= "$tag $valuestr ; "; # semicolon delimited with no '=' sign
}
chop $str; chop $str # remove the trailing semicolon and space
}
return $str;
}
=head2 gff_version
Title : _gff_version
Usage : $gffversion = $gffio->gff_version
Function:
Example :
Returns : The GFF version this parser will accept and emit.
Args : none
=cut
sub gff_version {
my ($self, $value) = @_;
if(defined $value && (($value == 1) || ($value == 2))) {
$self->{'GFF_VERSION'} = $value;
}
return $self->{'GFF_VERSION'};
}
# Make filehandles
=head2 newFh
Title : newFh
Usage : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format')
$feature = <$fh>; # read a feature object
print $fh $feature ; # write a feature object
Returns : filehandle tied to the Bio::Tools::GFF class
Args :
=cut
sub newFh {
my $class = shift;
return unless my $self = $class->new(@_);
return $self->fh;
}
=head2 fh
Title : fh
Usage : $obj->fh
Function:
Example : $fh = $obj->fh; # make a tied filehandle
$feature = <$fh>; # read a feature object
print $fh $feature; # write a feature object
Returns : filehandle tied to Bio::Tools::GFF class
Args : none
=cut
sub fh {
my $self = shift;
my $class = ref($self) || $self;
my $s = Symbol::gensym;
tie $$s,$class,$self;
return $s;
}
sub DESTROY {
my $self = shift;
$self->close();
}
sub TIEHANDLE {
my ($class,$val) = @_;
return bless {'gffio' => $val}, $class;
}
sub READLINE {
my $self = shift;
return $self->{'gffio'}->next_feature() unless wantarray;
my (@list, $obj);
push @list, $obj while $obj = $self->{'gffio'}->next_feature();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'gffio'}->write_feature(@_);
}
1;
]]>