Raw content of Bio::Variation::IO::xml
<![CDATA[# $Id: xml.pm,v 1.12.2.1 2003/03/01 17:23:43 jason Exp $
# BioPerl module for Bio::Variation::IO::xml
#
# Cared for by Heikki Lehvaslaiho <Heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Variation::IO::xml - XML sequence variation input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::Variation::IO class.
=head1 DESCRIPTION
This object can transform Bio::Variation::SeqDiff objects to and from XML
file databases.
The XML format, although consistent, is still evolving. The current
DTD for it is at L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>mutationsE<sol>DTDE<sol>seqDiff.dtd>.
=head1 REQUIREMENTS
To use this code you need the module XML::Twig which creates an
interface to XML::Parser to read XML and modules XML::Writer and
IO::String to write XML out.
=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 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 - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=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::Variation::IO::xml;
my $VERSION=1.1;
use vars qw(@ISA $seqdiff $var $prevdnaobj $prevrnaobj $prevaaobj);
use strict;
use XML::Twig;
use XML::Writer 0.4;
use IO::String;
use Bio::Variation::IO;
use Bio::Variation::SeqDiff;
use Bio::Variation::DNAMutation;
use Bio::Variation::RNAChange;
use Bio::Variation::AAChange;
use Bio::Variation::Allele;
# new() is inherited from Bio::Root::Object
@ISA = qw( Bio::Variation::IO );
# _initialize is where the heavy stuff will happen when new is called
sub new {
my ($class,@args) = @_;
my $self = bless {}, $class;
$self->_initialize(@args);
return $self;
}
sub _initialize {
my($self,@args) = @_;
return unless $self->SUPER::_initialize(@args);
}
=head2 next
Title : next
Usage : $haplo = $stream->next()
Function: returns the next seqDiff in the stream
Returns : Bio::Variation::SeqDiff object
Args : NONE
=cut
sub _seqDiff {
my ($t, $term)= @_;
$seqdiff->id( $term->att('id') );
$seqdiff->alphabet( $term->att('moltype') );
$seqdiff->offset( $term->att('offset') );
foreach my $child ($term->children) {
_variant($t, $child);
}
}
sub _variant {
my ($t, $term)= @_;
my $var;
my $att = $term->atts();
my ($variation_number, $change_number) = split /\./, $att->{number};
# if more than two alleles
if ($variation_number and $change_number and $change_number > 1 ) {
my $a3 = Bio::Variation::Allele->new;
$a3->seq( $term->first_child_text('allele_mut') )
if $term->first_child_text('allele_mut');
if ($term->gi eq 'DNA') {
$prevdnaobj->add_Allele($a3);
}
elsif ($term->gi eq 'RNA') {
$prevrnaobj->add_Allele($a3);
} else { # AA
$prevaaobj->add_Allele($a3);
}
} else { # create new variants
if ($term->gi eq 'DNA') {
$var = new Bio::Variation::DNAMutation;
}
elsif ($term->gi eq 'RNA') {
$var = new Bio::Variation::RNAChange;
} else { # AA
$var = new Bio::Variation::AAChange;
}
# these are always present
$var->start( $att->{start} );
$var->end( $att->{end});
$var->length($att->{len});
$var->mut_number( $att->{number});
$var->upStreamSeq($term->first_child_text('upFlank'));
$var->dnStreamSeq($term->first_child_text('dnFlank'));
$var->proof($term->first_child_text('proof'));
# region
my $region = $term->first_child('region');
if ($region) {
$var->region($region->text);
my $region_atts = $region->atts;
$var->region_value( $region_atts->{value} )
if $region_atts->{value};
$var->region_dist( $region_atts->{dist} )
if $region_atts->{dist};
}
# alleles
my $a1 = Bio::Variation::Allele->new;
$a1->seq($term->first_child_text('allele_ori') )
if $term->first_child_text('allele_ori');
$var->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($term->first_child_text('allele_mut') )
if $term->first_child_text('allele_mut');
$var->isMutation(1) if $term->att('isMutation');
$var->allele_mut($a2);
$var->add_Allele($a2);
$var->length( $term->att('length') );
$seqdiff->add_Variant($var);
# variant specific code
if ($term->gi eq 'DNA') {
$prevdnaobj = $var;
}
elsif ($term->gi eq 'RNA') {
my $codon = $term->first_child('codon');
if ($codon) {
my $codon_atts = $codon->atts;
$var->codon_table( $codon->att('codon_table') )
if $codon_atts->{codon_table} and $codon_atts->{codon_table} != 1;
$var->codon_pos( $codon->att('codon_pos') )
if $codon_atts->{codon_pos};
}
$prevdnaobj->RNAChange($var);
$var->DNAMutation($prevdnaobj);
$prevrnaobj = $var;
} else {
$prevrnaobj->AAChange($var);
$var->RNAChange($prevrnaobj);
$prevaaobj = $var;
}
}
}
sub next {
my( $self ) = @_;
local $/ = "</seqDiff>\n";
return unless my $entry = $self->_readline;
# print STDERR "|$entry|";
return unless $entry =~ /^\W*<seqDiff/;
$seqdiff = Bio::Variation::SeqDiff->new;
# create new parser object
my $twig_handlers = {'seqDiff' => \&_seqDiff };
my $t = new XML::Twig ( TwigHandlers => $twig_handlers,
KeepEncoding => 1 );
$t->parse($entry);
return $seqdiff;
}
=head2 write
Title : write
Usage : $stream->write(@haplos)
Function: writes the $seqDiff objects into the stream
Returns : 1 for success and 0 for error
Args : Bio::Variation::SeqDiff object
=cut
sub write {
my ($self,@h) = @_;
if( ! defined $h[0] ) {
$self->throw("Attempting to write with no information!");
}
my $str;
my $output = IO::String->new($str);
my $w = new XML::Writer(OUTPUT => $output, DATA_MODE => 1, DATA_INDENT => 4 );
foreach my $h (@h) {
#
# seqDiff
#
$h->alphabet || $self->throw("Moltype of the reference sequence is not set!");
my $hasAA = 0;
foreach my $mut ($h->each_Variant) {
$hasAA = 1 if $mut->isa('Bio::Variation::AAChange');
}
if ($hasAA) {
$w->startTag("seqDiff",
"id" => $h->id,
"moltype" => $h->alphabet,
"offset" => $h->offset,
"sysname" => $h->sysname,
"trivname" => $h->trivname
);
} else {
$w->startTag("seqDiff",
"id" => $h->id,
"moltype" => $h->alphabet,
"offset" => $h->offset,
"sysname" => $h->sysname
);
}
my @allvariants = $h->each_Variant;
#print "allvars:", scalar @allvariants, "\n";
my %variants = ();
foreach my $mut ($h->each_Variant) {
#print STDERR $mut->mut_number, "\t", $mut, "\t",
#$mut->proof, "\t", scalar $mut->each_Allele, "\n";
push @{$variants{$mut->mut_number} }, $mut;
}
foreach my $var (sort keys %variants) {
foreach my $mut (@{$variants{$var}}) {
#
# DNA
#
if( $mut->isa('Bio::Variation::DNAMutation') ) {
$mut->isMutation(0) if not $mut->isMutation;
my @alleles = $mut->each_Allele;
my $count = 0;
foreach my $allele (@alleles) {
$count++;
my ($variation_number, $change_number) = split /\./, $mut->mut_number;
if ($change_number and $change_number != $count){
$mut->mut_number("$change_number.$count");
}
$mut->allele_mut($allele);
$w->startTag("DNA",
"number" => $mut->mut_number,
"start" => $mut->start,
"end" => $mut->end,
"length" => $mut->length,
"isMutation" => $mut->isMutation
);
if ($mut->label) {
foreach my $label (split ', ', $mut->label) {
$w->startTag("label");
$w->characters($label);
$w->endTag;
}
}
if ($mut->proof) {
$w->startTag("proof");
$w->characters($mut->proof );
$w->endTag;
}
if ($mut->upStreamSeq) {
$w->startTag("upFlank");
$w->characters($mut->upStreamSeq );
$w->endTag;
}
#if ( $mut->isMutation) {
#if ($mut->allele_ori) {
$w->startTag("allele_ori");
$w->characters($mut->allele_ori->seq) if $mut->allele_ori->seq ;
$w->endTag;
#}
#if ($mut->allele_mut) {
$w->startTag("allele_mut");
$w->characters($mut->allele_mut->seq) if $mut->allele_mut->seq;
$w->endTag;
#}
#}
if ($mut->dnStreamSeq) {
$w->startTag("dnFlank");
$w->characters($mut->dnStreamSeq );
$w->endTag;
}
if ($mut->restriction_changes) {
$w->startTag("restriction_changes");
$w->characters($mut->restriction_changes);
$w->endTag;
}
if ($mut->region) {
if($mut->region_value and $mut->region_dist) {
$w->startTag("region",
"value" => $mut->region_value,
"dist" => $mut->region_dist
);
}
elsif($mut->region_value) {
$w->startTag("region",
"value" => $mut->region_value
);
}
elsif($mut->region_dist) {
$w->startTag("region",
"dist" => $mut->region_dist
);
} else {
$w->startTag("region");
}
$w->characters($mut->region );
$w->endTag;
}
$w->endTag; #DNA
}
}
#
# RNA
#
elsif( $mut->isa('Bio::Variation::RNAChange') ) {
$mut->isMutation(0) if not $mut->isMutation;
my @alleles = $mut->each_Allele;
my $count = 0;
foreach my $allele (@alleles) {
$count++;
my ($variation_number, $change_number) = split /\./, $mut->mut_number;
if ($change_number and $change_number != $count){
$mut->mut_number("$change_number.$count");
}
$mut->allele_mut($allele);
$w->startTag("RNA",
"number" => $mut->mut_number,
"start" => $mut->start,
"end" => $mut->end,
"length" => $mut->length,
"isMutation" => $mut->isMutation
);
if ($mut->label) {
foreach my $label (split ', ', $mut->label) {
$w->startTag("label");
$w->characters($label );
$w->endTag;
}
}
if ($mut->proof) {
$w->startTag("proof");
$w->characters($mut->proof );
$w->endTag;
}
if ($mut->upStreamSeq) {
$w->startTag("upFlank");
$w->characters($mut->upStreamSeq );
$w->endTag;
}
#if ( $mut->isMutation) {
if ($mut->allele_ori) {
$w->startTag("allele_ori");
$w->characters($mut->allele_ori->seq) if $mut->allele_ori->seq ;
$w->endTag;
}
if ($mut->allele_mut) {
$w->startTag("allele_mut");
$w->characters($mut->allele_mut->seq) if $mut->allele_mut->seq ;
$w->endTag;
}
#}
if ($mut->dnStreamSeq) {
$w->startTag("dnFlank");
$w->characters($mut->dnStreamSeq );
$w->endTag;
}
if ($mut->region eq 'coding') {
if (! $mut->codon_mut) {
$w->startTag("codon",
"codon_ori" => $mut->codon_ori,
"codon_pos" => $mut->codon_pos
);
} else {
$w->startTag("codon",
"codon_ori" => $mut->codon_ori,
"codon_mut" => $mut->codon_mut,
"codon_pos" => $mut->codon_pos
);
}
$w->endTag;
}
if ($mut->codon_table != 1) {
$w->startTag("codon_table");
$w->characters($mut->codon_table);
$w->endTag;
}
if ($mut->restriction_changes) {
$w->startTag("restriction_changes");
$w->characters($mut->restriction_changes);
$w->endTag;
}
if ($mut->region) {
if($mut->region_value and $mut->region_dist) {
$w->startTag("region",
"value" => $mut->region_value,
"dist" => $mut->region_dist
);
}
elsif($mut->region_value) {
$w->startTag("region",
"value" => $mut->region_value
);
}
elsif($mut->region_dist) {
$w->startTag("region",
"dist" => $mut->region_dist
);
} else {
$w->startTag("region");
}
$w->characters($mut->region );
$w->endTag;
}
$w->endTag; #RNA
}
}
#
# AA
#
elsif( $mut->isa('Bio::Variation::AAChange') ) {
$mut->isMutation(0) if not $mut->isMutation;
my @alleles = $mut->each_Allele;
my $count = 0;
foreach my $allele (@alleles) {
$count++;
my ($variation_number, $change_number) = split /\./, $mut->mut_number;
if ($change_number and $change_number != $count){
$mut->mut_number("$change_number.$count");
}
$mut->allele_mut($allele);
$w->startTag("AA",
"number" => $mut->mut_number,
"start" => $mut->start,
"end" => $mut->end,
"length" => $mut->length,
"isMutation" => $mut->isMutation
);
if ($mut->label) {
foreach my $label (split ', ', $mut->label) {
$w->startTag("label");
$w->characters($label );
$w->endTag;
}
}
if ($mut->proof) {
$w->startTag("proof");
$w->characters($mut->proof );
$w->endTag;
}
#if ( $mut->isMutation) {
if ($mut->allele_ori) {
$w->startTag("allele_ori");
$w->characters($mut->allele_ori->seq) if $mut->allele_ori->seq;
$w->endTag;
}
if ($mut->allele_mut) {
$w->startTag("allele_mut");
$w->characters($mut->allele_mut->seq) if $mut->allele_mut->seq;
$w->endTag;
}
#}
if ($mut->region) {
if($mut->region_value and $mut->region_dist) {
$w->startTag("region",
"value" => $mut->region_value,
"dist" => $mut->region_dist
);
}
elsif($mut->region_value) {
$w->startTag("region",
"value" => $mut->region_value
);
}
elsif($mut->region_dist) {
$w->startTag("region",
"dist" => $mut->region_dist
);
} else {
$w->startTag("region");
}
$w->characters($mut->region );
$w->endTag;
}
$w->endTag; #AA
}
}
}
}
}
$w->endTag;
$w->end;
$self->_print($str);
$output = undef;
return 1;
}
1;
]]>