Bio::Variation::IO xml
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Summary
Bio::Variation::IO::xml - XML sequence variation input/output stream
Package variables
No package variables defined.
Included modules
Bio::Variation::AAChange
Bio::Variation::Allele
Bio::Variation::DNAMutation
Bio::Variation::RNAChange
Bio::Variation::SeqDiff
IO::String
XML::Twig
XML::Writer 0 .4
Inherit
Bio::Variation::IO
Synopsis
Do not use this module directly. Use it via the Bio::Variation::IO class.
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 http://www.ebi.ac.uk/mutations/DTDE/seqDiff.dtd.
Methods
new
No description
Code
_initialize
No description
Code
_seqDiff
No description
Code
_variant
No description
Code
nextDescriptionCode
writeDescriptionCode
Methods description
nextcode    nextTop
 Title   : next
Usage : $haplo = $stream->next()
Function: returns the next seqDiff in the stream
Returns : Bio::Variation::SeqDiff object
Args : NONE
writecodeprevnextTop
 Title   : write
Usage : $stream->write(@haplos)
Function: writes the $seqDiff objects into the stream
Returns : 1 for success and 0 for error
Args : Bio::Variation::SeqDiff object
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;
    my $self = bless {}, $class;
    $self->_initialize(@args);
    return $self;
}
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  return unless $self->SUPER::_initialize(@args);
}
_seqDiffdescriptionprevnextTop
sub _seqDiff {
    my ($t, $term)= @_;
    $seqdiff->id( $term->att('id') );
    $seqdiff->alphabet( $term->att('moltype') );
    $seqdiff->offset( $term->att('offset') );

    foreach my $child ($term->children) {
	 _variant($t, $child);
    }
}
_variantdescriptionprevnextTop
sub _variant {
    my ($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') { $var = Bio::Variation::DNAMutation->new(); } elsif ($term->gi eq 'RNA') { $var = Bio::Variation::RNAChange->new(); } else { # AA
$var = Bio::Variation::AAChange->new(); } # 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; } }
}
nextdescriptionprevnextTop
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 $seqdiff;
}
writedescriptionprevnextTop
sub write {
    my ($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;
}
General documentation
REQUIREMENTSTop
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.
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 lists 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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _