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# BioPerl module for Bio::ClusterIO::dbsnp
#
# Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
# Human Genetics, UCLA Medical School, University of California, Los Angeles
# POD documentation - main docs before the code
=head1 NAME
Bio::ClusterIO::dbsnp - dbSNP input stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::ClusterIO class.
=head1 DESCRIPTION
Parse dbSNP XML files, one refSNP entry at a time. Note this handles dbSNPp
output generated by NBCI's eutils and does NOT parse output derived from
SNP's XML format (found at ftp://ftp.ncbi.nih.gov/snp/).
=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://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=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 the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Allen Day E<lt>allenday@ucla.eduE<gt>
=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::ClusterIO::dbsnp;
use strict;
use Bio::Root::Root;
use Bio::Variation::SNP;
use XML::SAX;
use Data::Dumper;
use IO::File;
use Time::HiRes qw(tv_interval gettimeofday);
use base qw(Bio::ClusterIO);
our $DEBUG = 0;
our %MAPPING = (
#the ones commented out i haven't written methods for yet... -Allen
'Rs_rsId' => 'id',
# 'Rs_taxId' => 'tax_id',
# 'Rs_organism' => 'organism',
'Rs_snpType' => {'type' => 'value'},
'Rs_sequence_observed' => 'observed',
'Rs_sequence_seq5' => 'seq_5',
'Rs_sequence_seq3' => 'seq_3',
# 'Rs_sequence_exemplarSs' => 'exemplar_subsnp',
'Rs_create_build' => 'ncbi_build',
#?? 'Rs_update_build' => 'ncbi_build',
# 'NSE-rs_ncbi-num-chr-hits' => 'ncbi_chr_hits',
# 'NSE-rs_ncbi-num-ctg-hits' => 'ncbi_ctg_hits',
# 'NSE-rs_ncbi-num-seq-loc' => 'ncbi_seq_loc',
# 'NSE-rs_ncbi-mapweight' => 'ncbi_mapweight',
# 'NSE-rs_ucsc-build-id' => 'ucsc_build',
# 'NSE-rs_ucsc-num-chr-hits' => 'ucsc_chr_hits',
# 'NSE-rs_ucsc-num-seq-loc' => 'ucsc_ctg_hits',
# 'NSE-rs_ucsc-mapweight' => 'ucsc_mapweight',
'Rs_het_value' => 'heterozygous',
'Rs_het-stdError' => 'heterozygous_SE',
'Rs_validation' => {'validated' => 'value'}, #??
# 'NSE-rs_genotype' => {'genotype' => 'value'},
'Ss_handle' => 'handle',
'Ss_batchId' => 'batch_id',
'Ss_locSnpId' => 'id',
# 'Ss_locSnpId' => 'loc_id',
# 'Ss_orient' => {'orient' => 'value'},
# 'Ss_buildId' => 'build',
'Ss_methodClass' => {'method' => 'value'},
# 'NSE-ss_accession_E' => 'accession',
# 'NSE-ss_comment_E' => 'comment',
# 'NSE-ss_genename' => 'gene_name',
# 'NSE-ss_assay-5_E' => 'seq_5',
# 'NSE-ss_assay-3_E' => 'seq_3',
# 'NSE-ss_observed' => 'observed',
# 'NSE-ss-popinfo_type' => 'pop_type',
# 'NSE-ss-popinfo_batch-id' => 'pop_batch_id',
# 'NSE-ss-popinfo_pop-name' => 'pop_name',
# 'NSE-ss-popinfo_samplesize' => 'pop_samplesize',
# 'NSE-ss_popinfo_est-het' => 'pop_est_heterozygous',
# 'NSE-ss_popinfo_est-het-se-sq' => 'pop_est_heterozygous_se_sq',
# 'NSE-ss-alleleinfo_type' => 'allele_type',
# 'NSE-ss-alleleinfo_batch-id' => 'allele_batch_id',
# 'NSE-ss-alleleinfo_pop-id' => 'allele_pop_id',
# 'NSE-ss-alleleinfo_snp-allele' => 'allele_snp',
# 'NSE-ss-alleleinfo_other-allele' => 'allele_other',
# 'NSE-ss-alleleinfo_freq' => 'allele_freq',
# 'NSE-ss-alleleinfo_count' => 'allele_count',
# 'NSE-rsContigHit_contig-id' => 'contig_hit',
# 'NSE-rsContigHit_accession' => 'accession_hit',
# 'NSE-rsContigHit_version' => 'version',
# 'NSE-rsContigHit_chromosome' => 'chromosome_hit',
# 'NSE-rsMaploc_asn-from' => 'asn_from',
# 'NSE-rsMaploc_asn-to' => 'asn_to',
# 'NSE-rsMaploc_loc-type' => {'loc_type' => 'value'},
# 'NSE-rsMaploc_hit-quality' => {'hit_quality' => 'value'},
# 'NSE-rsMaploc_orient' => {'orient' => 'value'},
# 'NSE-rsMaploc_physmap-str' => 'phys_from',
# 'NSE-rsMaploc_physmap-int' => 'phys_to',
'FxnSet_geneId' => 'locus_id', # does the code realise that there can be multiple of these
'FxnSet_symbol' => 'symbol',
'FxnSet_mrnaAcc' => 'mrna',
'FxnSet_protAcc' => 'protein',
'FxnSet_fxnClass' => {'functional_class' => 'value'},
#...
#...
#there are lots more, but i don't need them at the moment... -Allen
);
sub _initialize{
my ($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($usetempfile) = $self->_rearrange([qw(TEMPFILE)],@args);
defined $usetempfile && $self->use_tempfile($usetempfile);
# start up the parser factory
my $parserfactory = XML::SAX::ParserFactory->parser(
Handler => $self);
$self->{'_xmlparser'} = $parserfactory;
$DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
}
=head2 next_cluster
Title : next_cluster
Usage : $dbsnp = $stream->next_cluster()
Function: returns the next refSNP in the stream
Returns : Bio::Variation::SNP object representing composite refSNP
and its component subSNP(s).
Args : NONE
=cut
###
#Adapted from Jason's blastxml.pm
###
# you shouldn't have to preparse this; the XML is well-formed and refers
# accurately to a remote DTD/schema
sub next_cluster {
my $self = shift;
my $data = '';
my($tfh);
if( $self->use_tempfile ) {
$tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
$tfh->autoflush(1);
}
my $start = 1;
while( defined( $_ = $self->_readline ) ){
#skip to beginning of refSNP entry
if($_ !~ m{<Rs[^>]*>} && $start){
next;
} elsif($_ =~ m{<Rs[^>]*>} && $start){
$start = 0;
}
#slurp up the data
if( defined $tfh ) {
print $tfh $_;
} else {
$data .= $_;
}
#and stop at the end of the refSNP entry
last if $_ =~ m{</Rs>};
}
#if we didn't find a start tag
return if $start;
my %parser_args;
if( defined $tfh ) {
seek($tfh,0,0);
%parser_args = ('Source' => { 'ByteStream' => $tfh },
'Handler' => $self);
} else {
%parser_args = ('Source' => { 'String' => $data },
'Handler' => $self);
}
my $starttime;
my $result;
if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; }
eval {
$result = $self->{'_xmlparser'}->parse(%parser_args);
};
if( $@ ) {
$self->warn("error in parsing a report:\n $@");
$result = undef;
}
if( $DEBUG ) {
$self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime)));
}
return $self->refsnp;
}
=head2 SAX methods
=cut
=head2 start_document
Title : start_document
Usage : $parser->start_document;
Function: SAX method to indicate starting to parse a new document.
Creates a Bio::Variation::SNP
Returns : none
Args : none
=cut
sub start_document{
my ($self) = @_;
$self->{refsnp} = Bio::Variation::SNP->new;
}
sub refsnp {
return shift->{refsnp};
}
=head2 end_document
Title : end_document
Usage : $parser->end_document;
Function: SAX method to indicate finishing parsing a new document
Returns : none
Args : none
=cut
sub end_document{
my ($self,@args) = @_;
}
=head2 start_element
Title : start_element
Usage : $parser->start_element($data)
Function: SAX method to indicate starting a new element
Returns : none
Args : hash ref for data
=cut
sub start_element{
my ($self,$data) = @_;
my $nm = $data->{'Name'};
my $at = $data->{'Attributes'}->{'{}value'};
#$self->debug(Dumper($at)) if $nm = ;
if($nm eq 'Ss'){
$self->refsnp->add_subsnp;
return;
}
if(my $type = $MAPPING{$nm}){
if(ref $type eq 'HASH'){
#okay, this is nasty. what can you do?
$self->{will_handle} = (keys %$type)[0];
$self->{last_data} = $at->{Value};
} else {
$self->{will_handle} = $type;
$self->{last_data} = undef;
}
} else {
undef $self->{will_handle};
}
}
=head2 end_element
Title : end_element
Usage : $parser->end_element($data)
Function: Signals finishing an element
Returns : none
Args : hash ref for data
=cut
sub end_element {
my ($self,$data) = @_;
my $nm = $data->{'Name'};
my $at = $data->{'Attributes'};
my $method = $self->{will_handle};
if($method){
if($nm =~ /^Rs/ or $nm =~ /^NSE-SeqLoc/ or $nm =~ /^FxnSet/){
$self->refsnp->$method($self->{last_data});
} elsif ($nm =~ /^Ss/){
$self->refsnp->subsnp->$method($self->{last_data});
}
}
}
=head2 characters
Title : characters
Usage : $parser->characters($data)
Function: Signals new characters to be processed
Returns : characters read
Args : hash ref with the key 'Data'
=cut
sub characters{
my ($self,$data) = @_;
$self->{last_data} = $data->{Data}
if $data->{Data} =~ /\S/; #whitespace is meaningless -ad
}
=head2 use_tempfile
Title : use_tempfile
Usage : $obj->use_tempfile($newval)
Function: Get/Set boolean flag on whether or not use a tempfile
Example :
Returns : value of use_tempfile
Args : newvalue (optional)
=cut
sub use_tempfile{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_use_tempfile'} = $value;
}
return $self->{'_use_tempfile'};
}
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