Bio::ClusterIO::dbsnp - dbSNP input stream

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::ClusterIO::dbsnp - dbSNP input stream

SYNOPSIS

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Do not use this module directly. Use it via the Bio::ClusterIO class.

DESCRIPTION

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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/).

FEEDBACK

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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

Support

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 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://redmine.open-bio.org/projects/bioperl/

AUTHOR

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Allen Day <allenday@ucla.edu>

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

SAX methods

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

end_document

 Title   : end_document
 Usage   : $parser->end_document;
 Function: SAX method to indicate finishing parsing a new document
 Returns : none
 Args    : none

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

end_element

 Title   : end_element
 Usage   : $parser->end_element($data)
 Function: Signals finishing an element
 Returns : none
 Args    : hash ref for data

characters

 Title   : characters
 Usage   : $parser->characters($data)
 Function: Signals new characters to be processed
 Returns : characters read
 Args    : hash ref with the key 'Data'

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)
BioPerl documentation Contained in the BioPerl distribution. 
# 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


# 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);
}


###
#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;
}


sub start_document{
  my ($self) = @_;
  $self->{refsnp} = Bio::Variation::SNP->new;
}

sub refsnp {
  return shift->{refsnp};
}


sub end_document{
  my ($self,@args) = @_;
}


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};
  }
}


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});
	}
  }
}


sub characters{
  my ($self,$data) = @_;
  $self->{last_data} = $data->{Data}
    if $data->{Data} =~ /\S/; #whitespace is meaningless -ad
}


sub use_tempfile{
  my ($self,$value) = @_;
  if( defined $value) {
	$self->{'_use_tempfile'} = $value;
  }
  return $self->{'_use_tempfile'};
}

1;