Summary

Bio::ClusterIO::dbsnp - dbSNP input stream

Package variables

Included modules

Inherit

Bio::ClusterIO

Synopsis

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

Description

Parse dbSNP XML files, one refSNP entry at a time.

Methods

Methods description

 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

 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

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

 Title   : start_element
 Usage   : $parser->start_element($data)
 Function: SAX method to indicate starting a new element
 Returns : none
 Args    : hash ref for data

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

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

 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)

Methods code

BEGIN {

  %MAPPING = (
#the ones commented out i haven't written methods for yet... -Allen
			  'NSE-rs_refsnp-id'               => 'id',
#			  'NSE-rs_taxid'                   => 'tax_id',
#			  'NSE-rs_organism'                => 'organism',
			  'NSE-rs_snp-type'                => {'type' => 'value'},
			  'NSE-rs_observed'                => 'observed',
			  'NSE-rs_seq-5_E'                 => 'seq_5',
			  'NSE-rs_seq-3_E'                 => 'seq_3',
#			  'NSE-rs_seq-ss-exemplar'         => 'exemplar_subsnp',
			  'NSE-rs_ncbi-build-id'           => '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',
			  'NSE-rs_het'                     => 'heterozygous',
			  'NSE-rs_het-SE'                  => 'heterozygous_SE',
			  'NSE-rs_validated'               => {'validated' => 'value'},
			  'NSE-rs_genotype'                => {'genotype' => 'value'},

			  'NSE-ss_handle'                  => 'handle',
			  'NSE-ss_batch-id'                => 'batch_id',
			  'NSE-ss_subsnp-id'               => 'id',
#			  'NSE-ss_loc-snp-id'              => 'loc_id',
#			  'NSE-ss_orient'                  => {'orient' => 'value'},
#			  'NSE-ss_build-id'                => 'build',
			  'NSE-ss_method-class'            => {'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',

			  'NSE-FxnSet_locusid'             => 'locus_id',
			  'NSE-FxnSet_symbol'              => 'symbol',
			  'NSE-FxnSet_mrna-acc'            => 'mrna',
			  'NSE-FxnSet_prot-acc'            => 'protein',
			  'NSE-FxnSet_fxn-class-contig'    => {'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);
   $self->{'_xmlparser'} = new XML::Parser::PerlSAX();
   $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);

}

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!<NSE-rs>! && $start){
	  next;
	} elsif($_ =~ m!<NSE-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!</NSE-rs>!;
  }

  #if we didn't find a start tag
  return undef 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'};

  if($nm eq 'NSE-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];
	  my $valkey             = (values %$type)[0];
	  $self->{last_data}     = $at->{$valkey};
	} 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 =~ /^NSE-rs/ or $nm =~ /^NSE-SeqLoc/ or $nm =~ /^NSE-FxnSet/){
	  $self->refsnp->$method($self->{last_data});
	} elsif ($nm =~ /^NSE-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'};

}

General documentation

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/MailList.shtml - About the mailing lists

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/

Allen Day <allenday@ucla.edu>

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