Bio::ClusterIO dbsnp
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Summary
Bio::ClusterIO::dbsnp - dbSNP input stream
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Variation::SNP
Data::Dumper
IO::File
Time::HiRes qw ( tv_interval gettimeofday )
XML::SAX
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. 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/).
Methods
_initialize
No description
Code
next_clusterDescriptionCode
start_documentDescriptionCode
refsnp
No description
Code
end_documentDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
charactersDescriptionCode
use_tempfileDescriptionCode
Methods description
next_clustercode    nextTop
 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
start_documentcodeprevnextTop
 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_documentcodeprevnextTop
 Title   : end_document
Usage : $parser->end_document;
Function: SAX method to indicate finishing parsing a new document
Returns : none
Args : none
start_elementcodeprevnextTop
 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_elementcodeprevnextTop
 Title   : end_element
Usage : $parser->end_element($data)
Function: Signals finishing an element
Returns : none
Args : hash ref for data
characterscodeprevnextTop
 Title   : characters
Usage : $parser->characters($data)
Function: Signals new characters to be processed
Returns : characters read
Args : hash ref with the key 'Data'
use_tempfilecodeprevnextTop
 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
_initializedescriptionprevnextTop
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);
}
next_clusterdescriptionprevnextTop
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 $self->refsnp;
}
start_documentdescriptionprevnextTop
sub start_document {
  my ($self) = @_;
  $self->{refsnp} = Bio::Variation::SNP->new;
}
refsnpdescriptionprevnextTop
sub refsnp {
  return shift->{refsnp};
}
end_documentdescriptionprevnextTop
sub end_document {
  my ($self,@args) = @_;
}
start_elementdescriptionprevnextTop
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 $self->{will_handle}; }
}
end_elementdescriptionprevnextTop
sub end_element {
  my ($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($self->{last_data});
	}
  }
}
charactersdescriptionprevnextTop
sub characters {
  my ($self,$data) = @_;
  $self->{last_data} = $data->{Data}
    if $data->{Data} =~ /\S/; #whitespace is meaningless -ad
}
use_tempfiledescriptionprevnextTop
sub use_tempfile {
  my ($self,$value) = @_;
  if( defined $value) {
	$self->{'_use_tempfile'} = $value;
  }
  return $self->{'_use_tempfile'};
}

1;
}
General documentation
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 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 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/
AUTHORTop
Allen Day <allenday@ucla.edu>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
SAX methodsTop