Bio/ClusterIO/dbsnp.pm

   1 # BioPerl module for Bio::ClusterIO::dbsnp
   2 #
   3 # Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
   4 # Human Genetics, UCLA Medical School, University of California, Los Angeles
   5
   6 # POD documentation - main docs before the code
   7
   8 =head1 NAME
   9
  10 Bio::ClusterIO::dbsnp - dbSNP input stream
  11
  12 =head1 SYNOPSIS
  13
  14 Do not use this module directly.  Use it via the Bio::ClusterIO class.
  15
  16 =head1 DESCRIPTION
  17
  18 Parse dbSNP XML files, one refSNP entry at a time. Note this handles dbSNPp
  19 output generated by NBCI's eutils and does NOT parse output derived from
  20 SNP's XML format (found at ftp://ftp.ncbi.nih.gov/snp/).
  21
  22 =head1 FEEDBACK
  23
  24 =head2 Mailing Lists
  25
  26 User feedback is an integral part of the evolution of this and other
  27 Bioperl modules. Send your comments and suggestions preferably to one
  28 of the Bioperl mailing lists.  Your participation is much appreciated.
  29
  30   bioperl-l@bioperl.org                  - General discussion
  31   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  32
  33 =head2 Support
  34
  35 Please direct usage questions or support issues to the mailing list:
  36
  37 I<bioperl-l@bioperl.org>
  38
  39 rather than to the module maintainer directly. Many experienced and
  40 reponsive experts will be able look at the problem and quickly
  41 address it. Please include a thorough description of the problem
  42 with code and data examples if at all possible.
  43
  44 =head2 Reporting Bugs
  45
  46 Report bugs to the Bioperl bug tracking system to help us keep track
  47 the bugs and their resolution.  Bug reports can be submitted via the
  48 web:
  49
  50   https://github.com/bioperl/bioperl-live/issues
  51
  52 =head1 AUTHOR
  53
  54 Allen Day E<lt>allenday@ucla.eduE<gt>
  55
  56 =head1 APPENDIX
  57
  58 The rest of the documentation details each of the object
  59 methods. Internal methods are usually preceded with a _
  60
  61 =cut
  62
  63 # Let the code begin...
  64 package Bio::ClusterIO::dbsnp;
  65
  66 use strict;
  67 use Bio::Root::Root;
  68 use Bio::Variation::SNP;
  69 use XML::SAX;
  70 use Data::Dumper;
  71 use IO::File;
  72 use Time::HiRes qw(tv_interval gettimeofday);
  73
  74 use base qw(Bio::ClusterIO);
  75
  76 our $DEBUG = 0;
  77
  78 our %MAPPING = (
  79 #the ones commented out i haven't written methods for yet... -Allen
  80                           'Rs_rsId'               => 'id',
  81 #                         'Rs_taxId'                   => 'tax_id',
  82 #                         'Rs_organism'                => 'organism',
  83                           'Rs_snpType'                => {'type' => 'value'},
  84                           'Rs_sequence_observed'                => 'observed',
  85                           'Rs_sequence_seq5'                 => 'seq_5',
  86                           'Rs_sequence_seq3'                 => 'seq_3',
  87 #                         'Rs_sequence_exemplarSs'         => 'exemplar_subsnp',
  88                           'Rs_create_build'           => 'ncbi_build',
  89 #??                       'Rs_update_build'           => 'ncbi_build',
  90 #                         'NSE-rs_ncbi-num-chr-hits'       => 'ncbi_chr_hits',
  91 #                         'NSE-rs_ncbi-num-ctg-hits'       => 'ncbi_ctg_hits',
  92 #                         'NSE-rs_ncbi-num-seq-loc'        => 'ncbi_seq_loc',
  93 #                         'NSE-rs_ncbi-mapweight'          => 'ncbi_mapweight',
  94 #                         'NSE-rs_ucsc-build-id'           => 'ucsc_build',
  95 #                         'NSE-rs_ucsc-num-chr-hits'       => 'ucsc_chr_hits',
  96 #                         'NSE-rs_ucsc-num-seq-loc'        => 'ucsc_ctg_hits',
  97 #                         'NSE-rs_ucsc-mapweight'          => 'ucsc_mapweight',
  98
  99                           'Rs_het_value'                     => 'heterozygous',
 100                           'Rs_het-stdError'                  => 'heterozygous_SE',
 101                           'Rs_validation'               => {'validated' => 'value'}, #??
 102 #                         'NSE-rs_genotype'                => {'genotype' => 'value'},
 103
 104                           'Ss_handle'                  => 'handle',
 105                           'Ss_batchId'                => 'batch_id',
 106                           'Ss_locSnpId'               => 'id',
 107 #                         'Ss_locSnpId'              => 'loc_id',
 108 #                         'Ss_orient'                  => {'orient' => 'value'},
 109 #                         'Ss_buildId'                => 'build',
 110                           'Ss_methodClass'            => {'method' => 'value'},
 111 #                         'NSE-ss_accession_E'             => 'accession',
 112 #                         'NSE-ss_comment_E'               => 'comment',
 113 #                         'NSE-ss_genename'                => 'gene_name',
 114 #                         'NSE-ss_assay-5_E'               => 'seq_5',
 115 #                         'NSE-ss_assay-3_E'               => 'seq_3',
 116 #                         'NSE-ss_observed'                => 'observed',
 117
 118 #                         'NSE-ss-popinfo_type'            => 'pop_type',
 119 #                         'NSE-ss-popinfo_batch-id'        => 'pop_batch_id',
 120 #                         'NSE-ss-popinfo_pop-name'        => 'pop_name',
 121 #                         'NSE-ss-popinfo_samplesize'      => 'pop_samplesize',
 122 #                         'NSE-ss_popinfo_est-het'         => 'pop_est_heterozygous',
 123 #                         'NSE-ss_popinfo_est-het-se-sq'   => 'pop_est_heterozygous_se_sq',
 124
 125 #                         'NSE-ss-alleleinfo_type'         => 'allele_type',
 126 #                         'NSE-ss-alleleinfo_batch-id'     => 'allele_batch_id',
 127 #                         'NSE-ss-alleleinfo_pop-id'       => 'allele_pop_id',
 128 #                         'NSE-ss-alleleinfo_snp-allele'   => 'allele_snp',
 129 #                         'NSE-ss-alleleinfo_other-allele' => 'allele_other',
 130 #                         'NSE-ss-alleleinfo_freq'         => 'allele_freq',
 131 #                         'NSE-ss-alleleinfo_count'        => 'allele_count',
 132
 133 #                         'NSE-rsContigHit_contig-id'      => 'contig_hit',
 134 #                         'NSE-rsContigHit_accession'      => 'accession_hit',
 135 #                         'NSE-rsContigHit_version'        => 'version',
 136 #                         'NSE-rsContigHit_chromosome'     => 'chromosome_hit',
 137
 138 #                         'NSE-rsMaploc_asn-from'          => 'asn_from',
 139 #                         'NSE-rsMaploc_asn-to'            => 'asn_to',
 140 #                         'NSE-rsMaploc_loc-type'          => {'loc_type' => 'value'},
 141 #                         'NSE-rsMaploc_hit-quality'       => {'hit_quality' => 'value'},
 142 #                         'NSE-rsMaploc_orient'            => {'orient' => 'value'},
 143 #                         'NSE-rsMaploc_physmap-str'       => 'phys_from',
 144 #                         'NSE-rsMaploc_physmap-int'       => 'phys_to',
 145
 146                           'FxnSet_geneId'             => 'locus_id',  # does the code realise that there can be multiple of these
 147                           'FxnSet_symbol'              => 'symbol',
 148                           'FxnSet_mrnaAcc'            => 'mrna',
 149                           'FxnSet_protAcc'            => 'protein',
 150                           'FxnSet_fxnClass'    => {'functional_class' => 'value'},
 151
 152                           #...
 153                           #...
 154                           #there are lots more, but i don't need them at the moment... -Allen
 155                           );
 156
 157 sub _initialize{
 158    my ($self,@args) = @_;
 159    $self->SUPER::_initialize(@args);
 160    my ($usetempfile) = $self->_rearrange([qw(TEMPFILE)],@args);
 161    defined $usetempfile && $self->use_tempfile($usetempfile);
 162
 163   # start up the parser factory
 164   my $parserfactory = XML::SAX::ParserFactory->parser(
 165           Handler => $self);
 166   $self->{'_xmlparser'} = $parserfactory;
 167   $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
 168 }
 169
 170 =head2 next_cluster
 171
 172  Title   : next_cluster
 173  Usage   : $dbsnp = $stream->next_cluster()
 174  Function: returns the next refSNP in the stream
 175  Returns : Bio::Variation::SNP object representing composite refSNP
 176            and its component subSNP(s).
 177  Args    : NONE
 178
 179 =cut
 180
 181 ###
 182 #Adapted from Jason's blastxml.pm
 183 ###
 184
 185 # you shouldn't have to preparse this; the XML is well-formed and refers
 186 # accurately to a remote DTD/schema
 187
 188 sub next_cluster {
 189   my $self = shift;
 190   my $data = '';
 191   my($tfh);
 192
 193   if( $self->use_tempfile ) {
 194         $tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
 195         $tfh->autoflush(1);
 196   }
 197
 198   my $start = 1;
 199   while( defined( $_ = $self->_readline ) ){
 200         #skip to beginning of refSNP entry
 201         if($_ !~ m{<Rs[^>]*>} && $start){
 202           next;
 203         } elsif($_ =~ m{<Rs[^>]*>} && $start){
 204           $start = 0;
 205         }
 206
 207         #slurp up the data
 208         if( defined $tfh ) {
 209           print $tfh $_;
 210         } else {
 211           $data .= $_;
 212         }
 213
 214         #and stop at the end of the refSNP entry
 215         last if $_ =~ m{</Rs>};
 216   }
 217
 218   #if we didn't find a start tag
 219   return if $start;
 220
 221   my %parser_args;
 222   if( defined $tfh ) {
 223         seek($tfh,0,0);
 224         %parser_args = ('Source' => { 'ByteStream' => $tfh },
 225                                         'Handler' => $self);
 226   } else {
 227         %parser_args = ('Source' => { 'String' => $data },
 228                                         'Handler' => $self);
 229   }
 230
 231   my $starttime;
 232   my $result;
 233
 234   if(  $DEBUG ) {  $starttime = [ Time::HiRes::gettimeofday() ]; }
 235
 236   eval {
 237         $result = $self->{'_xmlparser'}->parse(%parser_args);
 238   };
 239
 240   if( $@ ) {
 241         $self->warn("error in parsing a report:\n $@");
 242         $result = undef;
 243   }
 244
 245   if( $DEBUG ) {
 246         $self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime)));
 247   }
 248
 249   return $self->refsnp;
 250 }
 251
 252 =head2 SAX methods
 253
 254 =cut
 255
 256 =head2 start_document
 257
 258  Title   : start_document
 259  Usage   : $parser->start_document;
 260  Function: SAX method to indicate starting to parse a new document.
 261            Creates a Bio::Variation::SNP
 262  Returns : none
 263  Args    : none
 264
 265 =cut
 266
 267 sub start_document{
 268   my ($self) = @_;
 269   $self->{refsnp} = Bio::Variation::SNP->new;
 270 }
 271
 272 sub refsnp {
 273   return shift->{refsnp};
 274 }
 275
 276 =head2 end_document
 277
 278  Title   : end_document
 279  Usage   : $parser->end_document;
 280  Function: SAX method to indicate finishing parsing a new document
 281  Returns : none
 282  Args    : none
 283
 284 =cut
 285
 286 sub end_document{
 287   my ($self,@args) = @_;
 288 }
 289
 290 =head2 start_element
 291
 292  Title   : start_element
 293  Usage   : $parser->start_element($data)
 294  Function: SAX method to indicate starting a new element
 295  Returns : none
 296  Args    : hash ref for data
 297
 298 =cut
 299
 300 sub start_element{
 301   my ($self,$data) = @_;
 302   my $nm = $data->{'Name'};
 303   my $at = $data->{'Attributes'}->{'{}value'};
 304
 305   #$self->debug(Dumper($at)) if $nm = ;
 306
 307   if($nm eq 'Ss'){
 308         $self->refsnp->add_subsnp;
 309         return;
 310   }
 311
 312   if(my $type = $MAPPING{$nm}){
 313         if(ref $type eq 'HASH'){
 314           #okay, this is nasty.  what can you do?
 315           $self->{will_handle}   = (keys %$type)[0];
 316           $self->{last_data}     = $at->{Value};
 317         } else {
 318           $self->{will_handle} = $type;
 319           $self->{last_data} = undef;
 320         }
 321   } else {
 322         undef $self->{will_handle};
 323   }
 324 }
 325
 326 =head2 end_element
 327
 328  Title   : end_element
 329  Usage   : $parser->end_element($data)
 330  Function: Signals finishing an element
 331  Returns : none
 332  Args    : hash ref for data
 333
 334 =cut
 335
 336 sub end_element {
 337   my ($self,$data) = @_;
 338   my $nm = $data->{'Name'};
 339   my $at = $data->{'Attributes'};
 340
 341   my $method = $self->{will_handle};
 342   if($method){
 343         if($nm =~ /^Rs/ or $nm =~ /^NSE-SeqLoc/ or $nm =~ /^FxnSet/){
 344           $self->refsnp->$method($self->{last_data});
 345         } elsif ($nm =~ /^Ss/){
 346           $self->refsnp->subsnp->$method($self->{last_data});
 347         }
 348   }
 349 }
 350
 351 =head2 characters
 352
 353  Title   : characters
 354  Usage   : $parser->characters($data)
 355  Function: Signals new characters to be processed
 356  Returns : characters read
 357  Args    : hash ref with the key 'Data'
 358
 359 =cut
 360
 361 sub characters{
 362   my ($self,$data) = @_;
 363   $self->{last_data} = $data->{Data}
 364     if $data->{Data} =~ /\S/; #whitespace is meaningless -ad
 365 }
 366
 367 =head2 use_tempfile
 368
 369  Title   : use_tempfile
 370  Usage   : $obj->use_tempfile($newval)
 371  Function: Get/Set boolean flag on whether or not use a tempfile
 372  Example :
 373  Returns : value of use_tempfile
 374  Args    : newvalue (optional)
 375
 376 =cut
 377
 378 sub use_tempfile{
 379   my ($self,$value) = @_;
 380   if( defined $value) {
 381         $self->{'_use_tempfile'} = $value;
 382   }
 383   return $self->{'_use_tempfile'};
 384 }
 385
 386 1;