lib/CXGN/SNP.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::SNP - a class to deal with SNP information.
   6
   7 =head1 DESCRIPTION
   8
   9 This class deals with a single SNP (Simple Nucleotide Polymorphism) - it can be used to store, modify, or delete information about a SNP. The term SNP is interpreted broadly and includes indels as well as polymorphisms that may include several nucleotides.
  10
  11 For SNP querying of aggregate information, use the L<CXGN::SNP::Query> class [not yet implemented].
  12
  13 It inherits from L<CXGN::DB::ModifiableI>.
  14
  15 SNPs are linked to sequences and accessions, and specify the base change. In addition, SNPs can be linked to markers that exploit that SNP, and to other meta information, such as who submitted the information, if it is experimentally verified, and the method of discovery.
  16
  17 =head1 AUTHOR
  18
  19 Lukas Mueller <lam87@cornell.edu>
  20
  21 =head1 FUNCTIONS
  22
  23 This class implements the following methods:
  24
  25 =cut
  26
  27 use strict;
  28
  29
  30 package CXGN::SNP;
  31
  32 use base qw | CXGN::DB::ModifiableI |;
  33
  34 =head2 new
  35
  36  Usage:
  37  Desc:
  38  Ret:
  39  Args:
  40  Side Effects:
  41  Example:
  42
  43 =cut
  44
  45 sub new {
  46     my $class = shift;
  47     my $dbh = shift;
  48     my $id = shift;
  49     my $self = $class->SUPER::new($dbh);
  50
  51     $self->set_snp_id($id);
  52     if ($id) {
  53         $self->fetch();
  54     }
  55
  56     return $self;
  57
  58 }
  59
  60 =head2 fetch
  61
  62  Usage:
  63  Desc:
  64  Ret:
  65  Args:
  66  Side Effects:
  67  Example:
  68
  69 =cut
  70
  71 sub fetch {
  72     my $self = shift;
  73     my $q = "SELECT snp_id,
  74                     reference_unigene_id,
  75                     reference_position,
  76                     primer_left_id,
  77                     primer_right_id,
  78                     reference_accession_id,
  79                     snp_accession_id,
  80                     reference_nucleotide,
  81                     snp_nucleotide,
  82                     sp_person_id,
  83                     modified_date,
  84                     create_date,
  85                     obsolete
  86                FROM sgn.snp
  87               WHERE snp_id = ?";
  88     my $h = $self->get_dbh()->prepare($q);
  89
  90     $h->execute($self->get_snp_id());
  91
  92     my ($snp_id, $reference_unigene_id, $reference_position, $primer_left_id, $primer_right_id, $reference_accession_id, $snp_accession_id, $reference_nucleotide, $snp_nucleotide, $sp_person_id, $modified_date, $create_date, $obsolete) = $h->fetchrow_array();
  93
  94     $self->set_snp_id($snp_id);
  95     $self->set_reference_unigene_id($reference_unigene_id);
  96     $self->set_reference_position($reference_position);
  97     $self->set_primer_left_id($primer_left_id);
  98     $self->set_primer_right_id($primer_right_id);
  99     $self->set_reference_accession_id($reference_accession_id);
 100     $self->set_snp_accession_id($snp_accession_id);
 101     $self->set_reference_nucleotide($reference_nucleotide);
 102     $self->set_snp_nucleotide($snp_nucleotide);
 103     $self->set_sp_person_id($sp_person_id);
 104     $self->set_modified_date($modified_date);
 105     $self->set_create_date($create_date);
 106     $self->set_obsolete($obsolete);
 107
 108
 109
 110 }
 111
 112
 113 =head2 store
 114
 115  Usage:
 116  Desc:
 117  Ret:
 118  Args:
 119  Side Effects:
 120  Example:
 121
 122 =cut
 123
 124 sub store {
 125     my $self = shift;
 126
 127     if ($self->get_snp_id()) {
 128         my $q = "UPDATE sgn.snp SET
 129                   reference_unigene_id=?,
 130                   reference_position=?,
 131                   primer_left_id=?,
 132                   primer_right_id=?,
 133                   reference_accession_id=?,
 134                   snp_accession_id=?,
 135                   reference_nucleotide=?,
 136                   snp_nucleotide=?,
 137                   sp_person_id=?,
 138                   modified_date=NOW(),
 139                   obsolete=?
 140                  WHERE
 141                   snp_id=?";
 142         my $h = $self->get_dbh()->prepare($q);
 143         $h->execute(
 144             $self->get_reference_unigene_id(),
 145             $self->get_reference_position(),
 146             $self->get_primer_left_id(),
 147             $self->get_primer_right_id(),
 148             $self->get_reference_accession_id(),
 149             $self->get_snp_accession_id(),
 150             $self->get_snp_nucleotide(),
 151             $self->get_sp_person_id(),
 152             $self->get_obsolete(),
 153             $self->get_snp_id()
 154             );
 155     }
 156     else {
 157         my $q = "INSERT INTO sgn.snp
 158                    (reference_unigene_id,
 159                     reference_position,
 160                     primer_left_id,
 161                     primer_right_id,
 162                     reference_accession_id,
 163                     snp_accession_id,
 164                     reference_nucleotide,
 165                     snp_nucleotide,
 166                     sp_person_id,
 167                     modified_date,
 168                     create_date,
 169                     obsolete)
 170                  VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, NOW(), NOW(), ?)";
 171         my $h = $self->get_dbh()->prepare($q);
 172         $h->execute();
 173
 174     }
 175
 176 }
 177
 178
 179
 180 =Head2_snp_id, set_snp_id
 181
 182  Usage:
 183  Desc:
 184  Property
 185  Side Effects:
 186  Example:
 187
 188 =cut
 189
 190 sub get_snp_id {
 191   my $self = shift;
 192   return $self->{snp_id};
 193 }
 194
 195 sub set_snp_id {
 196   my $self = shift;
 197   $self->{snp_id} = shift;
 198 }
 199
 200 =head2 accessors get_position, set_position
 201
 202  Usage:
 203  Desc:
 204  Property
 205  Side Effects:
 206  Example:
 207
 208 =cut
 209
 210 sub get_position {
 211   my $self = shift;
 212   return $self->{position};
 213 }
 214
 215 sub set_position {
 216   my $self = shift;
 217   $self->{position} = shift;
 218 }
 219 =head2 accessors get_reference_nucleotide, set_reference_nucleotide
 220
 221  Usage:
 222  Desc:
 223  Property
 224  Side Effects:
 225  Example:
 226
 227 =cut
 228
 229 sub get_reference_nucleotide {
 230   my $self = shift;
 231   return $self->{reference_nucleotide};
 232 }
 233
 234 sub set_reference_nucleotide {
 235   my $self = shift;
 236   $self->{reference_nucleotide} = shift;
 237 }
 238 =head2 accessors get_snp_nucleotide, set_snp_nucleotide
 239
 240  Usage:
 241  Desc:
 242  Property
 243  Side Effects:
 244  Example:
 245
 246 =cut
 247
 248 sub get_snp_nucleotide {
 249   my $self = shift;
 250   return $self->{snp_nucleotide};
 251 }
 252
 253 sub set_snp_nucleotide {
 254   my $self = shift;
 255   $self->{snp_nucleotide} = shift;
 256 }
 257
 258
 259 =head2 accessors get_reference_accession_id, set_reference_accession_id
 260
 261  Usage:
 262  Desc:
 263  Property
 264  Side Effects:
 265  Example:
 266
 267 =cut
 268
 269 sub get_reference_accession_id {
 270   my $self = shift;
 271   return $self->{reference_accession_id};
 272 }
 273
 274 sub set_reference_accession_id {
 275   my $self = shift;
 276   $self->{reference_accession_id} = shift;
 277 }
 278
 279 =head2 accessors get_snp_accession_id, set_snp_accession_id
 280
 281  Usage:
 282  Desc:
 283  Property
 284  Side Effects:
 285  Example:
 286
 287 =cut
 288
 289 sub get_snp_accession_id {
 290   my $self = shift;
 291   return $self->{snp_accession_id};
 292 }
 293
 294 sub set_snp_accession_id {
 295   my $self = shift;
 296   $self->{snp_accession_id} = shift;
 297 }
 298
 299
 300 =head2 accessors get_dbxrefs, set_dbxrefs
 301
 302  Usage:
 303  Desc:
 304  Property
 305  Side Effects:
 306  Example:
 307
 308 =cut
 309
 310 sub get_dbxrefs {
 311   my $self = shift;
 312   return $self->{dbxrefs};
 313 }
 314
 315 sub set_dbxrefs {
 316   my $self = shift;
 317   $self->{dbxrefs} = shift;
 318 }
 319
 320 =head2 add_marker
 321
 322  Usage:
 323  Desc:
 324  Ret:
 325  Args:
 326  Side Effects:
 327  Example:
 328
 329 =cut
 330
 331 sub add_marker {
 332
 333 }
 334
 335 =head2 get_markers
 336
 337  Usage:
 338  Desc:
 339  Ret:
 340  Args:
 341  Side Effects:
 342  Example:
 343
 344 =cut
 345
 346 sub get_markers {
 347
 348 }
 349
 350
 351
 352
 353 =head2 create_schema
 354
 355  Usage:
 356  Desc:
 357  Ret:
 358  Args:
 359  Side Effects:
 360  Example:
 361
 362 =cut
 363
 364 sub create_schema {
 365     my $class = shift;
 366     my $dbh = shift;
 367
 368     my $q = qq{
 369                 CREATE TABLE sgn.snp (
 370                                       snp_id serial primary key,
 371                                       reference_unigene_id bigint references sgn.unigene,
 372                                       reference_position bigint,
 373                                       primer_left_id bigint references sgn."sequence",
 374                                       primer_right_id bigint references sgn."sequence",
 375                                       reference_accession_id bigint references sgn.accession,
 376                                       snp_accession_id bigint references sgn.accession,
 377                                       reference_nucleotide varchar(1),
 378                                       snp_nucleotide varchar(1),
 379                                       sp_person_id bigint REFERENCES sgn_people.sp_person,
 380                                       modified_date timestamp with time zone,
 381                                       create_date timestamp with time zone,
 382                                       obsolete boolean default false
 383
 384                                       )
 385                 };
 386
 387     $dbh->do($q);
 388
 389     $dbh->do("GRANT SELECT, UPDATE, INSERT ON sgn.snp TO web_usr");
 390     $dbh->do("GRANT SELECT, UPDATE, INSERT ON snp_snp_id_seq TO web_usr");
 391
 392     my $p = qq {
 393                 CREATE TABLE sgn.snp_marker (
 394                                              snp_marker_id serial primary key,
 395                                              snp_id bigint references sgn.snp,
 396                                              marker_id bigint references sgn.marker
 397                                              )
 398                 };
 399
 400     $dbh->do($p);
 401
 402     $dbh->do("GRANT SELECT, UPDATE, INSERT ON sgn.snp_marker TO web_usr");
 403     $dbh->do("GRANT SELECT, UPDATE, INSERT ON sgn.snp_marker_snp_marker_id_seq TO web_usr");
 404
 405
 406     my $x = " CREATE TABLE sgn.snp_dbxref (
 407                  snp_dbxref_id serial primary key,
 408                  snp_id bigint references sgn.snp,
 409                  dbxref_id bigint references public.dbxref,
 410                  obsolete boolean,
 411                  sp_person_id bigint references sgn_people.sp_person,
 412                  create_date timestamp with time zone,
 413                  modified_date timestamp with time zone
 414               )";
 415
 416     $dbh->do($x);
 417
 418     $dbh->do("GRANT SELECT, UPDATE, INSERT ON sgn.snp_dbxref TO web_usr");
 419     $dbh->do("GRANT SELECT, UPDATE, INSERT ON sgn.snp_dbxref_snp_dbxref_id_seq TO web_usr");
 420
 421
 422
 423     $dbh->commit();
 424 }
 425
 426
 427
 428
 429 return 2; #haha