lib/CXGN/Genotype/DownloadFactory.pm

   1 package CXGN::Genotype::DownloadFactory;
   2
   3 =head1 NAME
   4
   5 CXGN::Genotype::DownloadFactory - an object factory to handle downloading genotypes across database. factory delegates between download types e.g. VCF, GenotypeMatrix
   6
   7 =head1 USAGE
   8
   9 my $geno = CXGN::Genotype::DownloadFactory->instantiate(
  10     'VCF',    #can be either 'VCF' or 'DosageMatrix'
  11     {
  12         bcs_schema=>$schema,
  13         people_schema=>$people_schema,
  14         cache_root_dir=>$cache_root,
  15         accession_list=>$accession_list,
  16         tissue_sample_list=>$tissue_sample_list,
  17         trial_list=>$trial_list,
  18         protocol_id_list=>$protocol_id_list,
  19         markerprofile_id_list=>$markerprofile_id_list,
  20         genotype_data_project_list=>$genotype_data_project_list,
  21         chromosome_list=>\@chromosome_numbers,
  22         start_position=>$start_position,
  23         end_position=>$end_position,
  24         marker_name_list=>['S80_265728', 'S80_265723'],
  25         genotypeprop_hash_select=>['DS', 'GT', 'DP'], #THESE ARE THE KEYS IN THE GENOTYPEPROP OBJECT
  26         protocolprop_top_key_select=>['reference_genome_name', 'header_information_lines', 'marker_names', 'markers'], #THESE ARE THE KEYS AT THE TOP LEVEL OF THE PROTOCOLPROP OBJECT
  27         protocolprop_marker_hash_select=>['name', 'chrom', 'pos', 'alt', 'ref'], #THESE ARE THE KEYS IN THE MARKERS OBJECT IN THE PROTOCOLPROP OBJECT
  28         limit=>$limit,
  29         offset=>$offset,
  30         compute_from_parents=>0, #If you want to compute the genotype for accessions given from parents in the pedigree. Useful for hybrids where parents are genotyped.
  31         forbid_cache=>0, #If you want to get a guaranteed fresh result not from the file cache
  32         prevent_transpose=>0, #Prevent transpose of DosageMatrix
  33         return_only_first_genotypeprop_for_stock=>1
  34     }
  35 );
  36 my $status = $geno->download();
  37
  38 =head1 DESCRIPTION
  39
  40
  41 =head1 AUTHORS
  42
  43  Nicolas Morales <nm529@cornell.edu>
  44
  45 =cut
  46
  47 use strict;
  48 use warnings;
  49
  50 sub instantiate {
  51     my $class = shift;
  52     my $type = shift;
  53     my $location = "CXGN/Genotype/Download/$type.pm";
  54     my $obj_class = "CXGN::Genotype::Download::$type";
  55     require $location;
  56     return $obj_class->new(@_);
  57 }
  58
  59 1;