lib/CXGN/GenotypeIO.pm

   1
   2 package CXGN::GenotypeIO;
   3
   4 use Moose;
   5 use JSON::Any;
   6 use Data::Dumper;
   7 use CXGN::Genotype;
   8
   9 use CXGN::GenotypeIOmain;
  10
  11 has 'format' => ( isa => 'Str',
  12                   is  => 'rw',
  13                   default => 'vcf', # or dosage
  14     );
  15
  16 has 'plugin' => ( isa => 'Ref',
  17                   is  => 'rw',
  18     );
  19
  20
  21
  22 sub BUILD {
  23     my $self = shift;
  24     my $args = shift;
  25
  26     my $plugin = CXGN::GenotypeIOmain->new();
  27
  28     if ($args->{format} eq "vcf") {
  29         $plugin->load_plugin("VCF");
  30     }
  31     elsif ($args->{format} eq "dosage") {
  32         $plugin->load_plugin("Dosage");
  33     }
  34     elsif ($args->{format} eq "dosage_transposed") {
  35         $plugin->load_plugin("DosageTransposed");
  36     }
  37     else {
  38         print STDERR "No valid format provided. Using vcf.\n";
  39         $plugin->load_plugin("VCF");
  40     }
  41     $plugin->file($args->{file});
  42
  43     my $data = $plugin->init($args);
  44
  45     $self->plugin($plugin);
  46
  47     #print STDERR "count = $data->{count}\n";
  48     #$self->count($data->{count});
  49     #$self->header($data->{header});
  50     #$self->current(0);
  51 }
  52
  53 sub next {
  54     my $self  =shift;
  55
  56     my ($markers, $rawscores, $accession_name) = $self->plugin()->next();
  57     if (keys(%$rawscores)==0) { return undef; }
  58     my $gt = CXGN::Genotype->new();
  59     $gt->name($accession_name);
  60     $gt->rawscores($rawscores);
  61     $gt->markers($self->markers());
  62
  63 #    print STDERR "NAME: $genotype\n";
  64 #    print STDERR join ", ", keys %$rawscores;
  65
  66     return $gt;
  67 }
  68
  69 sub accessions {
  70     my $self = shift;
  71     return $self->plugin()->accessions();
  72 }
  73
  74 sub observation_unit_names {
  75     my $self = shift;
  76     return $self->plugin()->observation_unit_names();
  77 }
  78
  79 sub header_information_lines {
  80     my $self = shift;
  81     return $self->plugin()->header_information_lines();
  82 }
  83
  84 sub markers {
  85     my $self = shift;
  86     #print STDERR "Markers now: ".Dumper($self->plugin()->markers())."\n";
  87     return $self->plugin()->markers();
  88 }
  89
  90 sub header {
  91     my $self = shift;
  92     #print STDERR "Markers now: ".Dumper($self->plugin()->markers())."\n";
  93     return $self->plugin()->header();
  94 }
  95
  96 sub close {
  97     my $self = shift;
  98     $self->plugin()->close();
  99 }
 100
 101 sub summary_stats {
 102     my $self = shift;
 103
 104     my $file = $self->plugin()->file();
 105     my $stats = $self->plugin()->summary_stats($file);
 106     return $stats;
 107 }
 108
 109
 110 1;