t/unit/CXGN/GenotypeIO.t

   1
   2 use strict;
   3 use Test::More;
   4 use Data::Dumper;
   5 use CXGN::GenotypeIO;
   6
   7 my $gtio = CXGN::GenotypeIO->new( { file => "t/data/cassava_test.vcf", format => 'vcf'});
   8
   9 is(scalar(@{$gtio->markers}), 15, "vcf marker count 1");
  10 is($gtio->markers->[0], "S1_14740", "vcf first marker name");
  11 is($gtio->markers->[-1], "S1_14911", "vcf last marker name");
  12 is($gtio->accessions->[0], "1002:250060174", "vcf first accession name");
  13 is($gtio->accessions->[-1], "Ug120191:250144197", "vcf last accession name");
  14 is(scalar(@{$gtio->accessions}), 9990, "vcf accession count");
  15 if (my $gt = $gtio->next()) {
  16     #print STDERR Dumper($gt->markers());
  17     is(scalar(@{$gt->markers()}), 15, "marker count in genotype");
  18 }
  19
  20 my $gtio2 = CXGN::GenotypeIO->new( { file => "t/data/dosage_transposed.csv", format=>'dosage_transposed' } );
  21
  22 #print STDERR "Markers: ".(Dumper($gtio->markers()))."\n";
  23 is(scalar(@{$gtio2->accessions()}), 9, "dosage_transposed accession count");
  24 is(scalar(@{$gtio2->markers()}), 3839, "dosage_transposed marker count");
  25
  26 is($gtio2->markers()->[0], "S10_14045", "dosage_transposed first marker");
  27 is($gtio2->markers()->[-1], "S10_23448593", "dosage_transposed last marker");
  28 is($gtio2->accessions()->[0], "1002.250060174", "dosage_transposed first accession");
  29 is($gtio2->accessions()->[-1], "1024.250060172", "dosage_transposed last accession");
  30
  31 my @gts;
  32 while(my $gt = $gtio2->next()) {
  33     print STDERR $gt->name()."\n";
  34     push @gts, $gt;
  35 }
  36
  37 is($gts[0]->name(), "1002.250060174", "genotype object accession name");
  38 is($gts[1]->rawscores()->{S10_131712}, 0.06, "genotype object markerscore 1");
  39 is($gts[7]->rawscores()->{S10_14045}, 0.2, "genotype object markerscore 2");
  40
  41 my $gtio3 = CXGN::GenotypeIO->new( { file => "t/data/dosage_transposed.csv", format=>'blablabla' });
  42
  43 done_testing();