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Extra checks on column values in qualitative data

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commit 7daa4d528882c9f9b3576180d0717d69d1dc053f 1 parent ef0c9eb
@kimrutherford authored
Showing with 16 additions and 0 deletions.
  1. +16 −0 lib/PomBase/Import/Qualitative.pm
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16 lib/PomBase/Import/Qualitative.pm
@@ -97,8 +97,24 @@ method load($fh)
my $type = $columns_ref->{"Type"};
my $during = $columns_ref->{"During"};
my $average_copies_per_cell = $columns_ref->{"Average copies per cell"};
+ if ($average_copies_per_cell eq 'NA') {
+ $average_copies_per_cell = undef;
+ }
my $range = $columns_ref->{"Range"};
+ if ($range eq 'NA') {
+ $range = undef;
+ }
my $qual_gene_ex_cell_distribution = $columns_ref->{"Evidence"};
+ if (lc $qual_gene_ex_cell_distribution eq 'population' or
+ lc $qual_gene_ex_cell_distribution eq 'population wide') {
+ $qual_gene_ex_cell_distribution = 'population_wide';
+ } else {
+ if (lc $qual_gene_ex_cell_distribution eq 'single cell') {
+ $qual_gene_ex_cell_distribution = 'single cell';
+ } else {
+ die qq(text in "Evidence" column not recognised: $qual_gene_ex_cell_distribution\n);
+ }
+ }
my $conditions = $columns_ref->{"Condition"};
my $source = $columns_ref->{"Source"};
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