Dataset Section

The configuration section for a dataset follows the general INI format. Its name must be dataset - this will indicate that it is a dataset configuration section. This configuration section must properly describe one dataset. Either this section or the ref:<study study_section> section must be present in the config file.

Example Configuration

[dataset]
enabled = yes

name = Dataset
id = dataset

studies = study

description = %(work_dir)s/data/description.md

hasDenovo = yes
hasTransmitted = no
hasComplex = no
hasCNV = no

commonReport = True
genotypeBrowser = True
phenotypeBrowser = True
enrichmentTool = False
phenotypeTool = False

[dataset]

The properties for this section are explained below.

name

name = <dataset name>

Name which will be used as a display name for the dataset. The default value is the value of the id property from the dataset.

id

id = <dataset identifier>

Identifier of the dataset.

studies

studies = <comma-separated list of study ids>

This property defines which studies are in the dataset. It’s format is a comma-separated list of study ids. You can see the study section configuration here.

description

description = <study description>

This property shows if the Dataset Description tab is enabled for the dataset. It can contain a description as a string in markdown format or as an absolute or relative path to a markdown file. You can see more about the Dataset Description tab here.

phenoDB

phenoDB = <pheno db name>

The corresponding pheno DB for the dataset. It must be a valid pheno DB id.

hasDenovo

hasDenovo = <boolean>

This property shows if the study contains variants with denovo inheritance. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if at least one of the studies’ hasDenovo property is True as well. This property takes a boolean value.

hasTransmitted

hasTransmitted = <boolean>

This property shows if the study contains variants with transmitted inheritance. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if at least one of the studies’ hasTransmitted property is True as well. This property takes a boolean value.

hasComplex

hasComplex = <boolean>

This property shows if the study contains variants with complex variant type. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if at least one of the studies’ hasComplex property is True as well. This property takes a boolean value.

hasCNV

hasCNV = <boolean>

This property shows if the study contains variants with CNV, CNV+ or CNV- effect types or CNV variant type. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if at least one of the studies’ hasCNV property is True as well. This property takes a boolean value.

commonReport

commonReport = <boolean>

This property shows if Dataset Statistics tab is enabled for the dataset. You can see more about Dataset Statistics tab here. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if all of the studies’ commonReport properties are True as well. This property takes a boolean value.

genotypeBrowser

genotypeBrowser = <boolean>

This property shows if Genotype Browser tab is enabled for the study. You can see more about Genotype Browser tab here. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if all of the studies’ genotypeBrowser properties are True as well. This property takes a boolean value.

phenotypeBrowser

phenotypeBrowser = <boolean>

This property shows if Phenotype Browser tab is enabled for the study. You can see more about Phenotype Browser tab here. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if all of the studies’ phenotypeBrowser properties are True as well. This property takes a boolean value.

enrichmentTool

enrichmentTool = <boolean>

This property shows if Enrichment Tool tab is enabled for the study. You can see more about Enrichment Tool tab here. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if all of the studies’ enrichmentTool properties are True as well. This property takes a boolean value.

phenotypeTool

phenotypeTool = <boolean>

This property shows if Phenotype Tool tab is enabled for the study. You can see more about Phenotype Tool tab here. It has default value if it is defined in all of the dataset’s defined studies and its value is True only if all of the studies’ phenotypeTool properties are True as well. This property takes a boolean value.

enabled

enabled = <boolean>

DEFAULT: True

This property enables the dataset. This property takes a boolean value.