Study Section

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

Example Configuration

[study]
enabled = yes

name = Study
id = study

prefix = data
file_format = vcf
description = %(work_dir)s/data/description.md

studyType = WE
year = 2019

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

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

[study]

The properties for this section are explained below.

name

name = <study name>

Name which will be used as display name for the study. Default value for it is the value of the id property from the study.

id

id = <study identifier>

Identifier of the study.

description

description = <study description>

This property shows if the Dataset Description tab is enabled for the study. 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.

prefix

prefix = <directory of data>

This property shows the location of the directory that contains the study’s data files. It can be an absolute or relative path. If it is a relative path, it must be relative to the directory containing the study’s configuration file.

file_format

file_format = <vcf / impala>

This property shows the file format of the study data files. Supported formats are impala and vcf. In the impala format, files are queried with the help of Apache Impala and the expected file format is Apache Parquet. On the other hand, if vcf is the chosen file format, files are expected to be valid tsv files in the VCF format. Querying in the VCF file format is implemented with the help of pandas.

phenoDB

phenoDB = <pheno db name>

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

studyType

studyType = <WE / WG / TG>

This property gives the type of the study. Possible types are:

WE - Whole Exome

WG - Whole Genome

TG - Targeted Genome

year

year = <YYYY>

This property specifies the release year of the study.

pubMed

pubMed = <id of PubMed article>

This property contains the id of an article from PubMed associated with the study. You can see more about PubMed on their website - https://www.ncbi.nlm.nih.gov/pubmed/.

hasDenovo

hasDenovo = <boolean>

This property specifies if the study contains variants with denovo inheritance. This property takes a boolean value.

hasTransmitted

hasTransmitted = <boolean>

This property specifies if the study contains variants with transmitted type inheritance. This property takes a boolean value.

hasComplex

hasComplex = <boolean>

This property specifies if the study contains variants with complex variant type. 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. This property takes a boolean value.

commonReport

commonReport = <boolean>

This property specifies if the Dataset Statistics tab is enabled for the study. You can see more about the Dataset Statistics tab here. This property takes a boolean value.

genotypeBrowser

genotypeBrowser = <boolean>

This property specifies if the Genotype Browser tab is enabled for the study. You can see more about the Genotype Browser tab here. This property takes a boolean value.

phenotypeBrowser

phenotypeBrowser = <boolean>

This property specifies if the Phenotype Browser tab is enabled for the study. You can see more about the Phenotype Browser tab here. This property takes a boolean value.

enrichmentTool

enrichmentTool = <boolean>

This property specifies if the Enrichment Tool tab is enabled for the study. You can see more about the Enrichment Tool tab here. This property takes a boolean value.

phenotypeTool

phenotypeTool = <boolean>

This property specifies if the Phenotype Tool tab is enabled for the study. You can see more about the Phenotype Tool tab here. This property takes a boolean value.

enabled

enabled = <boolean>

DEFAULT: True

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