config.yaml

data:
    GTEx: data/GTEx_Analysis_v8_eQTL/
    gwas: data/gwas-association-downloaded_2020-07-21-EFO_0010638-withChildTraits.tsv
    expression: data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz
    gencode: data/gencode.v26.GRCh38.genes.gtf
    loeuf: data/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz
    dice: data/dice/
    drugbank: 'data/drugbank/full database.xml'

analysis:
    snps: analysis/drug_response_combined_curated.txt
    gwas_snps: analysis/gwas.txt
    combined_snps: analysis/drug_response_combined_curated.txt
    curated_snps: analysis/drug_response_combined_curated_resolved_gene_range.txt
    genes_by_drugs: analysis/genes_by_drugs.txt

results:
    eqtls: results/eqtls/
    constrained_eqtls: results/eqtls/constrained/
    unconstrained_eqtls: results/eqtls/unconstrained/
    unconstrained_afc: results/eqtls/unconstrained/eqtls_afc.txt
    unconstrained_for_afc: results/eqtls/unconstrained/eqtls_for_afc.txt
    annotations_snps: results/haploreg/drug_response_combined_haploreg.txt
    annotations_genes: results/gencode/gene_annotations.txt
    loeuf: results/loeuf.txt
    dice: results/dice.txt
    population: results/population.txt
    drugbank: results/drugbank/
    druggable_genes: results/drugbank/genes.tsv
    asthma_drugs: results/drugbank/asthma_drugs.txt
    drugs: results/drugbank/drugs.txt
    drug_disease: results/drugbank/drug_disease.txt
    asthma_drug_interactions: results/drugbank/asthma_drug_interactions.txt
    bootstrap_drugs: results/drugbank/bootstrap_summary_drugs.txt
    bootstrap_genes: results/drugbank/bootstrap_summary.txt
    string_dir: results/stringdb/
    asthma_drugs_ppi: results/stringdb/string_asthma_drugs.txt
    asthma_drugs_ppi_bootstrap: results/stringdb/string_asthma_drugs.txt


tissues:
    lung: Lung
    blood: Whole_Blood
    list: ["Lung", "Whole_Blood"]