From 186b862063ce50ee1d282bc610196630c4ecac61 Mon Sep 17 00:00:00 2001 From: Brent Pedersen Date: Wed, 5 May 2021 14:47:00 +0200 Subject: [PATCH] update link in tsv help to new hpo file closes #91 --- src/slivarpkg/tsv.nim | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/slivarpkg/tsv.nim b/src/slivarpkg/tsv.nim index b626461..6b05874 100644 --- a/src/slivarpkg/tsv.nim +++ b/src/slivarpkg/tsv.nim @@ -182,7 +182,7 @@ proc main*(dropfirst:bool=false) = help("""convert filtered VCF to tab-separated-value spreadsheet for final filtering create a --gene-description file e.g. from human phenotype ontology with: - wget -qO - http://compbio.charite.de/jenkins/job/hpo.annotations.monthly/lastSuccessfulBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt | cut -f 2,3 > gene_desc.txt + wget -qO - http://purl.obolibrary.org/obo/hp/hpoa/phenotype_to_genes.txt | awk 'BEGIN{FS=OFS="\t"} (NR > 1) { print $4, $2 }' > gene_desc.txt or from clinvar with: wget -qO - ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/gene_condition_source_id | cut -f 2,5 | grep -v ^$'\t' > clinvar_gene_desc.txt or gene->pLI with: