Offline addons (#139)

* Update gene_name_mapping.R * add hpoFile option * fix hg38 on FRASER counting * doc hpoFile, files to download * add hpoFile option * doc hpoFile, files to download * vcf doc fixed * gene_biotype added * hpo term column can be blank Co-authored-by: Vicente <yepez@in.tum.de>
gagneurlab · Nov 12, 2020 · f0c37ca · f0c37ca
1 parent 5b9be6c
commit f0c37ca
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/drop/modules/aberrant-expression-pipeline/OUTRIDER/results.R b/drop/modules/aberrant-expression-pipeline/OUTRIDER/results.R
@@ -55,7 +55,7 @@ if(!is.null(gene_annot_dt$gene_name)){
 # Add HPO terms, requires online connection and for there to be annotated HPO terms
 sa <- fread(snakemake@config$sampleAnnotation)
 if(!is.null(sa$HPO_TERMS) & nrow(res) > 0){
-  if(!all(is.na(sa$HPO_TERMS))){
+  if(!all(is.na(sa$HPO_TERMS)) & ! all(sa$HPO_TERMS == '')){
     res <- add_HPO_cols(res, hpo_file = snakemake@params$hpoFile)
   }
 }

diff --git a/drop/modules/aberrant-splicing-pipeline/FRASER/07_extract_results_FraseR.R b/drop/modules/aberrant-splicing-pipeline/FRASER/07_extract_results_FraseR.R
@@ -92,7 +92,7 @@ if(length(res_junc) > 0){
   # add HPO overlap information
   sa <- fread(snakemake@config$sampleAnnotation)
   if(!is.null(sa$HPO_TERMS)){
-    if(!all(is.na(sa$HPO_TERMS))){
+    if(!all(is.na(sa$HPO_TERMS)) & ! all(sa$HPO_TERMS == '')){
       res_genes_dt <- add_HPO_cols(res_genes_dt, hpo_file = snakemake@params$hpoFile)
     }
   }

diff --git a/drop/template/Scripts/Pipeline/SampleAnnotation.R b/drop/template/Scripts/Pipeline/SampleAnnotation.R
@@ -81,6 +81,7 @@ unique(sa[,.(RNA_ID, DROP_GROUP)])$DROP_GROUP %>% strsplit(',') %>% unlist %>%
 # Obtain genes that overlap with HPO terms
 #+echo=F
 if(!is.null(sa$HPO_TERMS)){
+  if(!all(is.na(sa$HPO_TERMS)) & ! all(sa$HPO_TERMS == '')){
   sa2 <- sa[, .SD[1], by = RNA_ID]
 
   filename <- ifelse(is.null(snakemake@params$hpo_file), 
@@ -99,8 +100,8 @@ if(!is.null(sa$HPO_TERMS)){
          file.path(snakemake@config$root, 
                    'processed_data/sample_anno/genes_overlapping_HPO_terms.tsv'), 
          na = NA, sep = "\t", row.names = F, quote = F)
+  }
 }
-
 sa[, DROP_GROUP := gsub(' ', '', DROP_GROUP)]
 if(!is.null(sa$ICD_10))
   sa[, ICD_10 := toupper(ICD_10)]