From 8ae1644d615fdaa3718795ba1fb9d3c58b661f05 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 16:15:48 -0600
Subject: [PATCH] Try and fix CI countData
---
workflow/scripts/convertGeneSymbols.R | 4 ++--
workflow/tests/test_makeFeatureCounts.py | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/scripts/convertGeneSymbols.R b/workflow/scripts/convertGeneSymbols.R
index 05a1528..6cc5c0a 100644
--- a/workflow/scripts/convertGeneSymbols.R
+++ b/workflow/scripts/convertGeneSymbols.R
@@ -7,7 +7,7 @@ option_list=list(
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
-countTable <- read.csv(paste0(opt$repRID,"_countTable.csv"), stringsAsFactors=FALSE)
+countTable <- read.csv(paste0(opt$repRID,".countTable.csv"), stringsAsFactors=FALSE)
geneID <- read.delim("geneID.tsv", header=FALSE, stringsAsFactors=FALSE)
Entrez <- read.delim("Entrez.tsv", header=FALSE, stringsAsFactors=FALSE)
@@ -23,4 +23,4 @@ output <- merge(x=convert,y=countTable[,c("gene_name","gene_id","count","tpm")],
colnames(output) <- c("GENCODE_Gene_Symbol","NCBI_GeneID","Ensembl_GeneID","count","tpm")
output <- output[,c(1,3,2,4:5)]
-write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
+write.table(output,file=paste0(opt$repRID,"_tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py
index e67bca8..f6373b9 100644
--- a/workflow/tests/test_makeFeatureCounts.py
+++ b/workflow/tests/test_makeFeatureCounts.py
@@ -16,4 +16,4 @@ def test_makeFeatureCounts():
assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.tpmTable.csv'))
+ data_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))
--
GitLab