Update Snakefile

urmi-21 · Mar 6, 2021 · 0b062f4 · 0b062f4
1 parent 0ee3361
commit 0b062f4
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/case_studies/Covid_RNA-Seq/Snakemake/Snakefile b/case_studies/Covid_RNA-Seq/Snakemake/Snakefile
@@ -68,11 +68,11 @@ rule merge:
 		#gene counts
 		df_gene=df[['GeneID']+names].copy()
 		df_gene = df_gene.groupby(['GeneID'],as_index = False).sum()
-        df_gene['GeneID']=df_gene['GeneID'].str.split('.').str[0]
-        #add gene metadata
-        md=pd.read_csv('Ens_gene_metadata.txt',sep='\t',skiprows=0) 
-        md.rename(columns={ md.columns[0]: "GeneID" }, inplace = True)
-        df_gene=md.merge(df_gene, on=['GeneID'], how='right')
-        #reorder
-        df_gene = df_gene[ ['Gene name'] + [ col for col in df_gene.columns if col != 'Gene name' ] ]
+     		df_gene['GeneID']=df_gene['GeneID'].str.split('.').str[0]
+        	#add gene metadata
+        	md=pd.read_csv('Ens_gene_metadata.txt',sep='\t',skiprows=0) 
+        	md.rename(columns={ md.columns[0]: "GeneID" }, inplace = True)
+        	df_gene=md.merge(df_gene, on=['GeneID'], how='right')
+        	#reorder
+        	df_gene = df_gene[ ['Gene name'] + [ col for col in df_gene.columns if col != 'Gene name' ] ]
 		df_gene.to_csv(DIR+'/results_TPM_gene.tsv',sep='\t',index=False)