possible solution to the sed-newline issue on mac

assemble.sh

@@ -39,7 +39,8 @@ echo "Integration with ClinVar stored in ${genes_variants_out_path}"
 
 genes_line=`cat ${genes_variants_out_path} | grep "genes in total"`
 genes_out_path=${genes_variants_out_path/02-genes_variants/03-genes}
-echo ${genes_line#*:} | sed 's/\,/\n/g' > ${genes_out_path}
+#echo ${genes_line#*:} | sed 's/\,/\n/g' > ${genes_out_path}
+echo ${genes_line#*:} | tr ',' '\n' > ${genes_out_path}
 echo "Genes stored in ${genes_out_path}"
 
 minerva_genes_out_path=${RES_DIR}/04-minerva-genes-id_${ORPHANET_IDS_UNDERSCORE}.txt
@@ -47,7 +48,8 @@ $PYTHON_BIN $ASSOCIATIONS_DIR/minerva_genes.py -f ${genes_out_path} > ${minerva_
 
 var_line=`cat ${genes_variants_out_path} | grep "variants in total"`
 variants_out_path=${genes_variants_out_path/02-genes_variants/03-variants}
-echo ${var_line#*:} | sed 's/\,/\n/g' > ${variants_out_path}
+#echo ${var_line#*:} | sed 's/\,/\n/g' > ${variants_out_path}
+echo ${var_line#*:} | tr ',' '\n' > ${variants_out_path}
 echo "Variants stored in ${variants_out_path}"
 
 minerva_variants_out_path=${RES_DIR}/04-minerva-variants-id_${ORPHANET_IDS_UNDERSCORE}.txt