refactor disabling cloupe (for cellranger version 2 or 3) (0ceb6396) · Commits · github_fork / Universc

launch_universc.sh

+18 −15

Original line number	Diff line number	Diff line
		@@ -1542,12 +1542,6 @@ if [[ $lock -eq 0 ]]; then
		sed -i "s/#*#if gem_group == prev_gem_group/if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#*#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#*#assert np.array_equal(in_mc.get_barcodes(), barcodes)/assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py
		#restore cloupe generation
		if [[ $verbose ]]; then
		echo "restore cloupe"
		fi
		sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		elif [[ $lastcall_p == "default:10x" ]] \|\| [[ ! -f $lastcallfile ]]; then
		#disable checking barcodes
		if [[ $verbose ]]; then
		@@ -1556,17 +1550,26 @@ if [[ $lock -eq 0 ]]; then
		sed -i "s/if gem_group == prev_gem_group/#if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py
		fi
		fi
		if [[ $technology == "10x" ]] && [[ $barcodefile == "default:10x" ]]; then
		#restore cloupe generation
		if [[ $verbose ]]; then
		echo "restore cloupe"
		fi
		sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		elif [[ $lastcall_p == "default:10x" ]] \|\| [[ ! -f $lastcallfile ]]; then
		#disable cloupe generation
		if [[ $verbose ]]; then
		echo "diasble cloupe"
		fi
		# sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		# sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		sed -i '/output_for_cloupe/s/^/#/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		# sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro #
		sed -i '/output_for_cloupe/s/CLOUPE_PREPROCESS\.output_for_cloupe/"null"/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		sed -i '/out cloupe cloupe/ {s/^/#/g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		fi
		echo " ${cellrangerpath} set for $technology"
		fi

		#whitelist file name
		v2=737K-august-2016.txt

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