disable assert commands for custom barcode whitelist (8e52c7dc) · Commits · github_fork / Universc

launch_universc.sh

+43 −1

Original line number	Diff line number	Diff line
		@@ -326,6 +326,20 @@ if [[ $setup == "true" ]]
		fi
		echo "whitelist converted for 10x compatibility with version 3 kit"
		fi
		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]
		then
		#restore functions if other technology run previously
		last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`
		if [[ $last != $technology ]]
		then
		sed -i "s/#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/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" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		fi
		echo "$DIR restored for $technology"
		else
		echo "$DIR ready for $technology"
		fi
		elif [[ $technology == "nadia" ]]
		then
		#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)
		@@ -381,6 +395,20 @@ if [[ $setup == "true" ]]
		gzip -f 3M-february-2018.txt
		echo "whitelist converted for Nadia compatibility with version 3 kit"
		fi
		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]
		then
		#disable functions if 10x technology run previously
		last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`
		if [[ $last != "10x" ]]
		then
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/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" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		fi
		echo "$DIR restored for $technology"
		else
		echo "$DIR ready for $technology"
		fi
		elif [[ $technology == "icell8" ]]
		then
		#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)
		@@ -436,12 +464,26 @@ if [[ $setup == "true" ]]
		gzip -f 3M-february-2018.txt
		echo "whitelist converted for iCELL8 compatibility with version 3 kit"
		fi
		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]
		then
		#disable functions if 10x technology run previously
		last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`
		if [[ $last != "10x" ]]
		then
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/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" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		fi
		echo "$DIR restored for $technology"
		else
		echo "$DIR ready for $technology"
		fi
		else
		echo "Error: technology not supported"
		cd -
		exit 1
		fi
		echo $technology > .last_called
		echo $technology > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called
		cd -
		echo "setup complete"
		else

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