Command throw errors in scripts/flatten_roda.sh

[Minys233]

I downloaded the roda pdb subdir, with the following command

aws s3 cp --no-sign-request 's3://openfold/pdb' ./pdb --recursive

Then, following the readme, I ran the scripts/flatten_roda.sh and it keep throwing errors:

ls: cannot access 'a3m': No such file or directory
ls: cannot access 'hhr': No such file or directory
./scripts/flatten_roda.sh: 32: [[: not found
./scripts/flatten_roda.sh: 34: [[: not found
./scripts/flatten_roda.sh: 34: [[: not found

After a quick check, it turned out to be a bug at L32, where the ls command in this line elif [[ -z $(ls "${subdir}")]]; then will fail since $subdir equal to a3m or hhr here, without prefix path.

openfold/scripts/flatten_roda.sh

Lines 26 to 42 in ef0c9fa

	for chain_dir in $(ls "${RODA_DIR}"); do
	CHAIN_DIR_PATH="${RODA_DIR}/${chain_dir}"
	for subdir in $(ls "${CHAIN_DIR_PATH}"); do
	if [[ ! -d "$subdir" ]]; then
	echo "$subdir is not directory"
	continue
	elif [[ -z $(ls "${subdir}")]]; then
	continue
	elif [[ $subdir = "pdb" ]] || [[ $subdir = "cif" ]]; then
	mv "${CHAIN_DIR_PATH}/${subdir}"/* "${DATA_DIR}"
	else
	CHAIN_ALIGNMENT_DIR="${ALIGNMENT_DIR}/${chain_dir}"
	mkdir -p "${CHAIN_ALIGNMENT_DIR}"
	mv "${CHAIN_DIR_PATH}/${subdir}"/* "${CHAIN_ALIGNMENT_DIR}"
	fi
	done
	done

[Minys233]

It turns out that you should modify Line 29 to:

        if [[ ! -d "${CHAIN_DIR_PATH}/$subdir" ]]; then

and Line 32 to:

        elif [[ -z $(ls "${CHAIN_DIR_PATH}/${subdir}") ]]; then