Validate Hydra Store raw sequence data and metadata

Script name: validate_seq_data.py or validate_seq_data.sh

python source code

bash source code

Validates Ocean DNA raw sequence data against its corresponding metadata. The python script is faster than the bash script.

To download the script:

# download python script
wget https://github.com/dmacguigan/SI-Ocean-DNA/blob/main/scripts/data_management/raw_sequence_validate/validate_seq_data.py

# download bash script
wget https://github.com/dmacguigan/SI-Ocean-DNA/blob/main/scripts/data_management/raw_sequence_validate/validate_seq_data.sh

Run python validate_seq_data.py -h or bash validate_seq_data.sh -h to print the help documentation.

DESCRIPTION:
    Validates Ocean DNA raw sequence data against its corresponding metadata.
    This script checks for correct naming, file existence, and ensures that
    the contents of the metadata file and sequence data directory match.

ARGUMENTS:
  MAP_FILE
      Path to a text file mapping metadata to sequence data directories.
      It requires a header row (which is ignored). Each subsequent line
      should contain two space-separated columns:

      Column 1: The metadata CSV filename.
                - Must be in "/store/public/oceandna/raw_sequence_metadata"
                - Must end with "_mapfile.csv"
                - Its header must start with "ID,R1,R2,Taxon,UniqueID"

      Column 2: The raw sequence data directory name.
                - Must be in "/store/public/oceandna/raw_sequence_data"
                - Must contain one or more .fastq.gz files

OPTIONS:
  -h, --help
      Display this help message and exit.

Example MAP_FILE.