cowpi_get_and_prep_data.sh

#!/usr/bin/bash
yaml_config_output_file=$(realpath "${1}") # command line argument for output yaml configuration file for main script
cowpi_directory=$(realpath "${2}") # directory for cowpi output results to go
using_preclustered_data="${3}" # add a "y" or "n"
echo "${yaml_config_output_file}"
if [ ! -d "${cowpi_directory}" ] # checks if directory is present then produces it
then

    mkdir "${cowpi_directory}"

fi

# links to cowpi files download into array
cowpi_download_array=("https://zenodo.org/record/1252858/files/CowPi_V1.0_16S_precalculated.tab.gz?download=1" 
"https://zenodo.org/record/1252858/files/CowPi_V1.0_all_rumen_16S_combined.renamed.fas.gz?download=1"
"https://zenodo.org/record/1252858/files/CowPi_V1.0_ko_precalc1.tab.gz?download=1")

for download in "${cowpi_download_array[@]}" # loops over link array, downloads them, gives nice name and decompresses
do
    download_name=$(echo "${download}" | awk -F'/' '{print $NF}' | sed 's/?download=1//')
    download_path="${cowpi_directory}/${download_name}"
    wget "${download}" -O "${download_path}"
    gunzip "${download_path}"


done


cat "${cowpi_directory}/CowPi_V1.0_all_rumen_16S_combined.renamed.fas" | sed 's/-//g' > "${cowpi_directory}/CowPi_V1.0_all_rumen_16S_combined.fas" # removing the "-" to allow vsearch to work
if [ "${using_preclustered_data}" = "N" ]
then
    # array produced to produce configuration file, then adds the downloads produced above to the specific parts of the configuration file.
    yaml_configs_array=("copy_number_table_file: ${cowpi_directory}/CowPi_V1.0_16S_precalculated.tab" "ko_table: ${cowpi_directory}/CowPi_V1.0_ko_precalc1.tab" 
    "16s_sequence_table: ${cowpi_directory}/CowPi_V1.0_all_rumen_16S_combined.fas" "single_or_multiple_datasets:" "directory_of_datasets:" "threads:" "remove_chimeras:"
    "pre_clustered:")

    for config in "${yaml_configs_array[@]}" # for loop going over array to produce configuration file
    do
        
        echo "${config}" >> "${yaml_config_output_file}"

    done
else
    yaml_pre_clust_configs_array=("copy_number_table_file: ${cowpi_directory}/CowPi_V1.0_16S_precalculated.tab" "ko_table: ${cowpi_directory}/CowPi_V1.0_ko_precalc1.tab" \
    "16s_sequence_table: ${cowpi_directory}/CowPi_V1.0_all_rumen_16S_combined.fas" "single_or_multiple_datasets:" "directory_of_datasets:" "threads:" "remove_chimeras:" "pre_clustered: true" \
    "pre_clustered_files:"  "  fastq_cluster_file_path:" "  cluster_table_path:")

    for config in "${yaml_pre_clust_configs_array[@]}"
    do
        
        echo "${config}" >> "${yaml_config_output_file}"

    done
fi
rm "${cowpi_directory}/CowPi_V1.0_all_rumen_16S_combined.renamed.fas"