New pipeline update

OT2-setup/data/labware.csv

@@ -0,0 +1,25 @@
+protocol,location,labware,well_name,reactant,volume
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,A1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,B1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,C1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,D1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,E1,pJKR,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,F1,pJKR,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,G1,pJKR,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,H1,pJKR,20
+transformation,4,usascientific_96_wellplate_2.4ml_deep,A1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,B1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,C1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,D1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,E1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,F1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,G1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,H1,cells,300
+transformation,5,usascientific_96_wellplate_2.4ml_deep,A1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,B1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,C1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,D1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,E1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,F1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,G1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,H1,SOC,1500

OT2-setup/data/spotting-data.csv

@@ -0,0 +1,97 @@
+plate_location,source_well,destination_well,spotting_volume,agar_plate_weight
+1,A1,A1,5,33
+1,B1,B1,5,33
+1,C1,C1,5,33
+1,D1,D1,5,33
+1,E1,E1,5,33
+1,F1,F1,5,33
+1,G1,G1,5,33
+1,H1,H1,5,33
+1,A2,A2,5,33
+1,B2,B2,5,33
+1,C2,C2,5,33
+1,D2,D2,5,33
+1,E2,E2,5,33
+1,F2,F2,5,33
+1,G2,G2,5,33
+1,H2,H2,5,33
+1,A3,A3,5,33
+1,B3,B3,5,33
+1,C3,C3,5,33
+1,D3,D3,5,33
+1,E3,E3,5,33
+1,F3,F3,5,33
+1,G3,G3,5,33
+1,H3,H3,5,33
+1,A4,A4,5,33
+1,B4,B4,5,33
+1,C4,C4,5,33
+1,D4,D4,5,33
+1,E4,E4,5,33
+1,F4,F4,5,33
+1,G4,G4,5,33
+1,H4,H4,5,33
+1,A5,A5,5,33
+1,B5,B5,5,33
+1,C5,C5,5,33
+1,D5,D5,5,33
+1,E5,E5,5,33
+1,F5,F5,5,33
+1,G5,G5,5,33
+1,H5,H5,5,33
+1,A6,A6,5,33
+1,B6,B6,5,33
+1,C6,C6,5,33
+1,D6,D6,5,33
+1,E6,E6,5,33
+1,F6,F6,5,33
+1,G6,G6,5,33
+1,H6,H6,5,33
+1,A7,A7,5,33
+1,B7,B7,5,33
+1,C7,C7,5,33
+1,D7,D7,5,33
+1,E7,E7,5,33
+1,F7,F7,5,33
+1,G7,G7,5,33
+1,H7,H7,5,33
+1,A8,A8,5,33
+1,B8,B8,5,33
+1,C8,C8,5,33
+1,D8,D8,5,33
+1,E8,E8,5,33
+1,F8,F8,5,33
+1,G8,G8,5,33
+1,H8,H8,5,33
+1,A9,A9,5,33
+1,B9,B9,5,33
+1,C9,C9,5,33
+1,D9,D9,5,33
+1,E9,E9,5,33
+1,F9,F9,5,33
+1,G9,G9,5,33
+1,H9,H9,5,33
+1,A10,A10,5,33
+1,B10,B10,5,33
+1,C10,C10,5,33
+1,D10,D10,5,33
+1,E10,E10,5,33
+1,F10,F10,5,33
+1,G10,G10,5,33
+1,H10,H10,5,33
+1,A11,A11,5,33
+1,B11,B11,5,33
+1,C11,C11,5,33
+1,D11,D11,5,33
+1,E11,E11,5,33
+1,F11,F11,5,33
+1,G11,G11,5,33
+1,H11,H11,5,33
+1,A12,A12,5,33
+1,B12,B12,5,33
+1,C12,C12,5,33
+1,D12,D12,5,33
+1,E12,E12,5,33
+1,F12,F12,5,33
+1,G12,G12,5,33
+1,H12,H12,5,33

OT2-setup/data/spotting-parameters.json

@@ -0,0 +1,16 @@
+{
+    "transformation_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "agar_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "pipette_tiprack_name":"opentrons_96_tiprack_20ul",
+    "pipette_tiprack_slots":[6,5],
+    "pipette_name":"p20_multi_gen2",
+    "pipette_mount":"left",
+    "aspirate_rate":30,
+    "dispense_rate":60,
+    "aspirate_height":0.1,
+    "dispense_height":0.1,
+    "dead_volume": 1,
+    "plate_weight":14.11,
+    "agar_density":0.00095,
+    "spotting_height":0.5
+}

OT2-setup/data/transformation-data.csv

@@ -0,0 +1,33 @@
+dna_well,dna_volume,cells_well,cells_volume,soc_well,soc_volume,transformation_well
+A1,3,A2,30,A1,150,A1
+B1,3,B2,30,B1,150,B1
+C1,3,C2,30,C1,150,C1
+D1,3,D2,30,D1,150,D1
+E1,3,E2,30,E1,150,E1
+F1,3,F2,30,F1,150,F1
+G1,3,G2,30,G1,150,G1
+H1,3,H2,30,H1,150,H1
+A1,2,A2,20,A1,100,A2
+B1,2,B2,20,B1,100,B2
+C1,2,C2,20,C1,100,C2
+D1,2,D2,20,D1,100,D2
+E1,2,E2,20,E1,100,E2
+F1,2,F2,20,F1,100,F2
+G1,2,G2,20,G1,100,G2
+H1,2,H2,20,H1,100,H2
+A1,1,A2,10,A1,50,A3
+B1,1,B2,10,B1,50,B3
+C1,1,C2,10,C1,50,C3
+D1,1,D2,10,D1,50,D3
+E1,1,E2,10,E1,50,E3
+F1,1,F2,10,F1,50,F3
+G1,1,G2,10,G1,50,G3
+H1,1,H2,10,H1,50,H3
+A1,0,A2,30,A1,150,A4
+B1,0,B2,30,B1,150,B4
+C1,0,C2,30,C1,150,C4
+D1,0,D2,30,D1,150,D4
+E1,0,E2,30,E1,150,E4
+F1,0,F2,30,F1,150,F4
+G1,0,G2,30,G1,150,G4
+H1,0,H2,30,H1,150,H4

OT2-setup/data/transformation-parameters.json

@@ -0,0 +1,25 @@
+{
+    "init_temp":4,
+    "init_time":20,
+    "heat_temp":42,
+    "heat_time":30,
+    "cool_temp":4,
+    "cool_time":2,
+    "inc_temp":37,
+    "inc_time":60,
+    "dna_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "dna_plate_slot":1,
+    "cells_plate_name": "usascientific_96_wellplate_2.4ml_deep",
+    "cells_plate_slot":4,
+    "soc_plate_name": "usascientific_96_wellplate_2.4ml_deep",
+    "soc_plate_slot": 5,
+    "transformation_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "right_pipette_tiprack_name":"opentrons_96_tiprack_20ul",
+    "right_pipette_tiprack_slots":[2,3],
+    "right_pipette_name":"p20_multi_gen2",
+    "right_pipette_mount":"right",
+    "left_pipette_tiprack_name":"opentrons_96_tiprack_300ul",
+    "left_pipette_tiprack_slots":[6,9],
+    "left_pipette_name":"p300_multi_gen2",
+    "left_pipette_mount":"left"
+}

OT2-setup/generate-protocol.sh

@@ -0,0 +1,134 @@
+#!/bin/bash
+
+# Function to display usage information
+usage() {
+    echo "Usage: $0 experiment=experiment1,experiment2,... [csv_file=csv1,csv2,...] [json_file=json1,json2,...]"
+    exit 1
+}
+
+# Check if the correct number of arguments is provided
+if [ "$#" -lt 1 ]; then
+    usage
+fi
+
+# Set default values
+csv_files=""
+json_files=""
+
+# Parse command-line arguments
+for arg in "$@"; do
+    case $arg in
+        experiment=*)
+            experiment_types="${arg#*=}"
+            ;;
+        csv_file=*)
+            csv_files="${arg#*=}"
+            ;;
+        json_file=*)
+            json_files="${arg#*=}"
+            ;;
+        *)
+            echo "Error: Invalid argument: $arg"
+            usage
+            ;;
+    esac
+done
+
+# Function to check if a file exists
+check_file_exists() {
+    if [ ! -f "$1" ]; then
+        echo "Error: $1 file not found."
+        exit 1
+    fi
+}
+
+# Function to extract variable from JSON
+extract_variable_from_json() {
+    local json_file="$1"
+    local variable_name="$2"
+    local variable_line=$(grep "$variable_name" "$json_file")
+
+    # Extract the value part
+    local variable_value=$(echo "$variable_line" | cut -d '"' -f 4)
+    echo "$variable_value"
+}
+
+# Function to process each experiment type
+process_experiment_type() {
+    local experiment_type="$1"
+    local input_csv="$2"
+    local input_json="$3"
+
+    local template_py=""
+
+    case "$experiment_type" in
+        transformation)
+            template_py="./setup/protocol-templates/transformation-template.py"
+            ;;
+        spotting)
+            template_py="./setup/protocol-templates/spotting-template.py"
+            ;;
+        *)
+            echo "Error: Unsupported experiment type: $experiment_type"
+            exit 1
+            ;;
+    esac
+
+    # Check if the template Python file exists
+    check_file_exists "$template_py"
+
+    # If CSV file not specified, use default in "data" folder
+    if [ -z "$input_csv" ]; then
+        input_csv="data/${experiment_type}-data.csv"
+    fi
+    # If JSON file not specified, use default in "data" folder
+    if [ -z "$input_json" ]; then
+        input_json="data/${experiment_type}-parameters.json"
+    fi
+
+    # Check if the input CSV file exists
+    check_file_exists "$input_csv"
+    # Check if the input JSON file exists
+    check_file_exists "$input_json"
+
+    # Read contents of input CSV into a variable
+    csv_content=$(<"$input_csv")
+
+    # Define the content for protocol.py
+    new_content="csv_file = \"\"\"\n$csv_content\n\"\"\"\n\n"
+    # Read contents of input JSON into a variable and remove newlines
+    json_content="parameters_json = \"\"\"$(<"$input_json" tr -d '\n' | tr -d '[:space:]'| tr -d '[:space:]')\"\"\"\n"
+
+    # Extract the name from the template file
+    template_name=$(basename "$template_py" | sed 's/.*\([a-zA-Z]\)-template\.py/\1/')
+    # Generate the output file name in the "protocols" folder
+    output_folder="results"
+    output_file="${output_folder}/${experiment_type}-protocol.py"
+
+    # Create the protocols folder if it doesn't exist
+    mkdir -p "$output_folder"
+
+    # If the file exists, append the new content at the top
+    old_content=$(<"$template_py")
+    echo -e "$new_content$json_content$old_content" > "$output_file"
+    echo "Protocol for $experiment_type has been generated. Output file: $output_file"
+
+    # Get the transformation_plate_name and dna_plate_name from the parameters JSON
+    transformation_plate_name=$(extract_variable_from_json "$input_json" "transformation_plate_name")
+    dna_plate_name=$(extract_variable_from_json "$input_json" "dna_plate_name")
+
+    # Call the R scripts 
+    Rscript ./setup/create-labware/visualise-labware.R ./data/labware.csv "${output_folder}"
+    Rscript ./setup/create-labware/visualise-labware-2.R ./data/transformation-data.csv "${output_folder}"
+    Rscript ./setup/instruction-templates/transformation-instruction.R "./data/transformation-parameters.json" "${output_folder}/Instructions.pdf"
+}
+
+# Split comma-separated values into arrays
+IFS=',' read -ra experiment_type_array <<< "$experiment_types"
+IFS=',' read -ra csv_file_array <<< "$csv_files"
+IFS=',' read -ra json_file_array <<< "$json_files"
+
+# Process each experiment type
+for ((i=0; i<"${#experiment_type_array[@]}"; i++)); do
+    process_experiment_type "${experiment_type_array[i]}" "${csv_file_array[i]}" "${json_file_array[i]}"
+done