First working version sent to Dave.

set_positions.py

+import pandas
+import argparse
+import logging
+import os
+import sys
+
+logging.basicConfig(level=logging.INFO)
+
+def main(args):
+    
+    filename = args.filename
+    
+    if not os.path.isfile(filename):
+        raise IOError("File not found. Make sure the file '%s' exists and is readable." % (filename))
+
+    outfilename = args.out
+    
+    if outfilename.split(".")[-1] != "py":
+        raise RuntimeError("Output filename must have the extension '.py'. Aborting now, please restart.")
+    
+    if os.path.exists(outfilename):
+        logging.warning("%s exists and will be renamed to %s.", outfilename, outfilename+".old")
+        os.rename(src=outfilename, dst=outfilename+".old", src_dir_fd=None, dst_dir_fd=None)
+
+    logging.info("Reading positions from %s .", filename)
+    positions = pandas.read_csv(filename, sep=",")
+    
+    logging.debug("Positions = %s", repr(positions))
+    
+    with open("template_script.py", "r") as template:
+        template_lines = template.readlines()
+    
+    logging.debug("Old position line reads: %s", template_lines[2])
+    
+    new_positions_line = '    _all_values = json.loads("""{"uploaded_csv": "source_well, destination_well'
+    
+    for idx in positions.index:
+        new_positions_line += "\\\\n{},{}".format(positions.loc[idx, "source well"], positions.loc[idx, "destination well"])
+        
+    new_positions_line += '"}""")\n'
+    logging.debug("New positions line = %s", new_positions_line)
+    
+    template_lines[2] = new_positions_line
+    
+    logging.info("Writing robot script to %s", outfilename)
+    with open(outfilename, "w") as out:
+        for line in template_lines:
+            out.write(line)
+
+    logging.info("Done.")
+    
+    
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    
+    parser.add_argument("filename", type=str, metavar="FILENAME", help="Filename of csv file containing source and target positions on a well plate.")
+    parser.add_argument("--outfile", "-o", type=str, dest='out', metavar="OUT", help="(Optional) filename of generated script. Defaults to 'robot.py'.", default="robot.py", required=False)
+   
+    args = parser.parse_args()
+    
+    main(args)
+

template_script.py

+def get_values(*names):
+    import json
+    _all_values = json.loads("""{"uploaded_csv":"source well,destination well\\nA2,A2\\nA11,A11\\nB1,B2\\nB3,B3\\nB4,B4\\nB7,B5\\nB6,B6\\nB7,B7\\nB8,B8\\nB9,B9\\nB10,B10\\nB11,B11\\nC2,C2\\nC1,C3\\nC4,C4\\nC5,C5\\nC6,C6\\nA7,C7\\nC8,C8\\nC9,C9\\nC10,C10\\nC12,C11\\nD2,D2\\nD3,D3\\nD1,D4\\nD5,D5\\nD6,D6\\nD7,D7\\nD8,D8\\nD9,D9\\nD12,D10\\nD11,D11\\nE2,E2\\nE3,E3\\nE4,E4\\nE1,E5\\nE6,E6\\nA8,E7\\nE8,E8\\nE12,E9\\nE10,E10\\nE11,E11\\nF2,F2\\nF1,F3\\nF4,F4\\nF5,F5\\nF6,F6\\nF7,F7\\nH8,F8\\nF9,F9\\nF12,F10\\nF11,F11\\nG1,G2\\nG3,G3\\nG4,G4\\nG5,G5\\nG6,G6\\nH7,G7\\nG8,G8\\nG9,G9\\nG10,G10\\nG12,G11\\nH2,H2\\nH11,H11"}""")
+    return [_all_values[n] for n in names]
+
+
+import csv
+
+metadata = {
+    'protocolName': 'Cherrypicking Final',
+    'author': 'Steve <protocols@opentrons.com>',
+    'source': 'Custom Protocol Request',
+    'apiLevel': '2.9'
+}
+
+
+def run(ctx):
+
+    [uploaded_csv] = get_values(  # noqa: F821
+        "uploaded_csv")
+
+    # lines from uploaded csv file
+    [*csv_lines] = uploaded_csv.splitlines()
+    csv_reader = csv.DictReader(csv_lines)
+
+    # tips, p300 multi, p20 single, LB reservoir, source and destination plates
+    tips300 = [ctx.load_labware(
+     'opentrons_96_filtertiprack_200ul', str(slot)) for slot in [10, 11]]
+    p300m = ctx.load_instrument("p300_multi_gen2", 'left', tip_racks=tips300)
+
+    tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '7')]
+    p20s = ctx.load_instrument("p20_single_gen2", 'right', tip_racks=tips20)
+
+    # set default flow rates for p20 to match PD tool default values
+    p20s.flow_rate.aspirate = 3.78
+    p20s.flow_rate.dispense = 3.78
+
+    [lb, source, dest] = [ctx.load_labware(
+     labware, str(slot), display_name) for labware, slot, display_name in zip(
+     ['nest_1_reservoir_195ml', 'white_96well_plate_340ul',
+      'tpp_96well_plate_340ul'
+      ], [5, 8, 6], [
+      'NEST 1 WELL RESERVOIR 195 ML', 'SOURCE', 'DESTINATION'])]
+
+    # step 1: p300m transfer 198 ul LB to destination columns with same tips
+    p300m.transfer(198, lb['A1'].bottom(3), [
+     column[0].bottom(1.5) for column in dest.columns()])
+
+    # step 2: p300m mix 10 columns of SOURCE 80 ul 15X
+    for column in source.columns()[1:11]:
+        p300m.pick_up_tip()
+        p300m.mix(15, 80, column[0].bottom(2.5))
+        p300m.drop_tip()
+
+    # step 3: p20s 2 ul SOURCE A2, A11, 30 custom to DESTINATION top
+    # step 4: p20s 2 ul SOURCE 30 custom, H2, H11 to DESTINATION bottom
+    # top dispense of air gap volume to replicate PD tool behavior
+    for line in csv_reader:
+        p20s.pick_up_tip()
+        p20s.aspirate(2, source.wells_by_name()[line['source well']].bottom(2.5))
+        p20s.air_gap(2)
+        p20s.dispense(2, dest.wells_by_name()[line['destination well']].top())
+        p20s.dispense(
+         3, dest.wells_by_name()[line['destination well']].bottom(1.5))
+        p20s.mix(
+         5, 5, dest.wells_by_name()[line['destination well']].bottom(1.5))
+        p20s.drop_tip()
+
+    # step 5: p300m mix columns of DESTINATION 80 ul 5X
+    for column in dest.columns():
+        p300m.pick_up_tip()
+        p300m.mix(5, 80, column[0].bottom(1.5))
+        p300m.drop_tip()

test_positions.csv

+source well,destination well
+A2,A2
+A11,A11
+B2,B2
+B3,B3
+B4,B4
+B5,B5
+B6,B6
+B7,B7
+B8,B8
+B9,B9
+B10,B10
+B11,B11
+C2,C2
+C3,C3
+C4,C4
+C5,C5
+C6,C6
+C7,C7
+C8,C8
+C9,C9
+C10,C10
+C11,C11
+D2,D2
+D3,D3
+D4,D4
+D5,D5
+D6,D6
+D7,D7
+D8,D8
+D9,D9
+D10,D10
+D11,D11
+E2,E2
+E3,E3
+E4,E4
+E5,E5
+E6,E6
+E7,E7
+E8,E8
+E9,E9
+E10,E10
+E11,E11
+F2,F2
+F3,F3
+F4,F4
+F5,F5
+F6,F6
+F7,F7
+F8,F8
+F9,F9
+F10,F10
+F11,F11
+G2,G2
+G3,G3
+G4,G4
+G5,G5
+G6,G6
+G7,G7
+G8,G8
+G9,G9
+G10,G10
+G11,G11
+H2,H2
+H11,H11
\ No newline at end of file