Merge pull request #4987 from Opentrons/0845ab-check-readme

fix(protocols/0845ab): change how samples pool

protoBuilds/0845ab/0845ab.ot2.apiv2.py.json

@@ -1,5 +1,5 @@
 {
-    "content": "import math\nfrom opentrons import protocol_api\n\nmetadata = {\n    'protocolName': 'Digestion and Bead Cleanup',\n    'author': 'Rami Farawi <[email protected]>',\n    'source': 'Custom Protocol Request',\n    'apiLevel': '2.14'\n}\n\n\ndef run(ctx):\n\n    [num_samp, real_mode, p20_mount, m300_mount] = get_values(  # noqa: F821\n        \"num_samp\", \"real_mode\", \"p20_mount\", \"m300_mount\")\n\n    # num_samp = 48\n    num_col = math.ceil(num_samp/8)\n    #\n    # m300_mount = 'left'\n    # p20_mount = 'right'\n    #\n    # real_mode = True\n\n    # labware\n    mag_mod = ctx.load_module(\"magnetic module gen2\", 1)\n    try:\n        mag_plate = mag_mod.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt')  # noqa: E501\n\n    except FileNotFoundError:\n        mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')  # noqa: E501\n\n    try:\n        old_plate = ctx.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt', 2)  # noqa: E501\n    except FileNotFoundError:\n        old_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n                                     2)\n\n    tuberack = ctx.load_labware('opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', 3)  # noqa: E501\n\n    reservoir = ctx.load_labware('nest_12_reservoir_15ml', 6)\n    trash = ctx.load_labware('nest_1_reservoir_195ml', 8).wells()[0].top()\n    tmt_plate = ctx.load_labware('opentrons_96_tiprack_sarstedt_200ul', 9)\n\n    if not ctx.is_simulating:\n\n        hs_mod = ctx.load_module('heaterShakerModuleV1', 10)\n        hs_mod.close_labware_latch()\n    else:\n        dummy = ctx.load_labware('nest_12_reservoir_15ml', 10)\n        dummy = dummy\n\n    tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n               for slot in [4, 5]]\n    tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n              for slot in [7, 11]]\n\n    # pipettes\n    p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n    m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n                               tip_racks=tips300)\n\n    def slow_tip_withdrawal(pipette, well_location, to_center=False):\n        pipette.default_speed = 10\n        if to_center is False:\n            pipette.move_to(well_location.top())\n        else:\n            pipette.move_to(well_location.center())\n        pipette.default_speed = 400\n\n    def pick_up(pip):\n        try:\n            pip.pick_up_tip()\n        except protocol_api.labware.OutOfTipsError:\n            ctx.pause(f\"Replace empty tip rack for {pip}\")\n            pip.reset_tipracks()\n            pip.pick_up_tip()\n\n    # mapping\n    sample_cols = old_plate.rows()[0][:num_col]\n    dest_cols = mag_plate.rows()[0][:num_col]\n    dest_wells = [well for well in mag_plate.wells()[:num_samp]]\n\n    pool_well1 = tuberack['B1']\n    pool_well2 = tuberack['B2']\n    pool_well3 = tuberack['B3']\n\n    num_pools = int(num_samp/16)\n\n    all_pools = [pool_well1, pool_well2, pool_well3][:num_pools]\n\n    acn = reservoir['A1']\n    ethanol = reservoir['A2']\n\n    beads = tuberack['A1']\n    mm_teab = tuberack['A2']\n    ha = tuberack['A3']\n    formic_acid = tuberack['A4']\n\n    digestion_solution = tmt_plate['A12']\n\n    # protocol\n    ctx.comment('\\n---------------ADDING BEADS TO PLATES----------------\\n\\n')\n\n    pick_up(p20)\n    p20.mix(15, 20, beads, rate=1.5)\n    for well in dest_wells:\n        p20.aspirate(4, beads)\n        slow_tip_withdrawal(p20, beads)\n        p20.dispense(4, well)\n        p20.blow_out()\n    p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n    for s, d in zip(sample_cols, dest_cols):\n        pick_up(m300)\n        m300.aspirate(30, s)\n        m300.dispense(30, d)\n        m300.blow_out()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    ctx.comment('\\n---------------Transferring ACN----------------\\n\\n')\n    for col in dest_cols:\n        pick_up(m300)\n        m300.aspirate(70, acn)\n        m300.dispense(70, col)\n        m300.mix(3, 85, col, rate=0.7)\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    ctx.delay(minutes=2 if real_mode else 0.5)\n\n    mag_mod.engage(height_from_base=1)\n\n    ctx.delay(minutes=5 if real_mode else 0.5)\n\n    ctx.comment('\\n---------------Removing Super----------------\\n\\n')\n    pick_up(m300)\n    for col in dest_cols:\n        m300.aspirate(100, col, rate=0.1)\n        m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n        m300.dispense(110, trash)\n        ctx.delay(seconds=1.5)\n        m300.blow_out()\n    m300.drop_tip() if real_mode else m300.return_tip()\n\n    for _ in range(2):\n        ctx.comment('\\n---------------Adding Ethanol----------------\\n\\n')\n        pick_up(m300)\n        for col in dest_cols:\n            m300.aspirate(100, ethanol, rate=0.5)\n            slow_tip_withdrawal(m300, ethanol)\n            m300.dispense(100, col.top())\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n        ctx.comment('\\n---------------Removing Ethanol----------------\\n\\n')\n        pick_up(m300)\n        for col in dest_cols:\n            m300.aspirate(100, col, rate=0.1)\n            m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n            m300.dispense(110, trash)\n            ctx.delay(seconds=1.5)\n            m300.blow_out()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    mag_mod.disengage()\n\n    ctx.comment('\\n--------------ADDING Digestion Solution--------------\\n\\n')\n    for col in dest_cols:\n        pick_up(m300)\n        m300.aspirate(20, digestion_solution)\n        m300.dispense(20, col)\n        m300.mix(2, 15, col)\n        m300.blow_out()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    if not ctx.is_simulating:\n        hs_mod.open_labware_latch()\n    ctx.pause('Move plate to heater shaker')\n    if not ctx.is_simulating:\n        hs_mod.close_labware_latch()\n        hs_mod.set_and_wait_for_temperature(37)\n    ctx.pause('Overnight Digestion')\n    if not ctx.is_simulating:\n        hs_mod.deactivate_heater()\n        hs_mod.open_labware_latch()\n    ctx.pause(\"Move plate to magnetic module\")\n\n    mag_mod.engage(height_from_base=1)\n    ctx.delay(minutes=2 if real_mode else 0.5)\n\n    ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n    new_cols = mag_plate.rows()[0][num_col:num_col+num_col]\n    new_wells = [well for col in mag_plate.columns()[num_col:num_col+num_col]\n                 for well in col]\n\n    for s, d in zip(dest_cols, new_cols):\n        pick_up(m300)\n        m300.aspirate(20, s, rate=0.05)\n        m300.dispense(20, d)\n        m300.move_to(d.top())\n        ctx.delay(seconds=1.5)\n        m300.blow_out()\n        m300.touch_tip()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    tmt_wells = [well for col in tmt_plate.columns()[:num_col]\n                 for well in col]\n\n    for well in tmt_wells:\n        pick_up(p20)\n        p20.aspirate(5, mm_teab)\n        p20.dispense(5, well)\n        p20.mix(3, 9, well)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.comment('\\n-----From TMT Wells to Sample Wells----------\\n\\n')\n    for s, d in zip(tmt_wells, new_wells):\n        pick_up(p20)\n        p20.aspirate(9, s)\n        p20.dispense(9, d)\n        p20.mix(3, 20, d)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.delay(minutes=60 if real_mode else 0.5)\n\n    for well in new_wells:\n        pick_up(p20)\n        p20.aspirate(5, ha)\n        p20.dispense(5, well)\n        p20.mix(1, 20, well)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.delay(minutes=15 if real_mode else 0.5)\n    # WHAT IS POOL VOLUME?\n    print(all_pools)\n    ctx.comment('ddd')\n    for pool in all_pools:\n        pick_up(p20)\n        for well in new_wells:\n            for _ in range(2):\n                p20.aspirate(20, well)\n                p20.dispense(20, pool)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    for pool in all_pools:\n        pick_up(p20)\n        p20.aspirate(10, formic_acid)\n        p20.dispense(10, pool)\n        p20.mix(3, 20, pool)\n        p20.drop_tip() if real_mode else p20.return_tip()\n",
+    "content": "import math\nfrom opentrons import protocol_api\n\nmetadata = {\n    'protocolName': 'Digestion and Bead Cleanup',\n    'author': 'Rami Farawi <[email protected]>',\n    'source': 'Custom Protocol Request',\n    'apiLevel': '2.14'\n}\n\n\ndef run(ctx):\n\n    [num_samp, real_mode, p20_mount, m300_mount] = get_values(  # noqa: F821\n        \"num_samp\", \"real_mode\", \"p20_mount\", \"m300_mount\")\n\n    # num_samp = 48\n    num_col = math.ceil(num_samp/8)\n    #\n    # m300_mount = 'left'\n    # p20_mount = 'right'\n    #\n    # real_mode = True\n\n    # labware\n    mag_mod = ctx.load_module(\"magnetic module gen2\", 1)\n    try:\n        mag_plate = mag_mod.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt')  # noqa: E501\n\n    except FileNotFoundError:\n        mag_plate = mag_mod.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')  # noqa: E501\n\n    try:\n        old_plate = ctx.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt', 2)  # noqa: E501\n    except FileNotFoundError:\n        old_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n                                     2)\n\n    tuberack = ctx.load_labware('opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', 3)  # noqa: E501\n\n    reservoir = ctx.load_labware('nest_12_reservoir_15ml', 6)\n    trash = ctx.load_labware('nest_1_reservoir_195ml', 8).wells()[0].top()\n    tmt_plate = ctx.load_labware('opentrons_96_tiprack_sarstedt_200ul', 9)\n\n    if not ctx.is_simulating:\n\n        hs_mod = ctx.load_module('heaterShakerModuleV1', 10)\n        hs_mod.close_labware_latch()\n    else:\n        dummy = ctx.load_labware('nest_12_reservoir_15ml', 10)\n        dummy = dummy\n\n    tips300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n               for slot in [4, 5]]\n    tips20 = [ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n              for slot in [7, 11]]\n\n    # pipettes\n    p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n    m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n                               tip_racks=tips300)\n\n    def slow_tip_withdrawal(pipette, well_location, to_center=False):\n        pipette.default_speed = 10\n        if to_center is False:\n            pipette.move_to(well_location.top())\n        else:\n            pipette.move_to(well_location.center())\n        pipette.default_speed = 400\n\n    def pick_up(pip):\n        try:\n            pip.pick_up_tip()\n        except protocol_api.labware.OutOfTipsError:\n            ctx.pause(f\"Replace empty tip rack for {pip}\")\n            pip.reset_tipracks()\n            pip.pick_up_tip()\n\n    # mapping\n    sample_cols = old_plate.rows()[0][:num_col]\n    dest_cols = mag_plate.rows()[0][:num_col]\n    dest_wells = [well for well in mag_plate.wells()[:num_samp]]\n\n    pool_well1 = tuberack['B1']\n    pool_well2 = tuberack['B2']\n    pool_well3 = tuberack['B3']\n\n    num_pools = int(num_samp/16)\n\n    all_pools = [pool_well1, pool_well2, pool_well3][:num_pools]\n\n    acn = reservoir['A1']\n    ethanol = reservoir['A2']\n\n    beads = tuberack['A1']\n    mm_teab = tuberack['A2']\n    ha = tuberack['A3']\n    formic_acid = tuberack['A4']\n\n    digestion_solution = tmt_plate['A12']\n\n    # protocol\n    ctx.comment('\\n---------------ADDING BEADS TO PLATES----------------\\n\\n')\n\n    pick_up(p20)\n    p20.mix(15, 20, beads, rate=1.5)\n    for well in dest_wells:\n        p20.aspirate(4, beads)\n        slow_tip_withdrawal(p20, beads)\n        p20.dispense(4, well)\n        p20.blow_out()\n    p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n    for s, d in zip(sample_cols, dest_cols):\n        pick_up(m300)\n        m300.aspirate(30, s)\n        m300.dispense(30, d)\n        m300.blow_out()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    ctx.comment('\\n---------------Transferring ACN----------------\\n\\n')\n    for col in dest_cols:\n        pick_up(m300)\n        m300.aspirate(70, acn)\n        m300.dispense(70, col)\n        m300.mix(3, 85, col, rate=0.7)\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    ctx.delay(minutes=2 if real_mode else 0.5)\n\n    mag_mod.engage(height_from_base=1)\n\n    ctx.delay(minutes=5 if real_mode else 0.5)\n\n    ctx.comment('\\n---------------Removing Super----------------\\n\\n')\n    pick_up(m300)\n    for col in dest_cols:\n        m300.aspirate(100, col, rate=0.1)\n        m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n        m300.dispense(110, trash)\n        ctx.delay(seconds=1.5)\n        m300.blow_out()\n    m300.drop_tip() if real_mode else m300.return_tip()\n\n    for _ in range(2):\n        ctx.comment('\\n---------------Adding Ethanol----------------\\n\\n')\n        pick_up(m300)\n        for col in dest_cols:\n            m300.aspirate(100, ethanol, rate=0.5)\n            slow_tip_withdrawal(m300, ethanol)\n            m300.dispense(100, col.top())\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n        ctx.comment('\\n---------------Removing Ethanol----------------\\n\\n')\n        pick_up(m300)\n        for col in dest_cols:\n            m300.aspirate(100, col, rate=0.1)\n            m300.aspirate(10, col.bottom(z=0.5), rate=0.1)\n            m300.dispense(110, trash)\n            ctx.delay(seconds=1.5)\n            m300.blow_out()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    mag_mod.disengage()\n\n    ctx.comment('\\n--------------ADDING Digestion Solution--------------\\n\\n')\n    for col in dest_cols:\n        pick_up(m300)\n        m300.aspirate(20, digestion_solution)\n        m300.dispense(20, col)\n        m300.mix(2, 15, col)\n        m300.blow_out()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    if not ctx.is_simulating:\n        hs_mod.open_labware_latch()\n    ctx.pause('Move plate to heater shaker')\n    if not ctx.is_simulating:\n        hs_mod.close_labware_latch()\n        hs_mod.set_and_wait_for_temperature(37)\n    ctx.pause('Overnight Digestion')\n    if not ctx.is_simulating:\n        hs_mod.deactivate_heater()\n        hs_mod.open_labware_latch()\n    ctx.pause(\"Move plate to magnetic module\")\n\n    mag_mod.engage(height_from_base=1)\n    ctx.delay(minutes=2 if real_mode else 0.5)\n\n    ctx.comment('\\n---------------Transferring Sample----------------\\n\\n')\n    new_cols = mag_plate.rows()[0][num_col:num_col+num_col]\n    new_wells = [well for col in mag_plate.columns()[num_col:num_col+num_col]\n                 for well in col]\n\n    for s, d in zip(dest_cols, new_cols):\n        pick_up(m300)\n        m300.aspirate(20, s, rate=0.05)\n        m300.dispense(20, d)\n        m300.move_to(d.top())\n        ctx.delay(seconds=1.5)\n        m300.blow_out()\n        m300.touch_tip()\n        m300.drop_tip() if real_mode else m300.return_tip()\n\n    tmt_wells = [well for col in tmt_plate.columns()[:num_col]\n                 for well in col]\n\n    for well in tmt_wells:\n        pick_up(p20)\n        p20.aspirate(5, mm_teab)\n        p20.dispense(5, well)\n        p20.mix(3, 9, well)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.comment('\\n-----From TMT Wells to Sample Wells----------\\n\\n')\n    for s, d in zip(tmt_wells, new_wells):\n        pick_up(p20)\n        p20.aspirate(9, s)\n        p20.dispense(9, d)\n        p20.mix(3, 20, d)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.delay(minutes=60 if real_mode else 0.5)\n\n    for well in new_wells:\n        pick_up(p20)\n        p20.aspirate(5, ha)\n        p20.dispense(5, well)\n        p20.mix(1, 20, well)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    ctx.delay(minutes=15 if real_mode else 0.5)\n    # WHAT IS POOL VOLUME?\n    chunked_wells_of_16 = [new_wells[i:i+16]\n                           for i in range(0, len(new_wells), 16)]\n\n    for chunk, pool in zip(chunked_wells_of_16, all_pools):\n        pick_up(p20)\n        for well in chunk:\n            for _ in range(2):\n                p20.aspirate(20, well)\n                p20.dispense(20, pool)\n        p20.drop_tip() if real_mode else p20.return_tip()\n\n    for pool in all_pools:\n        pick_up(p20)\n        p20.aspirate(10, formic_acid)\n        p20.dispense(10, pool)\n        p20.mix(3, 20, pool)\n        p20.drop_tip() if real_mode else p20.return_tip()\n",
     "custom_labware_defs": [
         {
             "brand": {

protocols/0845ab/0845ab.ot2.apiv2.py

@@ -232,11 +232,12 @@ def pick_up(pip):
 
     ctx.delay(minutes=15 if real_mode else 0.5)
     # WHAT IS POOL VOLUME?
-    print(all_pools)
-    ctx.comment('ddd')
-    for pool in all_pools:
+    chunked_wells_of_16 = [new_wells[i:i+16]
+                           for i in range(0, len(new_wells), 16)]
+
+    for chunk, pool in zip(chunked_wells_of_16, all_pools):
         pick_up(p20)
-        for well in new_wells:
+        for well in chunk:
             for _ in range(2):
                 p20.aspirate(20, well)
                 p20.dispense(20, pool)