Merge pull request #135 from LondonBiofoundry/well-location-in-csv

implements new echo instruction pipeline

basicsynbio/cam/csv_export.py

@@ -7,14 +7,26 @@
 import csv
 
 
-def export_csvs(basic_build: BasicBuild, path: str = None):
+def export_csvs(
+    basic_build: BasicBuild,
+    path: str = None,
+    clip_plate_mapping: dict[str, list[str]] = None,
+    assembly_plate_mapping: dict[str, str] = None,
+):
     """Writes information about each clip_data and assembly to
     two dependent CSV files in the same folder the command
     is executed.
 
     Args:
         path (optional): path to zipped folder of csv files. If none defaults to
             working directory with a time stamped name, output csvs is created.
+        clip_plate_mapping (optional): A dictionary with keys containing clip
+            indicies and values containing lists of well locations's where the
+            clips are stored.
+        assembly_plate_mapping (optional): A dictionary with keys containing
+            assembly indicies and values containing the assemblies location plate
+            followed by a dash then the well locations for example {1:'0-A1',...}
+
 
     Returns:
         str: filepath of created zip containing the CSV files
@@ -35,6 +47,7 @@ def export_csvs(basic_build: BasicBuild, path: str = None):
             "Suffix ID",
             "Total assemblies",
             "Assembly indexes",
+            "Clip plate mapping",
         ]
         thewriter = csv.DictWriter(f, fieldnames=fieldnames)
         thewriter.writeheader()
@@ -55,10 +68,18 @@ def export_csvs(basic_build: BasicBuild, path: str = None):
                         basic_build.basic_assemblies.index(assembly) + 1
                         for assembly in clip_data[1]
                     ],
+                    "Clip plate mapping": clip_plate_mapping[str(index + 1)]
+                    if clip_plate_mapping
+                    else "N/A",
                 }
             )
     with open(Path.cwd() / "assemblies.csv", "w", newline="") as f:
-        fieldnames = ["Assembly Index", "Assembly ID", "Clip indexes"]
+        fieldnames = [
+            "Assembly Index",
+            "Assembly ID",
+            "Clip indexes",
+            "Assembly plate mapping",
+        ]
         thewriter = csv.DictWriter(f, fieldnames=fieldnames)
         thewriter.writeheader()
         for index, assembly in enumerate(basic_build.basic_assemblies):
@@ -70,6 +91,9 @@ def export_csvs(basic_build: BasicBuild, path: str = None):
                         basic_build.unique_clips.index(clip_reaction) + 1
                         for clip_reaction in assembly._clip_reactions
                     ],
+                    "Assembly plate mapping": assembly_plate_mapping[str(index + 1)]
+                    if assembly_plate_mapping
+                    else "N/A",
                 }
             )
     with zipfile.ZipFile(zip_path, "w") as my_zip:

basicsynbio/cam/echo_instructions.py

@@ -1,4 +1,5 @@
 from .main import BasicBuild
+from .csv_export import export_csvs
 import zipfile
 import os
 import pandas as pd
@@ -9,6 +10,9 @@
 import csv
 from functools import reduce
 from platemap import Plate, assign_source_wells, find_well, remove_volume
+from typing import Literal
+from collections import defaultdict
+
 
 CLIP_VOLUME = 500
 BUFFER_VOLUME = 500
@@ -21,6 +25,9 @@ def export_echo_assembly(
     buffer_well: str = "A1",
     water_well: str = "B1",
     alternate_well: bool = False,
+    assemblies_per_clip: int = 28,
+    clips_plate_size: Literal[6, 24, 96, 384, 1536] = 384,
+    assemblies_plate_size: Literal[6, 24, 96, 384, 1536] = 96,
 ) -> None:
     """Writes automation scripts for a echo liquid handler to build assemblies from clips.
 
@@ -30,6 +37,10 @@ def export_echo_assembly(
         buffer_well (optional): location in 6 well plate of assembly buffer.
         water_well (optional): location in 6 well plate of dH20.
         alternate_well (optional): specifies whether alternating wells are to be used in the input 384 well plate.
+        assemblies_per_clip (optional): number of assemblies each purified clip reaction can support.
+        clips_plate_size (optional): specifies the size of the clips plate. Defaults to 384
+        assemblies_plate_size (optional): specifiesthe size of the assemblies plates. Defaults to 96
+
 
     Returns:
         str: Path of zip file containing echo automation scripts
@@ -49,39 +60,60 @@ def export_echo_assembly(
             "Assembly Buffer Well location needs to be within the 6 well plate, between A1 - B3"
         )
 
-    source_plate = Plate(size=384, well_volume=40000, deadspace=20000)
-    destination_plate = Plate(size=96)
+    calculated_well_volume = assemblies_per_clip * CLIP_VOLUME
+    source_plate = Plate(
+        size=clips_plate_size, well_volume=calculated_well_volume, deadspace=0
+    )
+    destination_plate = Plate(size=assemblies_plate_size)
+
     try:
         assign_source_wells(
             source_plate,
             reduce(
                 lambda a, b: {**a, **b},
                 list(
                     map(
-                        lambda x: {x[0]: len(x[1][1] * CLIP_VOLUME)},
+                        lambda x: {x[0] + 1: len(x[1][1] * CLIP_VOLUME)},
                         enumerate(basic_build.clips_data.items()),
                     )
                 ),
             ),
             alternate_wells=alternate_well,
         )
+
     except:
         raise ValueError(
             """To many clips in the build to be handled by a single 384 
                 source plate, considering you alternate_well setting."""
         )
 
+    dd = defaultdict(list)
+
+    for d in list(
+        map(
+            lambda well_item: {well_item[1][1]["id"]: well_item[1][0]},
+            enumerate(
+                filter(lambda x: x[1]["total_volume"], source_plate.contents.items())
+            ),
+        )
+    ):
+        for key, value in d.items():
+            dd[str(key)].append(value)
+
+    clip_sourceplate_mapping = dict(dd)
+    assembly_outputplate_mapping = {}
+
     if path == None:
         now = datetime.now()
         zip_path = (
             Path.cwd() / f"Echo_Instructions_{now.strftime('%d-%m-%Y_%H.%M.%S')}.zip"
         )
     else:
         zip_path = path
-    for index, set_of_96_assemblies in enumerate(
+    for index, set_of_full_assemblies in enumerate(
         list(
-            basic_build.basic_assemblies[x : x + 96]
-            for x in range(0, len(basic_build.basic_assemblies), 96)
+            basic_build.basic_assemblies[x : x + assemblies_plate_size]
+            for x in range(0, len(basic_build.basic_assemblies), assemblies_plate_size)
         )
     ):
         with open(
@@ -94,14 +126,17 @@ def export_echo_assembly(
             thewriter_clips.writeheader()
             thewriter_water_buffer = csv.DictWriter(f2, fieldnames=fieldnames)
             thewriter_water_buffer.writeheader()
-            for index, assembly in enumerate(set_of_96_assemblies):
+            for assembly_index, assembly in enumerate(set_of_full_assemblies):
+                assembly_outputplate_mapping[
+                    str((index * assemblies_plate_size) + (assembly_index + 1))
+                ] = (str(index) + "-" + str(destination_plate.wells[assembly_index]))
                 for clip in [
-                    basic_build.unique_clips.index(clip_reaction)
+                    basic_build.unique_clips.index(clip_reaction) + 1
                     for clip_reaction in assembly._clip_reactions
                 ]:
                     thewriter_clips.writerow(
                         {
-                            "Destination Well": destination_plate.wells[index],
+                            "Destination Well": destination_plate.wells[assembly_index],
                             "Source Well": find_well(source_plate, clip, CLIP_VOLUME),
                             "Transfer Volume": CLIP_VOLUME,
                         }
@@ -113,14 +148,14 @@ def export_echo_assembly(
                     )
                 thewriter_water_buffer.writerow(
                     {
-                        "Destination Well": destination_plate.wells[index],
+                        "Destination Well": destination_plate.wells[assembly_index],
                         "Source Well": buffer_well,
                         "Transfer Volume": BUFFER_VOLUME,
                     }
                 )
                 thewriter_water_buffer.writerow(
                     {
-                        "Destination Well": destination_plate.wells[index],
+                        "Destination Well": destination_plate.wells[assembly_index],
                         "Source Well": water_well,
                         "Transfer Volume": TOTAL_VOLUME
                         - BUFFER_VOLUME
@@ -133,7 +168,17 @@ def export_echo_assembly(
                         ),
                     }
                 )
+    csv_zip = export_csvs(
+        basic_build, None, clip_sourceplate_mapping, assembly_outputplate_mapping
+    )
+    with zipfile.ZipFile(csv_zip, "r") as zip_ref:
+        zip_ref.extractall()
     with zipfile.ZipFile(zip_path, "w") as my_zip:
+        my_zip.write("clips.csv")
+        my_zip.write("assemblies.csv")
+        os.remove("clips.csv")
+        os.remove("assemblies.csv")
+        os.remove(csv_zip)
         for file in os.listdir(Path.cwd()):
             if file.startswith("echo_") and file.endswith(".csv"):
                 my_zip.write(file)

basicsynbio/cam/pdf_instructions.py

@@ -46,7 +46,7 @@ def pdf_instructions(
         basic_build: BasicBuild object the pdf lab instructions are written for.
         path (optional): path to zipped folder of csv files. If none defaults to
             working directory with a time stamped name, output csvs is created.
-        assemblies_per_clip (optional): amount of clips to be used in each assembly.
+        assemblies_per_clip (optional): number of assemblies each purified clip reaction can support.
 
     Returns:
         str: filepath of created pdf

tests/test_function_echo.py

@@ -43,6 +43,8 @@ def test_echo_instructions_small_build(small_build_example):
     )
     os.remove(Path.cwd() / "ECHO_CSVS" / "echo_clips_1.csv")
     os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_1.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "clips.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "assemblies.csv")
     os.rmdir(Path.cwd() / "ECHO_CSVS")
     expected_clips = [
         ["A1", "A1", 500],
@@ -80,6 +82,8 @@ def test_echo_instructions_small_build_useAllWell_False(small_build_example):
     )
     os.remove(Path.cwd() / "ECHO_CSVS" / "echo_clips_1.csv")
     os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_1.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "clips.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "assemblies.csv")
     os.rmdir(Path.cwd() / "ECHO_CSVS")
     expected_clips = [
         ["A1", "A1", 500],
@@ -142,6 +146,8 @@ def test_multiple_files_made_more_than_96_assemblies(promoter_assemblies_build):
     os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_1.csv")
     os.remove(Path.cwd() / "ECHO_CSVS" / "echo_clips_2.csv")
     os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_2.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "clips.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "assemblies.csv")
     os.rmdir(Path.cwd() / "ECHO_CSVS")
     expected_water_buffer_2 = [
         ["A1", "A1", 500],
@@ -334,6 +340,64 @@ def test_multiple_files_made_more_than_96_assemblies(promoter_assemblies_build):
     assert expected_water_buffer_2 == echo_water_buffer_2.to_numpy().tolist()
 
 
+def test_multiple_files_made_more_than_96_assemblies_clips_assignment(
+    promoter_assemblies_build,
+):
+    import zipfile
+    import os
+    import pandas as pd
+    import numpy as np
+    from pathlib import Path
+
+    echozippath = bsb.export_echo_assembly(promoter_assemblies_build)
+    with zipfile.ZipFile(echozippath, "r") as zip_ref:
+        try:
+            zip_ref.extractall("ECHO_CSVS")
+        finally:
+            zip_ref.close()
+            os.remove(echozippath)
+    echo_clips_csv = pd.read_csv(Path.cwd() / "ECHO_CSVS" / "clips.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_clips_1.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_1.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_clips_2.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_2.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "clips.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "assemblies.csv")
+    os.rmdir(Path.cwd() / "ECHO_CSVS")
+    echo_clips_first_clip_wells = "['A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1']"
+    assert echo_clips_first_clip_wells == echo_clips_csv.to_numpy().tolist()[0][-1]
+
+
+def test_multiple_files_made_more_than_96_assemblies_clips_assignment_with_alternate_wells(
+    promoter_assemblies_build,
+):
+    import zipfile
+    import os
+    import pandas as pd
+    import numpy as np
+    from pathlib import Path
+
+    echozippath = bsb.export_echo_assembly(
+        promoter_assemblies_build, alternate_well=True, clips_plate_size=1536
+    )
+    with zipfile.ZipFile(echozippath, "r") as zip_ref:
+        try:
+            zip_ref.extractall("ECHO_CSVS")
+        finally:
+            zip_ref.close()
+            os.remove(echozippath)
+    echo_clips_csv = pd.read_csv(Path.cwd() / "ECHO_CSVS" / "clips.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_clips_1.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_1.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_clips_2.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "echo_water_buffer_2.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "clips.csv")
+    os.remove(Path.cwd() / "ECHO_CSVS" / "assemblies.csv")
+    os.rmdir(Path.cwd() / "ECHO_CSVS")
+    echo_clips_first_clip_wells = "['A1', 'C1', 'E1', 'G1', 'I1', 'K1', 'M1']"
+    assert echo_clips_first_clip_wells == echo_clips_csv.to_numpy().tolist()[0][-1]
+
+
 def test_echo_instructions_too_many_clips(promoter_assemblies_build_more_than_384):
     import zipfile
     import os