def test_echo_instructions_too_many_clips(
promoter_assemblies_build_more_than_384):
import zipfile
import os
import pandas as pd
import numpy as np
from pathlib import Path
with pytest.raises(ValueError):
bsb.export_echo_assembly_instructions(
promoter_assemblies_build_more_than_384)
def test_echo_instruction_assert_buffer_water_well_errors(small_build_example):
with pytest.raises(
ValueError,
match=
"Water Well location needs to be within the 6 well plate, between A1 - B3",
):
echozippath = bsb.export_echo_assembly_instructions(
small_build_example, water_well="D1")
with pytest.raises(
ValueError,
match=
"Assembly Buffer Well location needs to be within the 6 well plate, between A1 - B3",
):
echozippath = bsb.export_echo_assembly_instructions(
small_build_example, buffer_well="D1")
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_instructions(
promoter_assemblies_build,
alternate_well=True,
clips_plate_size=1536,
assemblies_per_clip=28,
)
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_path(small_build_example):
from pathlib import Path
import os
zippath = Path.cwd() / "uniquezippath.zip"
realzippath = bsb.export_echo_assembly_instructions(small_build_example,
path=zippath)
os.remove(zippath)
assert zippath == realzippath
def test_echo_instructions_small_build_useAllWell_False(small_build_example):
import zipfile
import os
import pandas as pd
import numpy as np
from pathlib import Path
echozippath = bsb.export_echo_assembly_instructions(small_build_example,
alternate_well=True)
with zipfile.ZipFile(echozippath, "r") as zip_ref:
try:
zip_ref.extractall("ECHO_CSVS")
finally:
zip_ref.close()
os.remove(echozippath)
echo_clips = pd.read_csv(Path.cwd() / "ECHO_CSVS" / "echo_clips_1.csv")
echo_water_buffer = pd.read_csv(Path.cwd() / "ECHO_CSVS" /
"echo_water_buffer_1.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" / "clips.csv")
os.remove(Path.cwd() / "ECHO_CSVS" / "assemblies.csv")
os.rmdir(Path.cwd() / "ECHO_CSVS")
expected_clips = [
["A1", "A1", 500],
["A1", "C1", 500],
["B1", "E1", 500],
["B1", "C1", 500],
]
expected_water_buffer = [
["A1", "A1", 500],
["A1", "B1", 3500],
["B1", "A1", 500],
["B1", "B1", 3500],
]
assert expected_clips == echo_clips.to_numpy().tolist()
assert expected_water_buffer == echo_water_buffer.to_numpy().tolist()
def test_multiple_files_made_more_than_96_assemblies(
promoter_assemblies_build):
import zipfile
import os
import pandas as pd
import numpy as np
from pathlib import Path
echozippath = bsb.export_echo_assembly_instructions(
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 = pd.read_csv(Path.cwd() / "ECHO_CSVS" / "echo_clips_2.csv")
echo_water_buffer_2 = pd.read_csv(Path.cwd() / "ECHO_CSVS" /
"echo_water_buffer_2.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")
expected_water_buffer_2 = [
["A1", "A1", 500],
["A1", "B1", 3000],
["B1", "A1", 500],
["B1", "B1", 3000],
["C1", "A1", 500],
["C1", "B1", 3000],
["D1", "A1", 500],
["D1", "B1", 3000],
["E1", "A1", 500],
["E1", "B1", 3000],
["F1", "A1", 500],
["F1", "B1", 3000],
["G1", "A1", 500],
["G1", "B1", 3000],
["H1", "A1", 500],
["H1", "B1", 3000],
["A2", "A1", 500],
["A2", "B1", 3000],
["B2", "A1", 500],
["B2", "B1", 3000],
["C2", "A1", 500],
["C2", "B1", 3000],
["D2", "A1", 500],
["D2", "B1", 3000],
["E2", "A1", 500],
["E2", "B1", 3000],
["F2", "A1", 500],
["F2", "B1", 3000],
["G2", "A1", 500],
["G2", "B1", 3000],
["H2", "A1", 500],
["H2", "B1", 3000],
["A3", "A1", 500],
["A3", "B1", 3000],
["B3", "A1", 500],
["B3", "B1", 3000],
["C3", "A1", 500],
["C3", "B1", 3000],
["D3", "A1", 500],
["D3", "B1", 3000],
["E3", "A1", 500],
["E3", "B1", 3000],
["F3", "A1", 500],
["F3", "B1", 3000],
["G3", "A1", 500],
["G3", "B1", 3000],
["H3", "A1", 500],
["H3", "B1", 3000],
["A4", "A1", 500],
["A4", "B1", 3000],
["B4", "A1", 500],
["B4", "B1", 3000],
["C4", "A1", 500],
["C4", "B1", 3000],
["D4", "A1", 500],
["D4", "B1", 3000],
["E4", "A1", 500],
["E4", "B1", 3000],
["F4", "A1", 500],
["F4", "B1", 3000],
["G4", "A1", 500],
["G4", "B1", 3000],
["H4", "A1", 500],
["H4", "B1", 3000],
["A5", "A1", 500],
["A5", "B1", 3000],
["B5", "A1", 500],
["B5", "B1", 3000],
["C5", "A1", 500],
["C5", "B1", 3000],
["D5", "A1", 500],
["D5", "B1", 3000],
["E5", "A1", 500],
["E5", "B1", 3000],
["F5", "A1", 500],
["F5", "B1", 3000],
["G5", "A1", 500],
["G5", "B1", 3000],
["H5", "A1", 500],
["H5", "B1", 3000],
["A6", "A1", 500],
["A6", "B1", 3000],
["B6", "A1", 500],
["B6", "B1", 3000],
["C6", "A1", 500],
["C6", "B1", 3000],
["D6", "A1", 500],
["D6", "B1", 3000],
["E6", "A1", 500],
["E6", "B1", 3000],
["F6", "A1", 500],
["F6", "B1", 3000],
["G6", "A1", 500],
["G6", "B1", 3000],
["H6", "A1", 500],
["H6", "B1", 3000],
["A7", "A1", 500],
["A7", "B1", 3000],
["B7", "A1", 500],
["B7", "B1", 3000],
["C7", "A1", 500],
["C7", "B1", 3000],
["D7", "A1", 500],
["D7", "B1", 3000],
["E7", "A1", 500],
["E7", "B1", 3000],
["F7", "A1", 500],
["F7", "B1", 3000],
["G7", "A1", 500],
["G7", "B1", 3000],
["H7", "A1", 500],
["H7", "B1", 3000],
["A8", "A1", 500],
["A8", "B1", 3000],
["B8", "A1", 500],
["B8", "B1", 3000],
["C8", "A1", 500],
["C8", "B1", 3000],
["D8", "A1", 500],
["D8", "B1", 3000],
["E8", "A1", 500],
["E8", "B1", 3000],
["F8", "A1", 500],
["F8", "B1", 3000],
["G8", "A1", 500],
["G8", "B1", 3000],
["H8", "A1", 500],
["H8", "B1", 3000],
["A9", "A1", 500],
["A9", "B1", 3000],
["B9", "A1", 500],
["B9", "B1", 3000],
["C9", "A1", 500],
["C9", "B1", 3000],
["D9", "A1", 500],
["D9", "B1", 3000],
["E9", "A1", 500],
["E9", "B1", 3000],
["F9", "A1", 500],
["F9", "B1", 3000],
["G9", "A1", 500],
["G9", "B1", 3000],
["H9", "A1", 500],
["H9", "B1", 3000],
["A10", "A1", 500],
["A10", "B1", 3000],
["B10", "A1", 500],
["B10", "B1", 3000],
["C10", "A1", 500],
["C10", "B1", 3000],
["D10", "A1", 500],
["D10", "B1", 3000],
["E10", "A1", 500],
["E10", "B1", 3000],
["F10", "A1", 500],
["F10", "B1", 3000],
["G10", "A1", 500],
["G10", "B1", 3000],
["H10", "A1", 500],
["H10", "B1", 3000],
["A11", "A1", 500],
["A11", "B1", 3000],
["B11", "A1", 500],
["B11", "B1", 3000],
["C11", "A1", 500],
["C11", "B1", 3000],
["D11", "A1", 500],
["D11", "B1", 3000],
["E11", "A1", 500],
["E11", "B1", 3000],
["F11", "A1", 500],
["F11", "B1", 3000],
["G11", "A1", 500],
["G11", "B1", 3000],
["H11", "A1", 500],
["H11", "B1", 3000],
["A12", "A1", 500],
["A12", "B1", 3000],
["B12", "A1", 500],
["B12", "B1", 3000],
["C12", "A1", 500],
["C12", "B1", 3000],
["D12", "A1", 500],
["D12", "B1", 3000],
["E12", "A1", 500],
["E12", "B1", 3000],
]
assert expected_water_buffer_2 == echo_water_buffer_2.to_numpy().tolist()