implements new echo instruction pipeline

[Benedict-Carling]

Addresses #134

import basicsynbio as bsb
import zipfile
import os
import pandas as pd
from pathlib import Path

utr_linkers = ["UTR1-RBS1"]
promoter_assemblies = []
for utr_linker in utr_linkers:
    promoter_assemblies += [
        bsb.BasicAssembly(
            f"promoter_construct_{ind}_{utr_linker}",
            bsb.BASIC_SEVA_PARTS["v0.1"]["26"],
            bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMP"],
            promoter,
            bsb.BASIC_BIOLEGIO_LINKERS["v0.1"][utr_linker],
            bsb.BASIC_CDS_PARTS["v0.1"]["sfGFP"],
            bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMS"],
        )
        for ind, promoter in enumerate(bsb.BASIC_PROMOTER_PARTS["v0.1"].values())
    ]
my_build = bsb.BasicBuild(*promoter_assemblies)
echozippath = bsb.export_echo_assembly(
    my_build, alternate_well=True, clips_plate_size=1536
)

An example of the new zip file that is created when the above code is ran

Echo_Instructions_17-06-2021_16.54.28.zip

the following three arguments are added to echo_instructions

• 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,
  

the following arguments are added to csv_export

• clip_plate_mapping: dict = None,
  

• assembly_plate_mapping: dict = None,
  

The original echo_instruction unit tests have not been changed and still pass which is ideal, and new unit tests are added to check the new columns of the csv with and without alternate_wells

[hainesm6]

Some nice work @Benedict-Carling! Just wondering if it's feasible to do type hinting on the clip_plate_mapping and assembly_plate_mapping arguments? Just trying to figure out the format of them.

[Benedict-Carling]

Hi @hainesm6 Just did that! the clips contains a list as the same clip can be in multiple wells - the assemblies one is just a str as I don't think the same unique assembly can be in different wells if I'm not mistaken.

[hainesm6]

Just the one minor comment @Benedict-Carling. Great work!