import marimo

__generated_with = "0.14.16"
app = marimo.App(width="medium")


@app.cell
def _():
    import os
    from collections import Counter
    import marimo as mo
    import pandas as pd
    return mo, os, pd


@app.cell
def _(mo):
    mo.md(
        r"""
    # Search for Samples

    Not all QG samples have the `.mutations` files. It would be helpful to have some from those that were part of the historical QC service.

    Samples we have: `../data/qg_avail_dot_mutations.txt`
    """
    )
    return


@app.cell
def _():
    # pipeline runs used in the historical data (from repo)
    LB2_PIPELINE_RUNS = [
        "s3://quantgene-portland-lb/20221123-sp-pl34-hs2/lb-pl34-all-dev56/",
        "s3://quantgene-portland-lb/20221202-s1-pl36-hs2/lb-pl36-all-dev56/",
        "s3://quantgene-portland-lb/20221207-s2-pl37-hs2/lb-pl37-all-dev56/",
        "s3://quantgene-portland-lb/20230109-sp-pl41-hs2/lb-pl41-dev56/",
        "s3://quantgene-portland-lb/20230124-sp-pl42-hs2/lb-pl42-dev56/",
        # PL43 skipped, mostly Geneva samples with stats all over the place
        "s3://quantgene-portland-lb/20230210-sp-pl44-hs2/lb-pl44-dev59/",
        "s3://quantgene-portland-lb/20230224-s1-pl47-hs2/lb-pl47-dev59/",
        "s3://quantgene-portland-lb/20230316-s1-pl49-hs2/lb-pl49-dev59/",
        "s3://quantgene-portland-lb/20230330-sp-pl50-hs2/lb-pl50-dev59/",
        "s3://quantgene-portland-lb/20230417-s1-pl51-hs2/lb-pl51-dev59/",
        "s3://quantgene-portland-lb/20230512-sp-pl52-hs2/lb-pl52-prd-2-1-0/",
        "s3://quantgene-portland-lb/20230602-sp-pl53-hs2/lb-pl53-prd-2-1-1/",
        "s3://quantgene-portland-lb/20230615-sp-pl54-hs2/lb-pl54-prd-2-1-1/",
        "s3://quantgene-portland-lb/20230630-sp-pl55-hs2/lb-pl55-prd-2-1-1/",
        "s3://quantgene-portland-lb/20230721-sp-pl56-hs2/lb-pl56-prd212/",
        "s3://quantgene-portland-lb/20230811-sp-pl57-hs2/lb-pl57-prd212/",
        "s3://quantgene-portland-lb/20230901-sp-pl58-hs2/lb-pl58-prd212/",
        "s3://quantgene-portland-lb/20231027-sp-pl59-hs2/lb-pl59-prd212/",
        # PL60 skipped due to low amount of input reads in all samples
        "s3://quantgene-portland-lb/20240216-sp-pl61-hs2/lb-pl61-prd212/",
        # PL62 skipped due to low amount of input reads and insert size issues
        "s3://quantgene-portland-lb/20240516-s1-pl63-hs2/lb-pl63-prd212/",
        "s3://quantgene-portland-lb/20240529-sp-pl64-hs2/lb-pl64-prd212/",
    ]
    return (LB2_PIPELINE_RUNS,)


@app.cell
def _(pd):
    # hist samples
    qg_hist_data = pd.read_csv(
        "/home/darren/Documents/2_repos/serenomica/flowcell_qc/historical_data/historical_data_LB.csv",
        index_col=0,
    )
    qc_samples = list(set(qg_hist_data.index))
    qc_samples
    return (qc_samples,)


@app.cell
def _(LB2_PIPELINE_RUNS, os, qc_samples):
    with open("../data/qg_avail_dot_mutations.txt", "r") as handle:
        original, avail_samples, needed_samples = [], [], []
        for line in handle.readlines():
            fpath, samp = os.path.split(line.rstrip())

            fpath = str(fpath).replace("-lb//", "-lb/") + "/"
            samp = samp.strip(".mutations")

            original.append(line.rstrip())

            # skip non-prod versions
            if fpath not in LB2_PIPELINE_RUNS:
                continue

            avail_samples.append(samp)
            if samp in qc_samples:
                needed_samples.append(line.rstrip())
    print(
        f"Number of samples available from runs = {(n_avail := len(avail_samples))}"
    )
    print(f"Number of historical QC samples = {(n_qc := len(qc_samples))}")
    print(
        f"Number of historical QC samples available = {(n_needed := len(needed_samples))} ({round((n_needed / n_qc) * 100, 2)}%)"
    )
    return (needed_samples,)


@app.cell
def _(needed_samples):
    with open("../data/qg_needed.txt", "w") as whandle:
        whandle.writelines([i + "\n" for i in needed_samples])
    return


@app.cell
def _():
    return


if __name__ == "__main__":
    app.run()