eda.smk

configfile: "params-grid-exp.yaml"

from pathlib import Path
from concurrent.futures import ThreadPoolExecutor
from src.utils import MonitorValuesPlus
from src.msa import AnalyzerMSA
from tqdm import tqdm




# --- EDA MSA
rule eda_msa: 
    input: 
        path_msas=config["PATH_MSAS"]
    output:
        expand("{path_output}/analysis-msa/stats_msas.tsv", path_output=config["PATH_OUTPUT"]),
        expand("{path_output}/analysis-msa/problematic_files.tsv", path_output=config["PATH_OUTPUT"])
    run:
        path_output=config["PATH_OUTPUT"]
        mv = MonitorValuesPlus(list_vars=["path_msa","n_seqs","n_unique_seqs","n_identical_cols","n_cols", "perc_identical_cols"],
                                out_file=f"{path_output}/analysis-msa/stats_msas.tsv",
                                overwrite=True)

        mv_problems = MonitorValuesPlus(list_vars=["path_msa"],
                                        out_file=f"{path_output}/analysis-msa/problematic_files.tsv",
                                        overwrite=True)
        
        analyzer = AnalyzerMSA()
        def run(path_msa):
            "Function to run with ThreadPoolExecutor"
            try:
                n_cols, n_seqs, n_unique_seqs, n_identical_cols = analyzer(path_msa)
                perc_identical_cols = round(100*n_identical_cols/n_cols, 2)
                mv()
            except:     
                mv_problems()

        # list of (path to) msas
        # list_paths = list(Path(config["PATH_MSAS"]).glob("*.[fa]*"))

        # path msas
        SUBSET_HLA = ["A-3105", "B-3106", "C-3107", "DQA1-3117", "DQB1-3119", "DRB1-3123"]
        MSAS = list(Path(config["PATH_MSAS"]).glob("*.[fa]*"))
        
        list_paths = [path for path in MSAS if path.stem in SUBSET_HLA]
        print(MSAS)

        with ThreadPoolExecutor(max_workers=16) as pool:
            with tqdm(total=len(list_paths)) as progress:
                progress.set_description("Analyzing MSA")
                futures=[]
                for path_msa in list_paths:

                    future = pool.submit(run, path_msa)
                    future.add_done_callback(lambda p: progress.update())
                    futures.append(future)
                
                for future in futures:
                    future.result()