Antismash output filter EPS

"""
Select only BGCs with 4 or more genes that are related to (exo)polysaccharides
"""

import os
from builtins import any


def parse_genbank_antismash(input_dir,output_dir):
    classification_list = ["Alpha-amylase","Bac_transf",
                        "Capsule_synth","CBM_48","DegT_DnrJ_EryC1","dTDP_sugar_isom",
                        "Epimerase_2","Glycos_transf",
                        "Glyco_tran","Glyco_transf",
                        "MannoseP_isomer","PIG-L","Poly_export","Polysacc_synt",
                        "RmlD_sub_bind","Wzy_C"] # Sec_met classifications related to (exo)polysacharides
    begin_lijst = os.listdir(f"{input_dir}")
    bestand_lijst = []
    for file in begin_lijst:
        if ".gbk" in file and "fixed" not in file: # Only look at the GBK files and not the
            bestand_lijst.append(file)
    tuple_list = []
    for i in range(len(bestand_lijst)):
        with open(f"{input_dir}/{bestand_lijst[i]}") as f:
            file = f.readlines()
        sec_met_list = []
        for line in file:
            if "/sec_met_domain" in line:
                for k in classification_list:
                    if k in line:
                        line = line.strip().split(" ")[0][17:] # Print relevant sacharide related gene clusters
                        sec_met_list.append(line)
        if len(sec_met_list) > 3: # Select only with 4 or more gene clusters
            tuple_list.append((bestand_lijst[i],sec_met_list,len(sec_met_list))) # Create tuple from data entry
    a = sorted(tuple_list,key=lambda x: x[-1])[::-1] # Order list from low to high based on sacharide related count
    return a


if __name__ == "__main__":
    folder_path = "./antismash_analyser_input"
    with open("./antismash_analyser_output/output.txt","w+") as f:
        for folder in os.listdir(folder_path):
            print(folder)
            f.write("\n"+str(folder)+"\n")
            for i in parse_genbank_antismash(f"{folder_path}/{folder}", ""):
                print(i)
                f.write(str(i)+"\n")