currently working version

import os

import pickle

home_path = os.getcwd()

path_to_cds_pickle_files = f'{home_path}/{"CDS_pickles_sequential"}' # where the cds pickle files are, this one specifially uses the CDS_pickles_sequential folder
path_to_result = f'{home_path}/{"Test_folder/Test_cds_results"}' # where the result files will be dumped
path_to_algined_files = f'{home_path}/{"Test_folder/Test_peptide_input"}' # where the aligned files are kept
path_to_script_accessories =f'{home_path}/{"Script_accesories"}' # where a couple of accesory scripts are

def main():

    hop_to_species_shorthand = os.chdir(path_to_script_accessories) # this is the folder that has the dict in pickle format

    with open('cds_identifiers.pkl','rb') as cds_shorthand: # this opens the pickle file
        cds_shorthand_dict = pickle.load(cds_shorthand) # open the dict

    hop_to_aligned_files = os.chdir(path_to_algined_files) # hop to the peptide files

    list_of_aligned_files = os.listdir(path_to_algined_files) # make a list of the files in the peptide folder

    def test_species(current_peptide_header): # this is a prototype, this function is actually called inside current_peptide_header
        for key,value in cds_shorthand_dict.items():
            if key in current_peptide_header:
                return value

    for file in list_of_aligned_files: # go through the files
        hop_back_to_peptide_files = os.chdir(path_to_algined_files)
        with open(file,'rt') as current_peptide_file: # using with to not have to bother closing the files manaully
            current_peptide_headers = current_peptide_file.readlines() # turning it into an iterable object



            for current_peptide_header in current_peptide_headers: # opeing the peptide header line
                if current_peptide_header[0] == '>': # '>' makes sure that the header is actually a header
                    this_file = test_species(current_peptide_header)
                    map_sequence = key_vs_key(current_peptide_header,this_file,file)


def key_vs_key(current_peptide_header,this_file,file):

    file = os.path.splitext(file)[0]
    file = f'{path_to_result}/{file}.{"acds"}'

    hop_to_cds_pickles = os.chdir(path_to_cds_pickle_files)
    with open(this_file,'rb') as current_cds_pickle:
        current_pickle = pickle.load(current_cds_pickle)


    for Universal_header,cds_sequence in current_pickle.items():
        if Universal_header == current_peptide_header:
            with open(file,'a') as current_acds_file:
                current_acds_file.write(current_peptide_header)
                current_acds_file.write(cds_sequence)


main()