diff --git a/configs/dmmm.yaml b/configs/dmmm.yaml index 4ff108e..3c36336 100644 --- a/configs/dmmm.yaml +++ b/configs/dmmm.yaml @@ -46,12 +46,12 @@ datasets: # TODO: use old paramaters for datasets # HIV: https://github.com/Reed-CompBio/spras-benchmarking/blob/0293ae4dc0be59502fac06b42cfd9796a4b4413e/hiv-benchmarking/spras-config/config.yaml - label: dmmmhiv060 - node_files: ["processed_prize_060.txt"] + node_files: ["processed_prizes_060.txt"] edge_files: ["phosphosite-irefindex13.0-uniprot.txt"] other_files: [] data_dir: "datasets/hiv/processed" - label: dmmmhiv05 - node_files: ["processed_prize_05.txt"] + node_files: ["processed_prizes_05.txt"] edge_files: ["phosphosite-irefindex13.0-uniprot.txt"] other_files: [] data_dir: "datasets/hiv/processed" diff --git a/datasets/hiv/.gitignore b/datasets/hiv/.gitignore index e6a1bb2..390e292 100644 --- a/datasets/hiv/.gitignore +++ b/datasets/hiv/.gitignore @@ -1 +1,2 @@ -processed \ No newline at end of file +/processed +/Pickles diff --git a/datasets/hiv/README.md b/datasets/hiv/README.md new file mode 100644 index 0000000..a0bb7f3 --- /dev/null +++ b/datasets/hiv/README.md @@ -0,0 +1,15 @@ +# HIV dataset + +## Raw files + +See `raw/README.md`. + +## File organization + +See `Snakefile` for the way that all of the IO files are connected. + +1. `fetch.py` - This grabs the score files from https://doi.org/10.1371/journal.ppat.1011492 +1. `prepare.py` - This cleans up the prize files in `raw`; specifically to remove duplicates. +1. `name_mapping.py` - Converts from UniProt KB-ACID to UniProt KB to meet in the middle with `kegg_ortholog.py`. We chose UniProt KB for its generality. +1. `spras_formatting.py` - Formats the input files into a SPRAS-ready format. +1. `kegg_orthology.py` - This is used to generate the KEGG ortholog file for gold standards, but this has yet to be finalized. diff --git a/datasets/hiv/Scripts/Data_Prep.py b/datasets/hiv/Scripts/Data_Prep.py deleted file mode 100644 index 1aca432..0000000 --- a/datasets/hiv/Scripts/Data_Prep.py +++ /dev/null @@ -1,31 +0,0 @@ -import pandas -import pickle -import os - -prize_05 = pandas.read_csv('raw/prize_05.csv', sep='\t', lineterminator='\n') -prize_060 = pandas.read_csv('raw/prize_060.csv', sep='\t', lineterminator='\n') - -prize_05['Uniprot'] = prize_05['Uniprot'].str.split('-', expand=False).str[0] -prize_05 = prize_05.sort_values('Prize', - ascending=False).drop_duplicates('Uniprot').sort_index() - -prize_060['Uniprot'] = prize_060['Uniprot'].str.split('-', expand=False).str[0] -prize_060 = prize_060.sort_values('Prize', - ascending=False).drop_duplicates('Uniprot').sort_index() - -prize_060_nodes = prize_060['Uniprot'].tolist() -prize_05_nodes = prize_05['Uniprot'].tolist() - -nodeset = list(set(prize_05_nodes+prize_060_nodes)) - -df = { - "NodeIDs": nodeset, - "prize_05": prize_05, - "prize_060": prize_060 -} - -if not os.path.exists('./Pickles'): - os.makedirs('./Pickles') - -with open("Pickles/NodeIDs.pkl","wb") as file: - pickle.dump(df,file) diff --git a/datasets/hiv/Scripts/Kegg_Orthology.py b/datasets/hiv/Scripts/Kegg_Orthology.py deleted file mode 100644 index 9f1de1c..0000000 --- a/datasets/hiv/Scripts/Kegg_Orthology.py +++ /dev/null @@ -1,64 +0,0 @@ -from Bio.KEGG.KGML.KGML_parser import read -from bioservices import UniProt, KEGG -import pandas as pd -from more_itertools import chunked - -pathway = read(open("Raw_Data/ko03250.xml", 'r')) - -#Read in Kegg pathway data and keep only orthologs -entries_data = [] -for entry in pathway.entries.values(): - if entry.type == 'ortholog': - entries_data.append({ - 'name': entry.name - }) -entries_df = pd.DataFrame(entries_data) - -#Some orthologs have multiple ko codes in the same row -#The following two lines move all ko codes to individual rows -orthology_ids = entries_df['name'].str.split(' ').explode() -orthology_ids = orthology_ids.apply(lambda x: x.split(':')[1]).tolist() - -#Using bioservices KEGG class to map ortholog(ko) codes to human(hsa) codes -k = KEGG() -ko_hsa_map = k.link('hsa', '+'.join(orthology_ids)) -ko_hsa_dict = {x.split('\t')[0].split(':')[1]: x.split('\t')[1] for x in ko_hsa_map.split('\n')[:-1]} -ko_hsa_df = pd.DataFrame(ko_hsa_dict.items(),columns= ['KEGG_Orthology','HSA']) - -#Kegg .get is limited to 10 entries per call -#The following code chunks the hsa list into sets of 10 -#then calls the .get function on each which returns kegg api data in string format -hsa_chunked = list(chunked(ko_hsa_df['HSA'].tolist(),10)) -raw_uniprot = [] -for entry in hsa_chunked: - raw_uniprot.append(k.get('+'.join(entry)).split('\n///\n\n')) - -#Raw Kegg api data is filtered to obtain hsa and uniprot codes for each protein -#Note: Although bioservices .link and .conv return cleaner outputs, they do not support -#one to many relationships at this time. -#Note: bioservices also supplies a parser method for the kegg api but it is also broken at this time. -processed_uniprot = [] -for chunk in raw_uniprot: - for item in chunk: - item = item.split('\n') - processed_uniprot.append([(x.strip().split(' ')[1:],'hsa:'+(item[0].split(' '*7)[1])) - for x in item if 'UniProt' in x][0]) - -#Creates a dictionary where uniprot ids are keys and hsa ids are values -hsa_uniprot_dict = {} -for item in processed_uniprot : - for entry in item[0]: - hsa_uniprot_dict.update({'up:'+entry:item[1]}) - -#Creates a dataframe with uniprot and hsa values then merges with ko-hsa dataframe by hsa -hsa_uniprot_map = pd.DataFrame.from_dict(hsa_uniprot_dict.items()) -hsa_uniprot_map.columns = ['Uniprot','HSA'] -final_df = ko_hsa_df.merge(hsa_uniprot_map,on = 'HSA') -uniprotIDs = final_df['Uniprot'].apply(lambda x: x.split(':')[1]).tolist() - -#Filters the combined dataframe to include only rows where the uniprot code is in swissprot -u = UniProt() -tst = u.mapping(fr='UniProtKB', to='UniProtKB-Swiss-Prot',query = ','.join(uniprotIDs)) -failed_uniprot = pd.Series(list(set(tst['failedIds']))).apply(lambda x: 'up:'+x) - -final_df = final_df[~final_df['Uniprot'].isin(failed_uniprot)] diff --git a/datasets/hiv/Scripts/SPRAS_Formatting.py b/datasets/hiv/Scripts/SPRAS_Formatting.py deleted file mode 100644 index 837f52b..0000000 --- a/datasets/hiv/Scripts/SPRAS_Formatting.py +++ /dev/null @@ -1,28 +0,0 @@ -import pickle -from pathlib import Path -import os - -current_directory = Path(os.path.dirname(os.path.realpath(__file__))) -PROCESSED_DIR = current_directory.parent / 'processed' - -with open('Pickles/UniprotIDs.pkl', 'rb') as file: - UniprotIDs = pickle.load(file) - -UIDs = UniprotIDs["UniprotIDs"] -UMap= UniprotIDs["UniprotMap"] - -with open('Pickles/NodeIDs.pkl','rb') as file2: - prizes = pickle.load(file2) - -prize_05 = prizes["prize_05"] -prize_060 = prizes["prize_060"] - -prize_05['Uniprot'] = prize_05['Uniprot'].apply(lambda x: UMap.get(x)) -prize_060['Uniprot'] = prize_060['Uniprot'].apply(lambda x: UMap.get(x)) - -prize_05.columns = ['NODEID','prize'] -prize_060.columns = ['NODEID','prize'] - - -prize_05.to_csv(PROCESSED_DIR / 'processed_prize_05.txt', sep='\t', header=True, index=False) -prize_060.to_csv(PROCESSED_DIR / 'processed_prize_060.txt', sep='\t', header=True, index=False) diff --git a/datasets/hiv/Snakefile b/datasets/hiv/Snakefile index 14c1d6b..3cb0e62 100644 --- a/datasets/hiv/Snakefile +++ b/datasets/hiv/Snakefile @@ -1,17 +1,25 @@ rule all: input: - "processed/processed_prize_05.txt", - "processed/processed_prize_060.txt", + "processed/processed_prizes_05.txt", + "processed/processed_prizes_060.txt", "processed/phosphosite-irefindex13.0-uniprot.txt" +rule fetch: + output: + "raw/prizes_05.tsv", + "raw/prizes_060.tsv", + "raw/ko03250.xml" + shell: + "uv run scripts/fetch.py" + rule data_prep: input: - "raw/prize_05.csv", - "raw/prize_060.csv" + "raw/prizes_05.tsv", + "raw/prizes_060.tsv" output: "Pickles/NodeIDs.pkl" shell: - "uv run Scripts/Data_Prep.py" + "uv run scripts/prepare.py" rule name_mapping: input: @@ -19,17 +27,17 @@ rule name_mapping: output: "Pickles/UniprotIDs.pkl" shell: - "uv run Scripts/Name_Mapping.py" + "uv run scripts/name_mapping.py" rule spras_formatting: input: "Pickles/NodeIDs.pkl", "Pickles/UniprotIDs.pkl" output: - "processed/processed_prize_05.txt", - "processed/processed_prize_060.txt" + "processed/processed_prizes_05.txt", + "processed/processed_prizes_060.txt" shell: - "uv run Scripts/SPRAS_Formatting.py" + "uv run scripts/spras_formatting.py" rule copy_network: input: @@ -37,4 +45,4 @@ rule copy_network: output: "processed/phosphosite-irefindex13.0-uniprot.txt" shell: - "cp raw/phosphosite-irefindex13.0-uniprot.txt processed/phosphosite-irefindex13.0-uniprot.txt" \ No newline at end of file + "cp raw/phosphosite-irefindex13.0-uniprot.txt processed/phosphosite-irefindex13.0-uniprot.txt" diff --git a/datasets/hiv/raw/.gitignore b/datasets/hiv/raw/.gitignore new file mode 100644 index 0000000..1bf7803 --- /dev/null +++ b/datasets/hiv/raw/.gitignore @@ -0,0 +1,3 @@ +prizes_05.tsv +prizes_060.tsv +ko03250.xml diff --git a/datasets/hiv/raw/README.md b/datasets/hiv/raw/README.md new file mode 100644 index 0000000..e6b74a9 --- /dev/null +++ b/datasets/hiv/raw/README.md @@ -0,0 +1,10 @@ +# raw + +Some `raw` files are fetched from `../scripts/fetch.py`. + +The `phosphosite-irefindex13.0-uniprot.txt` is +a background interactome provided by SPRAS: https://github.com/Reed-CompBio/spras/blob/be8bc7f8d71880d7ce9c9ceeeddfefa6eb60c522/input/phosphosite-irefindex13.0-uniprot.txt. + +The `ko03250.xml` is from `https://www.kegg.jp/entry/ko03250`. Specifically, if you click on the pathway image in the entry, +you'll get to https://www.kegg.jp/pathway/ko03250, where you download the KGML file (which is formatted as a `.xml` file) +under `Download` -> `KGML`. (The final file is at https://www.kegg.jp/kegg-bin/download?entry=ko03250&format=kgml). diff --git a/datasets/hiv/raw/prize_05.csv b/datasets/hiv/raw/prize_05.csv deleted file mode 100644 index b0bc193..0000000 --- a/datasets/hiv/raw/prize_05.csv +++ /dev/null @@ -1,1127 +0,0 @@ -Uniprot Prize -B0YIW2 5.029365599650682 -Q99081 4.582688156260696 -P02765 4.027455886706566 -P69905 3.9558170656097413 -P06732 3.885427876677981 -B7ZKJ8 3.885427876677981 -P62805 3.885427876677981 -P23142 3.885427876677981 -H3BLZ8 3.7376592766836954 -Q9BU76 3.6456113515037165 -Q2KHT3 3.6456113515037165 -P02768 3.495543593199523 -Q8NBM4 3.4400540448812222 -Q5TEC6 3.4400540448812222 -Q92576 3.324208299637505 -Q9Y2R4 3.324208299637505 -P68363-2 3.324208299637505 -P61978-2 3.3188421301096285 -Q5T5H1 3.3188421301096285 -O75152 3.3188421301096285 -P11171 3.3010716433184752 -Q6PKG0 3.3010716433184752 -Q49A26 3.2919252118261477 -Q5T200 3.2919252118261477 -P02787 3.2382104940279395 -A0A0A0MTS7 3.238051370574229 -P49207 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+Associated paper for the prizes file: https://doi.org/10.1371/journal.ppat.1011492 +""" + +import urllib.request +import os +from pathlib import Path + +# https://stackoverflow.com/a/5137509/7589775 +hiv_path = Path(os.path.dirname(os.path.realpath(__file__))).parent + +base_url = "https://raw.githubusercontent.com/gitter-lab/hiv1-aurkb/ac9278d447e4188eea3bf4b24c4c4e0c19b0c6d9/Results/base_analysis/" +prizes_05_url = base_url + "prize_05.csv" +prizes_060_url = base_url + "prize_060.csv" + +def main(): + # Note: These files are .tsv, but have the wrong file extension .csv in the original data source. + urllib.request.urlretrieve(prizes_05_url, hiv_path / "raw" / "prizes_05.tsv") + urllib.request.urlretrieve(prizes_060_url, hiv_path / "raw" / "prizes_060.tsv") + + # and our final KGML file for the HIV pathway. + # KEGG requires a Referrer (server-CORS enforcement?) + # https://stackoverflow.com/a/46511429/7589775 + opener = urllib.request.build_opener() + opener.addheaders = [('Referer', 'https://www.kegg.jp/pathway/ko03250')] + urllib.request.install_opener(opener) + urllib.request.urlretrieve( + "https://www.kegg.jp/kegg-bin/download?entry=ko03250&format=kgml", + hiv_path / "raw" / "ko03250.xml") + +if __name__ == '__main__': + main() diff --git a/datasets/hiv/scripts/kegg_orthology.py b/datasets/hiv/scripts/kegg_orthology.py new file mode 100644 index 0000000..6b34351 --- /dev/null +++ b/datasets/hiv/scripts/kegg_orthology.py @@ -0,0 +1,70 @@ +from Bio.KEGG.KGML.KGML_parser import read +from bioservices import UniProt, KEGG +import pandas as pd +from more_itertools import chunked +from pathlib import Path +import os + +# https://stackoverflow.com/a/5137509/7589775 +hiv_path = Path(os.path.dirname(os.path.realpath(__file__)), '..') + +def main(): + pathway = read(open(hiv_path / "raw" / "ko03250.xml", "r")) + + # Read in Kegg pathway data and keep only orthologs + entries_data = [] + for entry in pathway.entries.values(): + if entry.type == "ortholog": + entries_data.append({"name": entry.name}) + entries_df = pd.DataFrame(entries_data) + + # Some orthologs have multiple ko codes in the same row + # The following two lines move all ko codes to individual rows + orthology_ids = entries_df["name"].str.split(" ").explode() + orthology_ids = orthology_ids.apply(lambda x: x.split(":")[1]).tolist() + + # Using bioservices KEGG class to map ortholog(ko) codes to human(hsa) codes + k = KEGG() + ko_hsa_map = k.link("hsa", "+".join(orthology_ids)) + ko_hsa_dict = {x.split("\t")[0].split(":")[1]: x.split("\t")[1] for x in ko_hsa_map.split("\n")[:-1]} + ko_hsa_df = pd.DataFrame(ko_hsa_dict.items(), columns=["KEGG_Orthology", "HSA"]) + + # Kegg .get is limited to 10 entries per call + # The following code chunks the hsa list into sets of 10 + # then calls the .get function on each which returns kegg api data in string format + hsa_chunked = list(chunked(ko_hsa_df["HSA"].tolist(), 10)) + raw_uniprot = [] + for entry in hsa_chunked: + raw_uniprot.append(k.get("+".join(entry)).split("\n///\n\n")) + + # Raw Kegg api data is filtered to obtain hsa and uniprot codes for each protein + # Note: Although bioservices .link and .conv return cleaner outputs, they do not support + # one to many relationships at this time. + # Note: bioservices also supplies a parser method for the kegg api but it is also broken at this time. + processed_uniprot = [] + for chunk in raw_uniprot: + for item in chunk: + item = item.split("\n") + processed_uniprot.append([(x.strip().split(" ")[1:], "hsa:" + (item[0].split(" " * 7)[1])) for x in item if "UniProt" in x][0]) + + # Creates a dictionary where uniprot ids are keys and hsa ids are values + hsa_uniprot_dict = {} + for item in processed_uniprot: + for entry in item[0]: + hsa_uniprot_dict.update({"up:" + entry: item[1]}) + + # Creates a dataframe with uniprot and hsa values then merges with ko-hsa dataframe by hsa + hsa_uniprot_map = pd.DataFrame.from_dict(hsa_uniprot_dict.items()) + hsa_uniprot_map.columns = ["Uniprot", "HSA"] + final_df = ko_hsa_df.merge(hsa_uniprot_map, on="HSA") + uniprotIDs = final_df["Uniprot"].apply(lambda x: x.split(":")[1]).tolist() + + # Filters the combined dataframe to include only rows where the uniprot code is in swissprot + u = UniProt() + tst = u.mapping(fr="UniProtKB", to="UniProtKB-Swiss-Prot", query=",".join(uniprotIDs)) + failed_uniprot = pd.Series(list(set(tst["failedIds"]))).apply(lambda x: "up:" + x) + + final_df = final_df[~final_df["Uniprot"].isin(failed_uniprot)] + +if __name__ == '__main__': + main() diff --git a/datasets/hiv/Scripts/Name_Mapping.py b/datasets/hiv/scripts/name_mapping.py similarity index 84% rename from datasets/hiv/Scripts/Name_Mapping.py rename to datasets/hiv/scripts/name_mapping.py index 9cace88..2674a13 100644 --- a/datasets/hiv/Scripts/Name_Mapping.py +++ b/datasets/hiv/scripts/name_mapping.py @@ -1,3 +1,8 @@ +""" +This code is almost fully copied from https://www.uniprot.org/help/id_mapping_prog, +with the only exception being at the top and bottom of `main`. +""" + import re import time import json @@ -17,35 +22,28 @@ def main(): - - with open('Pickles/NodeIDs.pkl', 'rb') as file: + # This is 1 of two major exceptions to this being example code from UniProt. + # See prepare.py for the NodeIDs generation: this is the deduplicated list of node IDs + # from the two prize files in `raw`. + with open("Pickles/NodeIDs.pkl", "rb") as file: NodeIDs = pickle.load(file)["NodeIDs"] - job_id = submit_id_mapping( - from_db="UniProtKB_AC-ID", to_db="UniProtKB", ids= NodeIDs - ) + job_id = submit_id_mapping(from_db="UniProtKB_AC-ID", to_db="UniProtKB", ids=NodeIDs) if check_id_mapping_results_ready(job_id): link = get_id_mapping_results_link(job_id) uniprot_results = get_id_mapping_results_search(link) uniprot_IDs = [] uniprot_map = {} - for i in uniprot_results.get('results'): + for i in uniprot_results.get("results"): uniprot_IDs.append((i.get("to").get("uniProtkbId"))) - uniprot_map.update({i.get("from"):i.get("to").get("uniProtkbId")}) - - df ={ - "UniprotIDs": uniprot_IDs, - "UniprotMap": uniprot_map - } - - with open("Pickles/UniprotIDs.pkl","wb") as file: - pickle.dump(df,file) - - return - + uniprot_map.update({i.get("from"): i.get("to").get("uniProtkbId")}) + df = {"UniprotIDs": uniprot_IDs, "UniprotMap": uniprot_map} + # Second major exception: we save the Uniprot IDs. + with open("Pickles/UniprotIDs.pkl", "wb") as file: + pickle.dump(df, file) def check_response(response): try: @@ -169,9 +167,7 @@ def get_id_mapping_results_search(url): else: size = 500 query["size"] = size - compressed = ( - query["compressed"][0].lower() == "true" if "compressed" in query else False - ) + compressed = query["compressed"][0].lower() == "true" if "compressed" in query else False parsed = parsed._replace(query=urlencode(query, doseq=True)) url = parsed.geturl() request = session.get(url) @@ -195,11 +191,9 @@ def get_id_mapping_results_stream(url): parsed = urlparse(url) query = parse_qs(parsed.query) file_format = query["format"][0] if "format" in query else "json" - compressed = ( - query["compressed"][0].lower() == "true" if "compressed" in query else False - ) + compressed = query["compressed"][0].lower() == "true" if "compressed" in query else False return decode_results(request, file_format, compressed) if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/datasets/hiv/scripts/prepare.py b/datasets/hiv/scripts/prepare.py new file mode 100644 index 0000000..a907bc1 --- /dev/null +++ b/datasets/hiv/scripts/prepare.py @@ -0,0 +1,38 @@ +import pandas +from pathlib import Path +import pickle +import os + +# https://stackoverflow.com/a/5137509/7589775 +hiv_path = Path(os.path.dirname(os.path.realpath(__file__)), '..') + +def main(): + # See `fetch.py` for information about these two files. + prize_05 = pandas.read_csv(hiv_path / "raw" / "prizes_05.tsv", sep="\t", lineterminator="\n") + prize_060 = pandas.read_csv(hiv_path / "raw" / "prizes_060.tsv", sep="\t", lineterminator="\n") + + # Some proteins in the original prize files have the syntax `majorIdentifier-N` where N denotes isoforms. + # We don't particurarly care about any particular isoform when doing pathway reconstruction, + # so we treat -N isoforms as duplicates and remove them. + prize_05["Uniprot"] = prize_05["Uniprot"].str.split("-", expand=False).str[0] + prize_060["Uniprot"] = prize_060["Uniprot"].str.split("-", expand=False).str[0] + + # We want to preserve the highest Prize column out of all of the isoform (and non-isoform) variants. + prize_05 = prize_05.sort_values("Prize", ascending=False).drop_duplicates("Uniprot").sort_index() + prize_060 = prize_060.sort_values("Prize", ascending=False).drop_duplicates("Uniprot").sort_index() + + prize_060_nodes = prize_060["Uniprot"].tolist() + prize_05_nodes = prize_05["Uniprot"].tolist() + nodeset = list(set(prize_05_nodes + prize_060_nodes)) + + # See `name_mapping.py`` for the NodeIDs storage motivation. + df = {"NodeIDs": nodeset, "prize_05": prize_05, "prize_060": prize_060} + + (hiv_path / "Pickles").mkdir(exist_ok=True) + + with open(hiv_path / "Pickles" / "NodeIDs.pkl", "wb") as file: + pickle.dump(df, file) + +if __name__ == '__main__': + main() + diff --git a/datasets/hiv/scripts/spras_formatting.py b/datasets/hiv/scripts/spras_formatting.py new file mode 100644 index 0000000..3efb3e0 --- /dev/null +++ b/datasets/hiv/scripts/spras_formatting.py @@ -0,0 +1,30 @@ +import pickle +from pathlib import Path +import os + +current_directory = Path(os.path.dirname(os.path.realpath(__file__))) +processed_directory = current_directory.parent / "processed" + +def main(): + # See name_mapping.py for the origin of this file + with open("Pickles/UniprotIDs.pkl", "rb") as file: + UniprotIDs = pickle.load(file) + UMap = UniprotIDs["UniprotMap"] + + with open("Pickles/NodeIDs.pkl", "rb") as file2: + prizes = pickle.load(file2) + prize_05 = prizes["prize_05"] + prize_060 = prizes["prize_060"] + + prize_05["Uniprot"] = prize_05["Uniprot"].apply(lambda x: UMap.get(x)) + prize_060["Uniprot"] = prize_060["Uniprot"].apply(lambda x: UMap.get(x)) + + # Format with SPRAS column names + prize_05.columns = ["NODEID", "prize"] + prize_060.columns = ["NODEID", "prize"] + + prize_05.to_csv(processed_directory / "processed_prizes_05.txt", sep="\t", header=True, index=False) + prize_060.to_csv(processed_directory / "processed_prizes_060.txt", sep="\t", header=True, index=False) + +if __name__ == '__main__': + main()