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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
author recetox
date Tue, 21 May 2024 07:44:25 +0000 (11 months ago)
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268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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1 import argparse
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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2 from collections import defaultdict
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3 from typing import Tuple
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5 import pandas as pd
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8 def parse_arguments() -> argparse.Namespace:
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9 """Parses command-line arguments.
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11 Returns:
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12 argparse.Namespace: Namespace with argument values as attributes.
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13 """
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14 parser = argparse.ArgumentParser(description='Rename annotated feature.')
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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15 parser.add_argument('--annotations_table_path', type=str, required=True, help='Path to the annotations table file.')
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16 parser.add_argument('--abundance_table_path', type=str, required=True, help='Path to the abundance table file.')
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17 parser.add_argument('--mode', type=str, choices=['single', 'multiple'], default='single', help='Mode to use for renaming. Can be "single" or "multiple".')
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18 parser.add_argument('--output_path', type=str, default='output.csv', help='Path to the output CSV file.')
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19 return parser.parse_args()
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22 def load_tables(annotations_table_path: str, abundance_table_path: str) -> Tuple[pd.DataFrame, pd.DataFrame]:
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23 """Loads annotation and abundance tables from files.
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25 Args:
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26 annotations_table_path (str): Path to the annotations table file.
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27 abundance_table_path (str): Path to the abundance table file.
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29 Returns:
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30 Tuple[pd.DataFrame, pd.DataFrame]: Tuple of DataFrames for annotations and abundance tables.
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31 """
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32 annotations_table = pd.read_table(annotations_table_path)
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33 abundance_table = pd.read_table(abundance_table_path)
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35 annotations_table.columns = annotations_table.columns.str.strip()
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36 abundance_table.columns = abundance_table.columns.str.strip()
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38 return annotations_table, abundance_table
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41 def rename_single(annotations_table: pd.DataFrame, abundance_table: pd.DataFrame) -> None:
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42 """Renames columns in abundance table based on single best match in annotations table.
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44 Args:
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45 annotations_table (pd.DataFrame): DataFrame of annotations.
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46 abundance_table (pd.DataFrame): DataFrame of abundance data.
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47 """
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48 scores_col = annotations_table.columns[-1]
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49 ref_idxs = annotations_table.groupby("query")[scores_col].idxmax()
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50 results = annotations_table.loc[ref_idxs]
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52 queries = results["query"]
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53 refs = results["reference"]
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55 mapping = dict(zip(queries, refs))
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56 abundance_table.rename(columns=mapping, inplace=True)
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59 def rename_multiple(annotations_table: pd.DataFrame, abundance_table: pd.DataFrame) -> None:
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60 """Renames columns in abundance table based on multiple matches in annotations table.
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62 Args:
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63 annotations_table (pd.DataFrame): DataFrame of annotations.
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64 abundance_table (pd.DataFrame): DataFrame of abundance data.
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65 """
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66 queries = annotations_table["query"]
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67 refs = annotations_table["reference"]
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69 mapping = defaultdict(list)
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70 for query, ref in zip(queries, refs):
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71 mapping[query].append(ref)
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73 for query, refs in mapping.items():
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74 new_column_name = ', '.join(refs)
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75 if query in abundance_table.columns:
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76 abundance_table.rename(columns={query: new_column_name}, inplace=True)
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79 def main() -> None:
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80 """Main function to parse arguments, load tables, rename columns, and save output."""
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81 args = parse_arguments()
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83 annotations_table, abundance_table = load_tables(args.annotations_table_path, args.abundance_table_path)
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85 if args.mode == "single":
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86 rename_single(annotations_table, abundance_table)
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87 else:
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88 rename_multiple(annotations_table, abundance_table)
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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89
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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90 abundance_table.to_csv(args.output_path, sep="\t", index=False)
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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91
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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92
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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93 if __name__ == "__main__":
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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94 main()