Mercurial > repos > recetox > table_pandas_rename_columns_regex

annotate utils.py @ 0:505a8e975968 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
author recetox
date Wed, 29 Jan 2025 15:35:08 +0000
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505a8e975968 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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diff changeset
1 import argparse
505a8e975968 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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2 from typing import Tuple
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5 import pandas as pd
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6
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8 class KeyValuePairsAction(argparse.Action):
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9 def __call__(self, parser, namespace, values, option_string=None):
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10 """
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11 Parse key=value pairs from the command line arguments.
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505a8e975968 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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13 Parameters:
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14 parser (argparse.ArgumentParser): The argument parser instance.
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15 namespace (argparse.Namespace): The namespace to hold the parsed values.
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16 values (list): The list of key=value pairs.
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17 option_string (str): The option string.
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19 Sets:
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20 namespace.dest (dict): A dictionary with 1-based column index as key and new column name as value.
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21 """
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22 key_value_pairs = {}
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23 for item in values:
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24 try:
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25 key, value = item.split("=")
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26 key_value_pairs[int(key)] = value # Convert key to integer
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27 except ValueError:
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28 parser.error(
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29 f"Invalid format for --rename: {item}. Expected format: key=value"
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30 )
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31 setattr(namespace, self.dest, key_value_pairs)
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34 class LoadDataAction(argparse.Action):
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35 def __call__(self, parser, namespace, values, option_string=None):
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36 file_path, file_extension = values
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37 file_extension = file_extension.lower()
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38 if file_extension == "csv":
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39 df = pd.read_csv(file_path)
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40 elif file_extension in ["tsv", "tabular"]:
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41 df = pd.read_csv(file_path, sep="\t")
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42 elif file_extension == "parquet":
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43 df = pd.read_parquet(file_path)
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44 else:
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45 raise ValueError(f"Unsupported file format: {file_extension}")
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46 setattr(namespace, self.dest, df)
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49 def write_csv(df: pd.DataFrame, file_path: str) -> None:
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50 """
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51 Write the dataframe to a CSV file.
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52
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53 Parameters:
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54 df (pd.DataFrame): The dataframe to write.
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55 file_path (str): The path to the output CSV file.
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56 """
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57 df.to_csv(file_path, index=False)
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60 def write_tsv(df: pd.DataFrame, file_path: str) -> None:
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61 """
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62 Write the dataframe to a TSV file.
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63
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64 Parameters:
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65 df (pd.DataFrame): The dataframe to write.
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66 file_path (str): The path to the output TSV file.
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67 """
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68 df.to_csv(file_path, sep="\t", index=False)
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71 def write_parquet(df: pd.DataFrame, file_path: str) -> None:
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72 """
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73 Write the dataframe to a Parquet file.
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74
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75 Parameters:
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76 df (pd.DataFrame): The dataframe to write.
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77 file_path (str): The path to the output Parquet file.
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78 """
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79 df.to_parquet(file_path, index=False)
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82 class StoreOutputAction(argparse.Action):
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83 def __call__(
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84 self,
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85 parser: argparse.ArgumentParser,
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86 namespace: argparse.Namespace,
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87 values: Tuple[str, str],
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88 option_string: str = None,
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89 ) -> None:
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90 """
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91 Custom argparse action to store the output function and file path based on file extension.
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92
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93 Parameters:
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94 parser (argparse.ArgumentParser): The argument parser instance.
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95 namespace (argparse.Namespace): The namespace to hold the parsed values.
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96 values (Tuple[str, str]): The file path and file extension.
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97 option_string (str): The option string.
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98 """
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99 file_path, file_extension = values
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100 file_extension = file_extension.lower()
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101 if file_extension == "csv":
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102 write_func = write_csv
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103 elif file_extension in ["tsv", "tabular"]:
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104 write_func = write_tsv
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105 elif file_extension == "parquet":
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106 write_func = write_parquet
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107 else:
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108 raise ValueError(f"Unsupported file format: {file_extension}")
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109 setattr(namespace, self.dest, (write_func, file_path))
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110
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111
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112 class SplitColumnIndicesAction(argparse.Action):
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113 def __call__(
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114 self,
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115 parser: argparse.ArgumentParser,
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116 namespace: argparse.Namespace,
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117 values: str,
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118 option_string: str = None,
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119 ) -> None:
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120 """
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121 Custom argparse action to split a comma-separated list of column indices and convert to 0-based indices.
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122
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123 Parameters:
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124 parser (argparse.ArgumentParser): The argument parser instance.
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125 namespace (argparse.Namespace): The namespace to hold the parsed values.
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126 values (str): The comma-separated list of 1-based column indices.
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127 option_string (str): The option string.
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128 """
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129 indices = [int(x) - 1 for x in values.split(",")] # Convert to 0-based indices
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130 setattr(namespace, self.dest, indices)