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to-csv-sd

  • accepts: sdc.api.SampleData
  • default extension: .csv

Saves the sample data in CSV format (row-wise).

usage: to-csv-sd [-h] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                 [-N LOGGER_NAME] [--skip]
                 [--split_ratios SPLIT_RATIOS [SPLIT_RATIOS ...]]
                 [--split_names SPLIT_NAMES [SPLIT_NAMES ...]]
                 [--split_group SPLIT_GROUP] [-o OUTPUT]
                 [--sample_id SAMPLE_ID] [--sample_data [SAMPLE_DATA ...]]
                 [--sample_data_prefix SAMPLE_DATA_PREFIX]

Saves the sample data in CSV format (row-wise).

options:
  -h, --help            show this help message and exit
  -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        The logging level to use. (default: WARN)
  -N LOGGER_NAME, --logger_name LOGGER_NAME
                        The custom name to use for the logger, uses the plugin
                        name by default (default: None)
  --skip                Disables the plugin, removing it from the pipeline.
                        (default: False)
  --split_ratios SPLIT_RATIOS [SPLIT_RATIOS ...]
                        The split ratios to use for generating the splits
                        (must sum up to 100) (default: None)
  --split_names SPLIT_NAMES [SPLIT_NAMES ...]
                        The split names to use for the generated splits.
                        (default: None)
  --split_group SPLIT_GROUP
                        The regular expression with a single group used for
                        keeping items in the same split, e.g., for identifying
                        the base name of a file or the sample ID. (default:
                        None)
  -o OUTPUT, --output OUTPUT
                        The CSV file to store the sample data in. (default:
                        None)
  --sample_id SAMPLE_ID
                        The name to use for the sample ID column. (default:
                        sample_id)
  --sample_data [SAMPLE_DATA ...]
                        The sample data names to store in CSV file. (default:
                        [])
  --sample_data_prefix SAMPLE_DATA_PREFIX
                        The prefix to use for the sample data columns.
                        (default: )

Available variables:

  • {HOME}: The home directory of the current user.
  • {CWD}: The current working directory.
  • {TMP}: The temp directory.
  • {INPUT_PATH}: The directory part of the current input, i.e., /some/where of input /some/where/file.txt.
  • {INPUT_NAMEEXT}: The name (incl extension) of the current input, i.e., file.txt of input /some/where/file.txt.
  • {INPUT_NAMENOEXT}: The name (excl extension) of the current input, i.e., file of input /some/where/file.txt.
  • {INPUT_EXT}: The extension of the current input (incl dot), i.e., .txt of input /some/where/file.txt.
  • {INPUT_PARENT_PATH}: The directory part of the parent directory of the current input, i.e., /some of input /some/where/file.txt.
  • {INPUT_PARENT_NAME}: The name of the parent directory of the current input, i.e., where of input /some/where/file.txt.