koza
Usage:
$ koza [OPTIONS] COMMAND [ARGS]...
Options:
--version--install-completion: Install completion for the current shell.--show-completion: Show completion for the current shell, to copy it or customize the installation.--help: Show this message and exit.
Commands:
split: Split a file by fieldstransform: Transform a source filevalidate: Validate a source file
koza split
Split a file by fields
Usage:
$ koza split [OPTIONS] FILE FIELDS
Arguments:
FILE: Path to the source kgx file to be split [required]FIELDS: Comma separated list of fields to split on [required]
Options:
--remove-prefixes / --no-remove-prefixes: Remove prefixes from the file names for values from the specified fields. (e.g, NCBIGene:9606 becomes 9606 [default: no-remove-prefixes]--output-dir TEXT: Path to output directory [default: output]--help: Show this message and exit.
koza transform
Transform a source file
Usage:
$ koza transform [OPTIONS]
Options:
--source TEXT: Source metadata file [required]--output-dir TEXT: Path to output directory [default: ./output]--output-format [tsv|jsonl|kgx]: Output format [default: tsv]--global-table TEXT: Path to global translation table--local-table TEXT: Path to local translation table--schema TEXT: Path to schema YAML for validation in writer--row-limit INTEGER: Number of rows to process (if skipped, processes entire source file)--debug / --quiet--log / --no-log: Optional log mode - set true to save output to ./logs [default: no-log]--help: Show this message and exit.
koza validate
Validate a source file
Usage:
$ koza validate [OPTIONS]
Options:
--file TEXT: Path or url to the source file [required]--format [csv|jsonl|json|yaml]: [default: csv]--delimiter TEXT: [default: ,]--header-delimiter TEXT--skip-blank-lines / --no-skip-blank-lines: [default: skip-blank-lines]--help: Show this message and exit.