joinem provides a CLI for fast, flexbile concatenation of tabular data using polars
- Free software: MIT license
- Repository: https://github.com/mmore500/joinem
- Documentation: https://github.com/mmore500/joinem/blob/master/README.md
python3 -m pip install joinem
- Lazily streams I/O to expeditiously handle numerous large files.
- Supports CSV and parquet input files.
- Due to current polars limitations, JSON and feather files are not supported.
- Input formats may be mixed.
- Supports output to CSV, JSON, parquet, and feather file types.
- Allows mismatched columns and/or empty data files with
--how diagonaland--how diagonal_relaxed. - Provides a progress bar with
--progress. - Add programatically-generated columns to output.
Pass input filenames via stdin, one filename per line.
find path/to/*.parquet path/to/*.csv | python3 -m joinem out.parquet
Output file type is inferred from the extension of the output file name. Supported output types are feather, JSON, parquet, and csv.
find -name '*.parquet' | python3 -m joinem out.json
Use --progress to show a progress bar.
ls -1 path/{*.csv,*.pqt} | python3 -m joinem out.csv --progress
If file columns may mismatch, use --how diagonal.
find path/to/ -name '*.csv' | python3 -m joinem out.csv --how diagonal
If some files may be empty, use --how diagonal_relaxed.
To run via Singularity/Apptainer,
ls -1 *.csv | singularity run docker://ghcr.io/mmore500/joinem out.feather
Add literal value column to output.
ls -1 *.csv | python3 -m joinem out.csv --with-column 'pl.lit(2).alias("two")'
Alias an existing column in the output.
ls -1 *.csv | python3 -m joinem out.csv --with-column 'pl.col("a").alias("a2")'
Apply regex on source datafile paths to create new column in output.
ls -1 path/to/*.csv | python3 -m joinem out.csv \
--with-column 'pl.lit(filepath).str.replace(r".*?([^/]*)\.csv", r"${1}").alias("filename stem")'
Read data from stdin and write data to stdout.
cat foo.csv | python3 -m joinem "/dev/stdout" --stdin --output-filetype csv --input-filetype csv
Advanced usage.
Write to parquet via stdout using pv to display progress, cast "myValue" column to categorical, and use lz4 for parquet compression.
ls -1 input/*.pqt | python3 -m joinem "/dev/stdout" --output-filetype pqt --with-column 'pl.col("myValue").cast(pl.Categorical)' --write-kwarg 'compression="lz4"' | pv > concat.pqt
usage: __main__.py [-h] [--version] [--progress] [--stdin] [--eager-read]
[--eager-write] [--with-column WITH_COLUMNS]
[--string-cache]
[--how {vertical,horizontal,diagonal,diagonal_relaxed}]
[--input-filetype INPUT_FILETYPE]
[--output-filetype OUTPUT_FILETYPE]
[--read-kwarg READ_KWARGS] [--write-kwarg WRITE_KWARGS]
output_file
CLI for fast, flexbile concatenation of tabular data using Polars.
positional arguments:
output_file Output file name
options:
-h, --help show this help message and exit
--version show program's version number and exit
--progress Show progress bar
--stdin Read data from stdin
--drop DROP Columns to drop.
--eager-read Use read_* instead of scan_*. Can improve performance
in some cases.
--eager-write Use write_* instead of sink_*. Can improve performance
in some cases.
--filter FILTERS Expression to be evaluated and passed to polars DataFrame.filter.
Example: 'pl.col("thing") == 0'
--with-column WITH_COLUMNS
Expression to be evaluated to add a column, as access
to each datafile's filepath as `filepath` and polars
as `pl`. Example:
'pl.lit(filepath).str.replace(r".*?([^/]*)\.csv",
r"${1}").alias("filename stem")'
--shrink-dtypes Shrink numeric columns to the minimal required datatype.
--string-cache Enable Polars global string cache.
--how {vertical,horizontal,diagonal,diagonal_relaxed}
How to concatenate frames. See
<https://docs.pola.rs/py-
polars/html/reference/api/polars.concat.html> for more
information.
--input-filetype INPUT_FILETYPE
Filetype of input. Otherwise, inferred. Example: csv,
parquet, json, feather
--output-filetype OUTPUT_FILETYPE
Filetype of output. Otherwise, inferred. Example: csv,
parquet
--read-kwarg READ_KWARGS
Additional keyword arguments to pass to pl.read_* or
pl.scan_* call(s). Provide as 'key=value'. Specify
multiple kwargs by using this flag multiple times.
Arguments will be evaluated as Python expressions.
Example: 'infer_schema_length=None'
--write-kwarg WRITE_KWARGS
Additional keyword arguments to pass to pl.write_* or
pl.sink_* call. Provide as 'key=value'. Specify
multiple kwargs by using this flag multiple times.
Arguments will be evaluated as Python expressions.
Example: 'compression="lz4"'
Provide input filepaths via stdin. Example: find path/to/ -name '*.csv' |
python3 -m joinem out.csv
If joinem contributes to a scholarly work, please cite it as
Matthew Andres Moreno. (2024). mmore500/joinem. Zenodo. https://doi.org/10.5281/zenodo.10701182
@software{moreno2024joinem,
author = {Matthew Andres Moreno},
title = {mmore500/joinem},
month = feb,
year = 2024,
publisher = {Zenodo},
doi = {10.5281/zenodo.10701182},
url = {https://doi.org/10.5281/zenodo.10701182}
}And don't forget to leave a star on GitHub!
