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Entab

What is everything were a/could be turned into a table?

Entab is a parsing framework to turn a variety of record-based scientific file formats into usable tabular data across a variety of programming languages.

Test status codecov Package on Crates.io Package on NPM Package on PyPI DOI

Formats

Entab supports reading a variety of bioinformatics, chemoinformatics, and other formats.

  • Agilent Chemstation CH, FID, MS, MWD, and UV formats
  • Agilent Masshunter DAD format1
  • FASTA and FASTQ sequence formats
  • FCS flow cytometry format
  • Inficon Hapsite mass specotrometry format
  • PNG image format
  • SAM and BAM alignment formats
  • Thermo continuous flow isotope mass spectrometry formats
  • Thermo RAW files
  • CSV & TSV files

CLI

Entab has a CLI that allows piping in arbitrary files and outputs TSVs. Install with:

cargo install entab-cli

Example usage to see how many records are in a file:

cat test.fa | entab | sed '1d' | wc -l

Bindings

There are bindings for two languages, Python and JavaScript, that support reading data streams and converting them into a series of records.

The Javascript library can be installed with:

npm install entab

The Python library can be installed with:

pip install entab

The R bindings can be installed from inside R with (note you will need Cargo and a Rust buildchain locally):

library(devtools)
devtools::install_github("bovee/entab", subdir="entab-r")

Priorities

  1. Handling many formats: Support as many record-based, streamable scientific formats as possible. Formats like HDF5 with complex headers and already existing, well-supported parsers are not considered a priority though.

  2. Correctness: Formats should be parsed with good error messages, consistant failure states, and well-tested code.

  3. Language bindings: Support using Entab from a decent selection of the programming languages currently used for science, data science, and related fields. Currently supporting Python, Javascript, and experimentally R with possible support for Julia in the future.

  4. Speed: Entab should be as fast as possible while still prioritizing the above issues. Parsers are split into two forms: a fast one that produces a specialized struct and a slow one that produces a generic record and is capable of being switched to at run time.

Website

There is a small demo of entab running in the browser that can open small files and plot the data in them.

Footnotes

  1. This format uses multiple files so it's not supported in streaming mode or in e.g. the JS bindings. ↩