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TAXonomic Profile Aggregation and STAndardisation

About

The main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.

Diagram of taxpasta functionality. On the left are a range of taxonomic profilers with hetereogeneous output types with a header of taxonomic profiles, then a range of colourful lines leading into a box with a single green line, the taxpasta logo plus three icons for Validation, Standardisation and Conversion, and finally a range of green lines spreading out to a range of file icons with various file types with a header of Standardised Tables.

Supported Taxonomic Profilers

Taxpasta currently supports standardisation and generation of comparable taxonomic tables for:

See supported profilers for more information.

Install

It's as simple as:

pip install taxpasta

Taxpasta is also available from the Bioconda channel

conda install -c bioconda taxpasta

and thus automatically generated Docker and Singularity BioContainers images also exist.

Optional Dependencies

Taxpasta supports a number of extras that you can install for additional features; primarily support for additional output file formats. You can install them by specifying a comma separated list within square brackets, for example,

pip install 'taxpasta[rich,biom]'
  • rich provides rich-formatted command line output and logging.
  • arrow supports writing output tables in Apache Arrow format.
  • parquet supports writing output tables in Apache Parquet format.
  • biom supports writing output tables in BIOM format.
  • ods supports writing output tables in ODS format.
  • xlsx supports writing output tables in Microsoft Excel format.
  • all includes all of the above.
  • dev provides all tools needed for contributing to taxpasta.

Usage

The main entry point for taxpasta is its command-line interface (CLI). You can interactively explore the offered commands through the help system.

taxpasta -h

See the Getting Started tutorial to get familiar with Taxpasta.

Taxpasta currently offers two commands corresponding to the main use-cases. You can find out more in the commands' documentation.

Standardise

Since the supported profilers all produce their own flavour of tabular output, a quick way to normalize such files, is to standardise them with taxpasta. You need to let taxpasta know what tool the file was created by. As an example, let's standardise a MetaPhlAn profile. (You can find an example file in our test data.)

curl -O https://raw.githubusercontent.com/taxprofiler/taxpasta/main/tests/data/metaphlan/MOCK_002_Illumina_Hiseq_3000_se_metaphlan3-db.metaphlan3_profile.txt

taxpasta standardise -p metaphlan -o standardised.tsv MOCK_002_Illumina_Hiseq_3000_se_metaphlan3-db.metaphlan3_profile.txt

With these minimal arguments, taxpasta produces a two column output consisting of

taxonomy_id count

You can count on the second column being integers 😉 Having such a simple and tidy table should make your downstream analysis much smoother to start out with. Please, have a look at the full getting started tutorial for a more thorough introduction.

Merge

Converting single tables is nice, but hopefully you have many shiny samples to analyze. The taxpasta merge command works similarly to standardise except that you provide multiple profiles as input. Grab a few more MOCK examples from our test data and try it out.

LOCATION=https://raw.githubusercontent.com/taxprofiler/taxpasta/main/tests/data/metaphlan
curl -O "${LOCATION}/MOCK_001_Illumina_Hiseq_3000_se_metaphlan3-db.metaphlan3_profile.txt"
curl -O "${LOCATION}/MOCK_002_Illumina_Hiseq_3000_se_metaphlan3-db.metaphlan3_profile.txt"
curl -O "${LOCATION}/MOCK_003_Illumina_Hiseq_3000_se_metaphlan3-db.metaphlan3_profile.txt"

taxpasta merge -p metaphlan -o merged.tsv MOCK_*.metaphlan3_profile.txt

The output of the merge command has one column for the taxonomy identifier and one more column for each input profile. Again, please have a look at the full getting started tutorial for a more thorough introduction.

Citation

If you use TAXPASTA in your academic work, please cite our article in the Journal of Open Source Software.

Beber, M. E., Borry, M., Stamouli, S., & Fellows Yates, J. A. (2023). TAXPASTA: TAXonomic Profile Aggregation and STAndardisation. Journal of Open Source Software, 8(87), 5627. https://doi.org/10.21105/joss.05627

Acknowledgments

Many thanks to:

  • Copyright © 2022, 2023, Moritz E. Beber, Maxime Borry, James A. Fellows Yates, and Sofia Stamouli.
  • Free software distributed under the Apache Software License 2.0.