Package: taxpasta
TAXonomicProfileAggregation andSTAndardisationPackageMetaAutomationAboutThe main purpose of taxpasta is tostandardisetaxonomic 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 takethe lessons learntto 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 alsomergethem
across samples for thesameprofiler into a single table.Supported Taxonomic ProfilersTaxpasta currently supports standardisation and generation of comparable
taxonomic tables for:BrackenCentrifugeDIAMONDganonKaijuKraken2KrakenUniqMEGAN6/MALTMetaPhlAnmOTUsSeesupported profilersfor more information.InstallIt's as simple as:pipinstalltaxpastaTaxpasta is also available from theBiocondachannelcondainstall-cbiocondataxpastaand thus automatically generatedDockerandSingularityBioContainersimages also exist.Optional DependenciesTaxpasta 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,pipinstall'taxpasta[rich,biom]'richprovidesrich-formatted command line output and logging.arrowsupports writing output tables inApache Arrowformat.parquetsupports writing output tables inApache Parquetformat.biomsupports writing output tables inBIOMformat.odssupports writing output tables inODSformat.xlsxsupports writing output tables inMicrosoft Excelformat.allincludes all of the above.devprovides all tools needed for contributing to taxpasta.UsageThe main entry point for taxpasta is its command-line interface (CLI). You can interactively
explore the offered commands through the help system.taxpasta-hTaxpasta currently offers two commands corresponding to the mainuse-cases. You can find out more in thecommands'
documentation.StandardiseSince thesupported profilersall 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 ourtest
data.)curl-Ohttps://raw.githubusercontent.com/taxprofiler/taxpasta/main/tests/data/metaphlan/MOCK_002_Illumina_Hiseq_3000_se_metaphlan3-db.metaphlan3_profile.txt
taxpastastandardise-pmetaphlan-ostandardised.tsvMOCK_002_Illumina_Hiseq_3000_se_metaphlan3-db.metaphlan3_profile.txtWith these minimal arguments, taxpasta produces a two column output consisting oftaxonomy_idcountYou can count on the second column being integers :wink:. Having such a simple
and tidy table should make your downstream analysis much smoother to start out
with. Please have a look at the fullgetting
startedtutorial for a more thorough introduction.MergeConverting single tables is nice, but hopefully you have many shiny samples to
analyze. Thetaxpasta mergecommand works similarly tostandardiseexcept
that you provide multiple profiles as input. You can grab a few more 'MOCK' examples from
ourtest
dataand
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"taxpastamerge-pmetaphlan-omerged.tsvMOCK_*.metaphlan3_profile.txtThe output of themergecommand has one column for the taxonomic identifier and
one more column for each input profile. Again, have a look at the fullgetting
startedtutorial for a more thorough introduction.CitationIf you use TAXPASTA in your academic work, please cite ourarticle 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.05627AcknowledgmentsMany thanks to:nf-corefor bringing the original developers togetherZandra Fagernäsfor the logo designCopyrightCopyright © 2022, 2023, Moritz E. Beber, Maxime Borry, James A. Fellows
Yates, and Sofia Stamouli.Free software distributed under theApache Software License
2.0.