taxpasta: TAXonomic Profile Aggregation and STAndardisation

[Midnighter]

Submitting Author: Moritz E. Beber (@Midnighter)
All current maintainers: (@Midnighter, @sofstam, @jfy133)
Package Name: taxpasta
One-Line Description of Package: TAXonomic Profile Aggregation and STAndardisation
Repository Link: https://github.com/taxprofiler/taxpasta
Version submitted: 0.2.1
Editor: @ctb
Reviewer 1: @snacktavish
Reviewer 2: @bluegenes
Archive: https://github.com/taxprofiler/taxpasta/releases/tag/0.4.0
JOSS DOI:
Version accepted: 0.4.0
Date accepted (month/day/year): 07/05/2023

---

Code of Conduct & Commitment to Maintain Package

• I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package after should it be accepted.
• I have read and will commit to package maintenance after the review as per the pyOpenSci Policies Guidelines.

Description

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. In future, we also intend to offer
methods for forming a consensus for the same sample analyzed by different
profilers.

Scope

• Please indicate which category or categories.
  Check out our package scope page to learn more about our
  scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

  • Data retrieval
  • Data extraction
  • Data processing/munging
  • Data deposition
  • Data validation and testing
  • Data visualization **
  • Workflow automation
  • Citation management and bibliometrics
  • Scientific software wrappers
  • Database interoperability

Domain Specific & Community Partnerships

- [ ] Geospatial
- [ ] Education
- [ ] Pangeo

Community Partnerships

If your package is associated with an
existing community please check below:

• Pangeo
  • My package adheres to the Pangeo standards listed in the pyOpenSci peer review guidebook

** Please fill out a pre-submission inquiry before submitting a data visualization package.*

• For all submissions, explain how the and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each):

  • Who is the target audience and what are scientific applications of this package?

    Taxpasta is a tool for anyone working with taxonomic profiles from metagenomic sequencing experiments. Mostly that means ecologists, bioinformaticians, statisticians. Taxpasta's main application is to standardise profiles from a range of different tools. Having a singular format facilitates downstream analyses. Taxpasta is used, for example, in the upcoming taxprofiler pipeline implemented in nextflow. There, it also serves to combine the profiles of many samples into a single file.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ?

    The BIOM format was created with the intention of standardizing a storage format for microbiome analyses. However, creating this format was entirely left to the user. Taxpasta conveniently knows how to read profiles from a range of tools and can also produce BIOM output.

    Some of the taxonomic profilers also come with scripts to convert their output into another format but none of them support such a wide range of tools as taxpasta does.

  • If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted:

Technical checks

For details about the pyOpenSci packaging requirements, see our packaging guide. Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• uses an OSI approved license.
• contains a README with instructions for installing the development version (development version is described in CONTRIBUTING.rst).
• includes documentation with examples for all functions.
• contains a tutorial with examples of its essential functions and uses.
• has a test suite.
• has continuous integration setup, such as GitHub Actions CircleCI, and/or others.

Publication Options

• Do you wish to automatically submit to the Journal of Open Source Software? If so:

JOSS Checks

• The package has an obvious research application according to JOSS's definition in their submission requirements. Be aware that completing the pyOpenSci review process does not guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS.
• The package is not a "minor utility" as defined by JOSS's submission requirements: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria.
• The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
• The package is deposited in a long-term repository with the DOI:

Note: JOSS accepts our review as theirs. You will NOT need to go through another full review. JOSS will only review your paper.md file. Be sure to link to this pyOpenSci issue when a JOSS issue is opened for your package. Also be sure to tell the JOSS editor that this is a pyOpenSci reviewed package once you reach this step.

Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

This option will allow reviewers to open smaller issues that can then be linked to PR's rather than submitting a more dense text based review. It will also allow you to demonstrate addressing the issue via PR links.

• Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.

Confirm each of the following by checking the box.

• I have read the author guide.
• I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed.

Please fill out our survey

• Last but not least please fill out our pre-review survey. This helps us track
  submission and improve our peer review process. We will also ask our reviewers
  and editors to fill this out.

P.S. *Have feedback/comments about our review process? Leave a comment here

Editor and Review Templates

The [editor template can be found here][Editor Template].

The [review template can be found here][Review Template].

[lwasser]

hey there 👋 @Midnighter welcome to pyopensci and thank you for this submission! i just wanted to say hello so you know that we see this submission and will be getting back to you shortly! i also am looking into forms for the submission template as well - many thanks for that suggestion! More soon!

[NickleDave]

Welcome @Midnighter @sofstam @jfy133!
I'm adding initial checks for this package.

Glad to see this as someone who develops a similar tool (for a different domain!).

Looks like most everything is there.

I do want to request one thing before we proceed with a review though:
can you please add at least one full tutorial?

Something like the "Examples" section in the Pynteny docs here (which also has a CLI interface): https://robaina.github.io/Pynteny/examples/example_cli/

(These docs were in place before we began the Pynteny review, which is why I'm providing them as an example of what we need to see before we start.)

I would suggest a sort of walkthrough of the main use case for taxpasta. This might be a simplified version of something you're using it for in research already.

I have provided some other feedback below but adding an initial tutorial is the only thing that's necessary at this time.

Editor in Chief checks

Hi there! Thank you for submitting your package for pyOpenSci
review. Below are the basic checks that your package needs to pass
to begin our review. If some of these are missing, we will ask you
to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements below.

• Installation The package can be installed from a community repository such as PyPI (preferred), and/or a community channel on conda (e.g. conda-forge, bioconda).
  • @Midnighter given the domain you're targeting, maybe it be good to publish a distribution package on bioconda and/or conda forge?
  • The package imports properly into a standard Python environment import package-name.
• Fit The package meets criteria for fit and overlap.
  • yes this is clearly a data munging package
• Documentation The package has sufficient online documentation to allow us to evaluate package function and scope without installing the package. This includes:
  • User-facing documentation that overviews how to install and start using the package.
    • I would strongly suggest adding a more general description of the package right at the top of the index page, that even a non-generalist (like me) can understand. What do people use taxonomic profiles for in your field? Why would it help me to be able to convert between formats? Links to Wikipedia pages, review articles, etc., would be helpful here. Ideally with a brief example of a table, like those shown in the command docs ("taxpasta is an interoperability tool for working with taxonomic profiles, that look something like this:"
    • There are install instructions but no real examples on the landing/index page. At a minimum the output of taxpasta -h could be shown and additionally a brief snippet. If the main usage is the CLI, then perhaps demos of usage could be shown with a tool like asciicinema
      • Also the output of taxpasta -h was truncated for me. See below. Not sure it would be clear to a new user what consensus and merge commands do because of the ellipsis. From the docs I guess this is because your cli package imports text from somewhere else? Is there a way to not truncate? Maybe just give a briefer summary?

$ taxpasta -h
Usage: taxpasta [OPTIONS] COMMAND [ARGS]...

  TAXonomic Profile Aggregation and STAndardisation

Options:
  --version                       Print only the current tool version and
                                  exit.
  -l, --log-level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
                                  Set the desired log level.  [default: INFO]
  --install-completion [bash|zsh|fish|powershell|pwsh]
                                  Install completion for the specified shell.
  --show-completion [bash|zsh|fish|powershell|pwsh]
                                  Show completion for the specified shell, to
                                  copy it or customize the installation.
  -h, --help                      Show this message and exit.

Commands:
  consensus    Form a consensus for the same sample but from different...
  merge        Standardise and merge two or more taxonomic profiles into...
  standardise  Standardise a taxonomic profile (alias: 'standardize').

• Short tutorials that help a user understand how to use the package and what it can do for them.
  • There are some snippet-like examples in documentation for commands of the command-line interface but I do not find more extensive tutorials
• API documentation (documentation for your code's functions, classes, methods and attributes): this includes clearly written docstrings with variables defined using a standard docstring format. We suggest using the Numpy docstring format.
• Core GitHub repository Files
  • README The package has a README.md file with clear explanation of what the package does, instructions on how to install it, and a link to development instructions.
  • Contributing File The package has a CONTRIBUTING.md file that details how to install and contribute to the package.
    • @Midnighter is there a link to the CONTRIBUTING.rst in the README? I'm not finding it. If not, I'd suggest adding it.
  • Code of Conduct The package has a Code of Conduct file.
    • inside the .github directory
  • License The package has an OSI approved license.
    NOTE: We prefer that you have development instructions in your documentation too.
• Issue Submission Documentation All of the information is filled out in the YAML header of the issue (located at the top of the issue template).
• Automated tests Package has a testing suite and is tested via GitHub actions or another Continuous Integration service.
• Repository The repository link resolves correctly.
• Package overlap The package doesn't entirely overlap with the functionality of other packages that have already been submitted to pyOpenSci.
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly.
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

• Initial onboarding survey was filled out
  We appreciate each maintainer of the package filling out this survey individually. 🙌
  Thank you authors in advance for setting aside five to ten minutes to do this. It truly helps our organization. 🙌

---

---

Editor comments

This is not required in checks but I would suggest adding example data to taxpasta.
Since you are working with tabular data that I'd guess can be failry lightweight, it should be relatively painless to add and it will really help people understand package usage. (Unless I'm wrong and the taxonomic profiles are like 100 MB each. In that case, see next paragraph.)
Again see the Pynteny example where they work with example data (not suggesting you need to add a download command but just showing you why built-in data is useful: https://robaina.github.io/Pynteny/examples/example_cli/#download-pgap-profile-hmm-database)

For my own library I just add the files directly to the package and then access with importlib.resources, see this issue: vocalpy/crowsetta#90
Some libraries have adopted the pooch library for data, e.g. scikit-image: https://scikit-image.org/docs/stable/api/skimage.data.html. Might be worth snooping their issues to help you figure out how to implement if you decide to adopt it.

[NickleDave]

Also @sofstam @jfy133 could you both please fill out the pre-review survey?
I have a reply for @Midnighter but not you I think.
https://forms.gle/F9mou7S3jhe8DMJ16
It's just a brief (5-10m) survey to help us understand how we're doing as an org. Thank you! 🙏

[Midnighter]

Hi @NickleDave,

Thank you for your review and comments. Adding a tutorial and improving the docs mostly makes sense to me. I will work on adding those.

The tables are indeed small, still I'm a little hesitant to distribute them with the package. However, pandas should be able to just load a table from a URL so that's maybe a way to go.

• Please note that taxpasta is already on bioconda https://bioconda.github.io/recipes/taxpasta/README.html#package-package%20'taxpasta' We need to document this, of course.
• I will also publish the package on Zenodo.

[jfy133]

Also @sofstam @jfy133 could you both please fill out the pre-review survey? I have a reply for @Midnighter but not you I think. https://forms.gle/F9mou7S3jhe8DMJ16 It's just a brief (5-10m) survey to help us understand how we're doing as an org. Thank you! pray

oops, sorry - from the second page most of the questions seemed to be about the package and I assume Moritz had already provided all that info.

I've filled it out, but left pretty much all the optional questions empty as either you have that info from Moritz, and/or submitting via pyOpenSci is Moritz' initative so I'm not that familiar/involved with python etc.

One comment though: I noticed that the options in your 'What background best describes you cultural identity?' question is extremely N. American focused. Unfortunately I don't have a good solution for you, but you may not be getting a particularly good overview of this - e.g. Asian spans half the world with many equally large sub-divisons as the Pacific Islanders, and also grouping 'Black' and African-American is also arguably unfair as they also can have a large difference in backgrounds/problems etc. For example see what official surveys from UK use: https://www.ethnicity-facts-figures.service.gov.uk/style-guide/ethnic-groups

[Midnighter]

@NickleDave regarding your comments on taxpasta -h the truncation is automatically created by typer. It looks better if you also install rich. I'll look into shortening the summaries such that they are not truncated by typer in the default view.

[NickleDave]

Thank you for your review and comments. Adding a tutorial and improving the docs mostly makes sense to me. I will work on adding those.

Great, thank you @Midnighter. Your other comments re: tables, bioconda, Zenodo, and the truncation all sound good. Would it be worth making rich a dependency so you don't have to special case typer behavior?

oops, sorry - from the second page most of the questions seemed to be about the package and I assume Moritz had already provided all that info.

I've filled it out, but left pretty much all the optional questions empty as either you have that info from Moritz, and/or submitting via pyOpenSci is Moritz' initative so I'm not that familiar/involved with python etc.

One comment though: I noticed that the options in your 'What background best describes you cultural identity?' question is extremely N. American focused.

Thank you @jfy133 I hear you and I will relay this to our executive director @lwasser. Your feedback is helpful; this is definitely a version 0.1 of the survey and I'm sure we can improve it to not be US-centric, and to encompass people who are core contributors to a project even if they are not primarily Python developers.

[Midnighter]

Would it be worth making rich a dependency so you don't have to special case typer behavior?

At the moment, it's an extra dependency that can be installed with taxpasta[rich]. (Come to think of it, we should document all of those.) The reason that it's not default is that where taxpasta originated, as a CLI tool for a nextflow pipeline, fancy terminal output is really not needed. We should definitely recommend installing that for interactive work, though.

[NickleDave]

where taxpasta originated, as a CLI tool for a nextflow pipeline, fancy terminal output is really not needed.

Understood!

Btw @Midnighter could I ask you to link this review issue on any issues you raise to make changes before review? By adding a link to the issue on the taxpasta repo, so that GitHub cross references them.

Just to help us track. Thank you 🙏