taxpasta: TAXonomic Profile Aggregation and STAndardisation

Midnighter commented 1 year ago

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

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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
- [x] 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

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[ ] Pangeo
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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.
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lwasser commented 1 year ago

Update: i just fixed our template AND the text here in the header of this issue.

Midnighter commented 1 year ago

Dear @ctb,

You can have a look at our draft for JOSS if you like, but as @lwasser mentioned this is not required to complete the review process here. Either way, we look forward to your final comments.

Midnighter commented 1 year ago

FYI, we just released version 0.4.0 that wraps the changes from the reviews, as well as further issues discovered by users.

ctb commented 1 year ago

ok, here goes:

🎉 taxpasta has been approved by pyOpenSci! Thank you @Midnighter for submitting and many thanks to @snacktavish @bluegenes for reviewing this package! 😸

Author Wrap Up Tasks

There are a few things left to do to wrap up this submission:

[x] Activate Zenodo watching the repo if you haven't already done so.
[x] Tag and create a release to create a Zenodo version and DOI.
[x] Add the badge for pyOpenSci peer-review to the README.md of taxpasta. The badge should be [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/84).
[x] Please fill out the post-review survey. All maintainers and reviewers should fill this out.
[x] Add taxpasta to the pyOpenSci website. @Midnighter , please open a pr to update this file: to add your package and name to the list of contributors.
[ ] @snacktavish @bluegenes if you have time and are open to being listed on our website, please add yourselves to this file via a pr so we can list you on our website as contributors!

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[ ] Invite the maintainers to submit a blog post highlighting their package. Feel free to use / adapt language found in this comment to help guide the author.
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jfy133 commented 1 year ago

Added badge and confirm I've filled out the post-review survey!

Kevin-Mattheus-Moerman commented 1 year ago

@ctb @lwasser :wave: I am an editor for JOSS and processing the JOSS side of things. Can you clarify if this review is fully complete and this submission has passed review? The reason I ask is that many of the boxes :point_up: are not ticked.

ctb commented 1 year ago

Yes, it has passed review! At least one reviewer has checked all the criteria.

Kevin-Mattheus-Moerman commented 1 year ago

@ctb thanks for the reply. Note though that @NickleDave Editor in Chief checks set has unchecked boxes :point_up:, and so does your Author Wrap Up Tasks and Editor Final Checks set. It seems to me like most of these can just be ticked? If so I think it would be best if your group makes a habit of ticking them (perhaps you still can now), so that somebody studying this review issue is not confused about the software/review lacking anything.

ctb commented 1 year ago

@ctb thanks for the reply. Note though that @NickleDave Editor in Chief checks set has unchecked boxes ☝️, and so does your Author Wrap Up Tasks and Editor Final Checks set. It seems to me like most of these can just be ticked? If so I think it would be best if your group makes a habit of ticking them (perhaps you still can now), so that somebody studying this review issue is not confused about the software/review lacking anything.

there are so many check boxes 😆

but also, I think:

Invite the maintainers to submit a blog post highlighting their package.

could maybe best happen after JOSS paper is available. Similarly,

If the author submits to JOSS...

I felt needed to wait until there was a JOSS issue. In addition, I don't think the authors have the ability to check off those boxes so it had to wait until THEY did the work and then I noticed that they had done so => check the boxes.

For the other checklist items like adding badges and so on, those were done after I signed off on the review and I don't get notified of PRs etc. referencing this issue so barring monitoring this issue manually or being tagged in on the PRs, I'm not sure how I would go about knowing I should check them off...

(I don't mean to be defensive - I am just explaining where we are and why, and confirming to myself that I had read the unchecked boxes and made the decision not to check them off yet, instead of missing them entirely, which was also certainly a possibility!)

jfy133 commented 1 year ago

In addition, I don't think the authors have the ability to check off those boxes so it had to wait until THEY did the work and then I noticed that they had done so => check the boxes.

Correct, at least I was unable to tick of the boxes of what was meant to be our tasks (as authors)

lwasser commented 1 year ago

ahhhh ok lessons learned here that we need a way for authors to check their boxes AND/OR we need fewer of them . thank you all for the feedback!!! i hadn't considered that authors would NOT be able to check those author list boxes - we will have to come up with a better approach! i'm open to suggestions.

and it looks like taxpasta was accepted by JOSS - hooray. 🎉 🎉

jfy133 commented 1 year ago

:tada: ! Thanks @lwasser !

lwasser commented 1 year ago

awesome! ok i'll close this issue now. Friends - if anyone from this review (reviewers, maintainers etc) is interested in joining our slack community please email me at leah at pyopensci.org or reply here if your email is available on your github and i can add you!! we'd love to have all of you there!

Kevin-Mattheus-Moerman commented 1 year ago

@lwasser One of the JOSS AEiCs here. Thanks for the great work with pyOpenSci. On the checkboxes, yes I recommend a single set of checkboxes which are all ticked before acceptance in pyOpenSci. This way it is super clear that if they are all ticked things are completed/acceptable. This way people viewing the review issue do not get the wrong idea. If the authors cannot check them perhaps the editor can do it once completed. We sometimes have to do that with JOSS. Also, I believe just 1 reviewer complete the review here. Do you have guidelines/documentation on your policies on this somewhere for pyOpenSci? I would recommend that you adopt that at least 2 reviewers should complete the review. Thanks.

pyOpenSci / software-submission