[REVIEW]: Dnaapler: A tool to reorient circular microbial genomes

[editorialbot]

Submitting author: @gbouras13 (George Bouras)
Repository: https://github.com/gbouras13/dnaapler
Branch with paper.md (empty if default branch):
Version: v0.5.0
Editor: @fboehm
Reviewers: @mkerin, @vinisalazar
Archive: 10.5281/zenodo.10251242

Status

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Markdown: [![status](https://joss.theoj.org/papers/e6b4ba465b709fc372e640b1f2351f6f/status.svg)](https://joss.theoj.org/papers/e6b4ba465b709fc372e640b1f2351f6f)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mkerin & @vinisalazar, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fboehm know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @mkerin

📝 Checklist for @vinisalazar

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (538.5 files/s, 71943.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          12            522            483           1974
Markdown                        12            281              0            650
TeX                              1             14              0            145
YAML                             6             18             10            133
TOML                             1              7              0             38
-------------------------------------------------------------------------------
SUM:                            32            842            493           2940
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/s13059-015-0849-0 is OK
- 10.1101/pdb.top17 is OK
- 10.1016/S0022-2836(05)80360-2 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1371/journal.pcbi.1005595 is OK
- 10.1093/nargab/lqab067 is OK
- 10.1186/s13059-021-02483-z is OK
- 10.1101/2023.04.04.535632 is OK
- 10.1093/bioinformatics/btad409 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 981

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[mkerin]

Review checklist for @mkerin

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/gbouras13/dnaapler?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@gbouras13) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[vinisalazar]

Review checklist for @vinisalazar

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/gbouras13/dnaapler?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@gbouras13) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[vinisalazar]

The authors present a tool for automated reorientation of microbial genomes. The implementation is simple and elegant, with high code quality, and employs best practices for scientific software.

This is a high quality submission and I wholly recommend it for publication in JOSS.

Having this said, my only concern with the manuscript (and the accompanying software documentation) is the lack of actual example usages of the software, either on artificial or real-world data. Although the authors demonstrate how to utilise the different subcommands, there is no explicit demonstration of what the software does, that is, showing an output representing a reoriented genome. The testing suite in the software package contains example data that can presumably be used to demonstrate this. Although I don't think that this should be a blocker to accepting the manuscript, I believe that the manuscript and/or the documentation would be greatly enriched by this addition. One suggestion would be to show figures comparing "no treatment" vs "reoriented" genomes on a genome browser such as Geneious.

Some additional points:

• I would suggest renaming the mystery subcommand as random as that is more descriptive of what it does.
• I understand that Dnaapler reorients genomes by placing specific marker genes at the start. But how does it decide the order of the remaining genes, does it follow the order that they were in the original FASTA file? Is there any guarantee that this is the actual order of CDSs in the genome?
• Edit: the authors may also consider adding the citations of the third-party dependencies to the "citation" command, or some sort of disclaimer that the software relies on third-party software that would also have to be cited.

[fboehm]

@vinisalazar @mkerin - thank you for starting the reviews and your initial comments. @gbouras13 - please feel free to reply to the suggestions above (and the opened github issues). Please let us know if you have any questions or need clarifications. Thanks again!

[mkerin]

Hi all - I have now finished my review.

I think dnaapler is a strong submission to JOSS. The library has through documentation, appears to be well tested, and I can see how separating out the re-orientation of bacterial genomes into a separate library is a valuable contribution to the community.

I have left 5 boxes in the checklist unticked, which represent areas where I have outstanding questions / comments:

• For the authorship/community guidelines/references, I have opened issues in the dnaapler repo which I believe are minor only & should be straight forward to resolve.
• On testing the functionality of dnaapler, I performed basic checks using the test .fasta file to verify that dnaapler conserves the order of the dna sequence during reorientation. For example, if transMystery() and transAll() are functions that transform genomes accordinging to dnaapler mystery and dnaapler all respectively, then transAll(fasta) == transAll(transMystery(fasta)). However the logs suggested that dnaapler was not actually using BLAST as expected - so it would be great in @gbouras13 could clarify if this is expected (see issue in dnaapler repo for more details).
• On the example usage, I agree with @vinisalazar that it would be useful to see examples using real world data & accompanying visualizations of the original & reorientated sequences - if this is not too burdensome.

Once these points are resolved then I will be happy to recommended this paper for publication in JOSS.

[mkerin]

Also - just in case it's helpful to know in advance - I have good availability to respond to comments etc for the next 2 weeks, but from the 20th November I will be on vacation & will likely have limited internet access.

[gbouras13]

@vinisalazar and @mkerin,

Thank you so much for your reviews. We will aim to respond to all your questions today - especially yours @mkerin as a priority.

Edit: almost made it through all of them today but not quite.

George

[gbouras13]

Regarding the visualisation/example data question, we think this is feasible to include in the manuscript. We will include an example chromosome and phage visualised by the plot output options in Bakta and Pharokka respectively (with some manual annotation to make the dnaA/terL obvious - it will be clearer for phage due to the genome size).

We will also outline tests and examples explicitly in the documentation using data in the tests directory.

[gbouras13]

I also note that dnaapler all and dnaapler largest have been added since v0.2.0 (submission in August), so I have added explanation of them to the table and paper - especially dnaapler all which I anticipate is the most useful command.

[mkerin]

@editorialbot generate pdf

[fboehm]

@gbouras13 - it looks like two of the dois for your references have preceding text that needs to be removed. Would you please edit the bib file by deleting the "https://doi.org/" from the two doi entries?

[fboehm]

IN other words, the doi field in the bib entry should be merely: 10.1099/mgen.0.001128 (for example)

[fboehm]

Also, @gbouras13 - the software repo (https://github.com/gbouras13/dnaapler) and the software archive (https://doi.org/10.5281/zenodo.10251242) need to use the same license. It looks to me that the github repo uses MIT license, while the zenodo archive, I think, lists a creative commons license. Am I interpreting this accurately?

[fboehm]

I'm thinking that the zenodo page's "Rights" section should list MIT license.

[gbouras13]

Hi @fboehm ,

Thanks for this - I have updated the zenodo page's rights to MIT and fixed those 2 spurious dois

[gbouras13]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/s13059-015-0849-0 is OK
- 10.1101/pdb.top17 is OK
- 10.1016/S0022-2836(05)80360-2 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1371/journal.pcbi.1005595 is OK
- 10.1093/nargab/lqab067 is OK
- 10.1186/s13059-021-02483-z is OK
- 10.1093/bioinformatics/btad586 is OK
- 10.1093/bioinformatics/btad409 is OK
- 10.1099/mgen.0.001128 is OK
- 10.1093/bioinformatics/btac776 is OK
- 10.1099/mgen.0.000685 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[fboehm]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[fboehm]

lines 73 & 74: use lower case letters in continuous integration and continuous integration
@gbouras13 - can you fix this small issue? Otherwise, the text of the pdf looks good.

[fboehm]

Also, the dois all resolve to the intended targets.

[gbouras13]

All fixed @fboehm thanks for picking up the typos

[fboehm]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[fboehm]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/s13059-015-0849-0 is OK
- 10.1101/pdb.top17 is OK
- 10.1016/S0022-2836(05)80360-2 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1371/journal.pcbi.1005595 is OK
- 10.1093/nargab/lqab067 is OK
- 10.1186/s13059-021-02483-z is OK
- 10.1093/bioinformatics/btad586 is OK
- 10.1093/bioinformatics/btad409 is OK
- 10.1099/mgen.0.001128 is OK
- 10.1093/bioinformatics/btac776 is OK
- 10.1099/mgen.0.000685 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4866, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@gbouras13 As AEiC I will now help process this work for acceptance in JOSS (apologies for the delay). I have checked the paper, this review, your repository, and the archive link. All seems in order. I will now proceed to process this for acceptance.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Bouras
  given-names: George
  orcid: "https://orcid.org/0000-0002-5885-4186"
- family-names: Grigson
  given-names: Susanna R.
  orcid: "https://orcid.org/0000-0003-4738-3451"
- family-names: Papudeshi
  given-names: Bhavya
  orcid: "https://orcid.org/0000-0001-5359-3100"
- family-names: Mallawaarachchi
  given-names: Vijini
  orcid: "https://orcid.org/0000-0002-2651-8719"
- family-names: Roach
  given-names: Michael J.
  orcid: "https://orcid.org/0000-0003-1488-5148"
doi: 10.5281/zenodo.10251242
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bouras
    given-names: George
    orcid: "https://orcid.org/0000-0002-5885-4186"
  - family-names: Grigson
    given-names: Susanna R.
    orcid: "https://orcid.org/0000-0003-4738-3451"
  - family-names: Papudeshi
    given-names: Bhavya
    orcid: "https://orcid.org/0000-0001-5359-3100"
  - family-names: Mallawaarachchi
    given-names: Vijini
    orcid: "https://orcid.org/0000-0002-2651-8719"
  - family-names: Roach
    given-names: Michael J.
    orcid: "https://orcid.org/0000-0003-1488-5148"
  date-published: 2024-01-11
  doi: 10.21105/joss.05968
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5968
  title: "Dnaapler: A tool to reorient circular microbial genomes"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05968"
  volume: 9
title: "Dnaapler: A tool to reorient circular microbial genomes"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05968 joss-papers#4897
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05968
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@gbouras13 congratulations on this JOSS publication!

Thanks for editing @fboehm, and a special thanks to the reviewers: @mkerin, @vinisalazar

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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