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[REVIEW]: CPgeneProfiler: A lightweight R package to profile the Carbapenamase genes from genome assemblies #2473

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: @ramadatta (Prakki Sai Rama Sridatta) Repository: https://github.com/ramadatta/CPgeneProfiler Version: v2.1.1 Editor: @will-rowe Reviewer: @fmaguire, @boasvdp Archive: 10.5281/zenodo.4076089

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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

@fmaguire & @boasvdp, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @fmaguire

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @boasvdp

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fmaguire, @boasvdp it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1093/bioinformatics/btx364 may be missing for title: UpSetR: an R package for the visualization of intersecting sets and their properties
- https://doi.org/10.1186/1471-2105-10-421 may be missing for title: BLAST+: architecture and applications
- https://doi.org/10.1186/s13073-014-0090-6 may be missing for title: SRST2: rapid genomic surveillance for public health and hospital microbiology labs
- https://doi.org/10.1093/jac/dks261 may be missing for title: Identification of acquired antimicrobial resistance genes
- https://doi.org/10.1093/nar/gkw1009 may be missing for title: MEGARes: an antimicrobial resistance database for high throughput sequencing
- https://doi.org/10.1093/nar/gkw1004 may be missing for title: CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
- https://doi.org/10.1128/aac.01310-13 may be missing for title: ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
- https://doi.org/10.1099/mgen.0.000131 may be missing for title: ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
- https://doi.org/10.3389/fpubh.2019.00242 may be missing for title: Using genomics to track global antimicrobial resistance
- https://doi.org/10.1093/ofid/ofx176 may be missing for title: Prevalence of carbapenem-resistant Gram-negative infections in the United States predominated by Acinetobacter baumannii and Pseudomonas aeruginosa
- https://doi.org/10.1016/j.jinf.2018.11.003 may be missing for title: Whole genome sequencing detects inter-facility transmission of carbapenem-resistant Klebsiella pneumoniae
- https://doi.org/10.1128/aac.02282-18 may be missing for title: Cocarriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single sequence type 11 carbapenem-resistant Klebsiella pneumoniae isolate
- https://doi.org/10.1093/cid/ciz824 may be missing for title: Epidemiology and diagnostics of carbapenem resistance in gram-negative bacteria

INVALID DOIs

- None
will-rowe commented 4 years ago

@ramadatta - please can you add the flagged DOIs to your paper references

ramadatta commented 4 years ago

@ramadatta - please can you add the flagged DOIs to your paper references

@will-rowe, @boasvdp, @fmaguire Thank you so much for kindly agreeing to review the submission!

@will-rowe - I have added the missing DOIs in the paper now and tested the build.

fmaguire commented 4 years ago

@whedon commands

whedon commented 4 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository
fmaguire commented 4 years ago

Overview

In this tool the author's provide an R package that generates some potentially useful diagnostic plots for AMR researchers with limited data analysis/visualisation experience and an interest in carbapenemase genes. Unfortunately, the utility of this tool is currently hampered by its lack of modularity, choice of AMR database, and limited ease of installation/dependency management. While there are no existing AMR detection tools that do exactly the same summary/analysis that this package provides, there are several that provide more comprehensive AMR profiling (more than just carbapenemases), some visualisation, and generation of outputs that can be visualised as the analyst sees fit with relatively little work.

With improved documentation, a fairly major overhaul to improve modularity and packaging (listed below) CPgeneProfiler could represent a handy set of visualisation utilities for this targeted research/public health group. However, as it currently stands CPgeneProfiler isn't widely applicable outside the specific internal analytical use-case for which it was developed.

Installation

Functionality

Documentation

Software Paper

ramadatta commented 4 years ago

@fmaguire We sincerely appreciate your comprehensive review. We will go through each of them and come back at the earliest. Thank you!

will-rowe commented 4 years ago

Thanks @fmaguire - that's an excellent review.

@ramadatta - feel free to begin working on these points now. @boasvdp will also be providing feedback so please keep an eye out for that too.

I'm due to go on annual leave for a week next week. I'll check back in here when I'm back but please ping another editor if you need assistance next week.

ramadatta commented 4 years ago

@will-rowe Sure. Thank you very much!

boasvdp commented 4 years ago

Hi all,

I'm on annual leave at this moment, but will be back in a week. I'll do the review before the end of next week (July 24).

@ramadatta Are there any specific things you'd like extra feedback/attention on?

ramadatta commented 4 years ago

@boasvdp Thank you very much! Nothing specific for me at the moment. Will begin working on with @fmaguire points.

boasvdp commented 4 years ago

General

The described tool identifies carbapenemase genes from assembled bacterial genomes and produces additional plots, especially aimed at co-carriage. The identification of carbapenemase genes is possible through other tools, but I am unaware of any tools which produce the additional plots that are included in the CPgeneProfiler output. The tool is installable (although this could be improved) and does what it promises. However, improvements are possible and in some cases necessary.

One major outstanding question for me is the 'audience' for this software. What level of bioinformatics expertise would you expect for people using your tool? Is this a tool for bioinformaticians, or is this intended for molecular biologists with some R experience? This influences some of the suggestions I have made below, as some will apply more or less depending on the bioinformatics expertise of the audience you're aiming for.

I support all notions made by @fmaguire above, and will try to provide additional feedback where needed.

Installation

Functionality

Documentation

Software paper

ramadatta commented 4 years ago

@boasvdp - Thank you so much for the comments!

I actually intended to make this package helpful to biologists who have only little experience in R. I am working on the package currently and trying to make it modular. I also appreciate both of your suggestions on changing the database and working on this. I am making an effort to make the functionality more flexible. Thanks again!

will-rowe commented 4 years ago

Thank you very much for your review @boasvdp.

@ramadatta - please let us know when you have had chance to respond to these comments and are ready for us to take another look over your submission.

will-rowe commented 4 years ago

Hey @ramadatta - can you let me know how you are getting on please? No pressure, just chasing up!

ramadatta commented 4 years ago

Thanks @will-rowe - I am almost done with the comments on functionality from both the authors. I am working on installation portion.

will-rowe commented 4 years ago

Hi @ramadatta - just another ping to see how you are getting on?

ramadatta commented 4 years ago

Hi @will-rowe - thank you. I am in the process of documenting the package. Once I am done with this, I will start editing the final paper possibly this weekend and aim to submit soon.

ramadatta commented 4 years ago

Hi @will-rowe - just an update on manuscript. I am almost done with manuscript and awaiting my collaborator's go-ahead to submit. Thank you.

will-rowe commented 4 years ago

Hi @ramadatta - just checking in again to see how you are progressing? Thanks!

ramadatta commented 4 years ago

Dear @will-rowe - Due to some unforeseen circumstances, I am not able to submit the manuscript within the timeframe expected before. I sincerely apologize for this delay. If it is possible, could I kindly request an extension for a week or two? Thank you very much for your consideration.

will-rowe commented 4 years ago

That's fine from my point of view. I'll check back in a couple of weeks unless I hear from you sooner

ramadatta commented 3 years ago

Thanks so much @will-rowe for understanding.

ramadatta commented 3 years ago

Dear @will-rowe @fmaguire @boasvdp - Thank you so much for giving us time to work through the comments and submit the manuscript. We have tried our best to resolve the issues raised by both of the reviewers and re-submitted the updated manuscript. In regards to this, we kindly request the reviewers to review our updated comments.

will-rowe commented 3 years ago

@whedon generate pdf

will-rowe commented 3 years ago

@whedon check references

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fmicb.2020.00052 is OK
- 10.1093/nar/gkz935 is OK
- 10.1093/jac/dkx217 is OK
- 10.1093/jac/dkaa345 is OK
- 10.1093/jac/dkw184 is OK
- 10.1186/s12859-018-2336-6 is OK
- 10.1093/bioinformatics/btx364 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1186/s13073-014-0090-6 is OK
- 10.1093/jac/dks261 is OK
- 10.1093/nar/gkw1009 is OK
- 10.1093/nar/gkz1010 is OK
- 10.1093/nar/gkw1004 is OK
- 10.1128/aac.01310-13 is OK
- 10.1099/mgen.0.000131 is OK
- 10.3389/fpubh.2019.00242 is OK
- 10.1093/ofid/ofx176 is OK
- 10.1016/j.diagmicrobio.2012.11.009 is OK
- 10.1128/AAC.00296-11 is OK
- 10.1016/j.jinf.2018.11.003 is OK
- 10.1128/genomeA.00199-18 is OK
- 10.1128/aac.02282-18 is OK
- 10.1093/cid/ciz824 is OK
- 10.1128/JCM.02086-16 is OK

MISSING DOIs

- None

INVALID DOIs

- None
will-rowe commented 3 years ago

Hi @ramadatta. Many thanks for your thorough responses to the comments. In my opinion you have satisfied the reviewer comments. That being said, if @fmaguire or @boasvdp would like to give their thoughts on your responses, that would be most welcome.

I have a request and a question:

fmaguire commented 3 years ago

I've updated the checklist in light of the changes. Only minor issue is that when @ramadatta makes the explicit "statement of need" section in the paper it could do with being added to the README as well.

Apart from that, all good from my end, @ramadatta did a great job thoroughly addressing the comments. The tool and its documentation is much improved from their work.

ramadatta commented 3 years ago

Dear @will-rowe - thank you very much for your comment.

Thanks for providing the example paper for adding statement of need section in paper. We will edit our manuscript accordingly.

We do agree, it is very helpful for users to install of package through conda. In regards to this, we did try to package the recipe. But for some reason, I had trouble getting this in Bioconda.

We sincerely appreciate and are thankful to you for offering help to get it packaged. At the moment, I have meta.yaml file and if possible could I kindly request to get pointers from you to work on packaging this. Thank you very much!

fmaguire commented 3 years ago

From the bioconda linter (https://app.circleci.com/pipelines/github/bioconda/bioconda-recipes/31534/workflows/2aeaba6e-e261-4314-b570-17b5cb046873/jobs/120863), the following seem to be the issues:


should_be_noarch_generic: The recipe should be build as `noarch`
ERROR: recipes/cpgeneprofiler/meta.yaml:2:
folder_and_package_name_must_match: The recipe folder and package name
do not match.
WARNING: recipes/cpgeneprofiler/meta.yaml:28:
gpl_requires_license_distributed: The recipe packages GPL software but
is missing copy of license.
ERROR: recipes/cpgeneprofiler/meta.yaml:9: build_number_needs_reset:
The recipe build number should be reset to 0```

On Fri, 9 Oct 2020 at 00:28, Prakki Rama <notifications@github.com> wrote:

> Dear @will-rowe <https://github.com/will-rowe> - thank you very much for
> your comment.
>
> Thanks for providing the example paper for adding statement of need
> section in paper. We will edit our manuscript accordingly.
>
> We do agree, it is very helpful for users to install of package through
> conda. In regards to this, we did try to package the recipe
> <https://github.com/openjournals/joss-reviews/files/5352239/meta_yaml.txt>.
> But for some reason, I had trouble getting this in Bioconda
> <https://github.com/bioconda/bioconda-recipes/pull/24047>.
>
> We sincerely appreciate and are thankful to you for offering help to get
> it packaged. At the moment, I have meta.yaml
> <https://github.com/openjournals/joss-reviews/files/5352239/meta_yaml.txt>
> file and if possible could I kindly request to get pointers from you to
> work on packaging this.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/openjournals/joss-reviews/issues/2473#issuecomment-705946398>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAM6WROL6XWKRZOSBCFEANDSJZ7N7ANCNFSM4OXGMBOQ>
> .
>

-- 
Dr. Finlay Maguire
Donald Hill Fellow in Computer Science
Dalhousie University
-----------------------------------------
Website: finlaymagui.re
ramadatta commented 3 years ago

Dear @fmaguire - Thanks! Will look into this.

boasvdp commented 3 years ago

Hi @ramadatta, all issues have been addressed appropriately in my opinion. I have updated my checklist.

I agree adding this to bioconda would be great!

ramadatta commented 3 years ago

Dear @will-rowe @fmaguire - Thank you. We have now made the statement of purpose more explicit in the paper and documentation. Please kindly review our updated manuscript and synopsis section in documentation.

@fmaguire @boasvdp - I will restart working on conda packaging. Thank you for the advice.

will-rowe commented 3 years ago

@whedon generate pdf

will-rowe commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fmicb.2020.00052 is OK
- 10.1093/nar/gkz935 is OK
- 10.1093/jac/dkx217 is OK
- 10.1093/jac/dkaa345 is OK
- 10.1093/jac/dkw184 is OK
- 10.1186/s12859-018-2336-6 is OK
- 10.1093/bioinformatics/btx364 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1186/s13073-014-0090-6 is OK
- 10.1093/jac/dks261 is OK
- 10.1093/nar/gkw1009 is OK
- 10.1093/nar/gkz1010 is OK
- 10.1093/nar/gkw1004 is OK
- 10.1128/aac.01310-13 is OK
- 10.1099/mgen.0.000131 is OK
- 10.3389/fpubh.2019.00242 is OK
- 10.1093/ofid/ofx176 is OK
- 10.1016/j.diagmicrobio.2012.11.009 is OK
- 10.1128/AAC.00296-11 is OK
- 10.1016/j.jinf.2018.11.003 is OK
- 10.1128/genomeA.00199-18 is OK
- 10.1128/aac.02282-18 is OK
- 10.1093/cid/ciz824 is OK
- 10.1128/JCM.02086-16 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

will-rowe commented 3 years ago

Thanks @ramadatta - this looks good. I think we can move toward acceptance!

If you can now tag a new release, archive it (zenodo) and then report back here with the version and DOI.

I've got the recipe building (thanks @fmaguire for the linting report). I will wait for your new release before we make the bioconda PR

ramadatta commented 3 years ago

Thank you so much @will-rowe. Will start working on the new release and the archive.

I sincerely thank @fmaguire @boasvdp for their comprehensive reviews by which I had a wonderful opportunity to learn several new things.

ramadatta commented 3 years ago

Dear @will-rowe - I have a tag now for the CPgeneProfiler v2.1.1 and the DOI is: 10.5281/zenodo.4076089

Could I kindly know, if I can recheck and do a minor editing in the manuscript for one last time before being published? Many thanks.

will-rowe commented 3 years ago

Thanks @ramadatta. Please can you update the Zenodo repo author list to match the author list of your paper

will-rowe commented 3 years ago

@whedon set v2.1.1 as version

whedon commented 3 years ago

OK. v2.1.1 is the version.

will-rowe commented 3 years ago

Sorry - missed the question re. editing. Sure you can - I will wait before flagging this paper to the editor in chief. Let me know when you are ready for the paper to be accepted. You will need another release/DOI if you make edits, so let me know what they are.

will-rowe commented 3 years ago

Bioconda recipe is ready to be reviewed and merged (see here). I had to add the dependencies to the meta.yaml, add the license and sort a name conflict. I also set the recipe to build from your releases, rather than the master branch, which I think is preferred by Bioconda.

ramadatta commented 3 years ago

Sorry - missed the question re. editing. Sure you can - I will wait before flagging this paper to the editor in chief. Let me know when you are ready for the paper to be accepted. You will need another release/DOI if you make edits, so let me know what they are.

Thank you very much @will-rowe - I just made a minor edit at visualize the set intersections of cocarriage of CP genes in the manuscript.

Also, as you suggested, I have updated the CPgeneProfiler v2.1.1 release and updated the Zenodo repo author list. Thank you so much for the Bioconda request.

Please let me know if I missed anything else from my side. Else, I kindly request the editor for the manuscript to accepted.