-
-
Notifications
You must be signed in to change notification settings - Fork 36
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[REVIEW]: Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. #4296
Comments
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
|
|
Wordcount for |
|
@Gab0, @standage: Thanks for agreeing to review. Please carry out your review in this issue by first creating a checklist ( If you have any questions or concerns please let me know. |
Review checklist for @standageConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
|
Review checklist for @Gab0Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
|
The author describes Pyrodigal, a software package implementing a Python interface to the widely-adopted gene prediction program Prodigal. The Prodigal source code is bundled with Pyrodigal and compiled as a Python extension, which Pyrodigal accesses directly via a Python interface rather than indirect system calls to a separate executable. In addition to Python bindings, the author describes performance optimizations made to Prodigal’s core scoring procedure. Prodigal is the de facto standard for prokaryotic gene prediction in the genome informatics community, and Python is the community’s de facto general-purpose scripting language. Exposing Prodigal’s internals comprehensively and efficiently to Python programs is a valuable contribution, as underscored by Pyrodigal's usage statistics and its integration into various published workflows. I am happy to endorse this submission for publication at JOSS.
|
Hi @mikldk, no concerns from me on this submission so I think this concludes my review! |
OverviewThis project consists of Cython bindings to the widely used prokaryotic ORF finder software The premise is interesting, allowing The performance claims over CPU time, RAM use and storage use can be useful when analyzing large sets of genomes, a scenario that has become increasingly common over the last years. The paper includes all the required information. It also includes interesting details about performance optimizations done on top of the SetupThe
From these I tested the There seems to be two undocumented installation methods:
Both methods works nicely. The local build works after pulling all the submodules to the local repository. TestsI wrote a quick comparison test for [ ] However, in this run, calling I would like to ask the author a few questions about these benchmark results:
a) b)
Suggestions
Summary
The project is solid overall. My review status is |
Hi @Gab0 , thanks for the review! A few answers / updates:
I added the AUR installation method recently, that's why it's not documented, but after your review updated the documentation to mention it, so it will be rendered on the website with the next release. Installing from source is not covered in the
No, the two snippets are not equivalent, because in the command line invocation you called Pyrodigal/Prodigal in single mode (which trains and predicts on the same sequence) but in the script you used the meta mode (as shown by the first line,
Pyrodigal is not thought to perform I/O, which is why I included examples with Biopython and Scikit-Bio, which are two general purpose libraries for bioinformatics, and can be used to load data from FASTA or GenBank files.
I have linted the Python sources with |
@althonos Cool, I'll address each remaining topic:
Ok, so all my concerns have been addressed. My suggestions about working examples and documentation updates can be implemented in future releases if the author feels they will improve the package. My review is completed, and I endorse this submission for publication at JOSS. (@mikldk) |
@Gab0, @standage: Thank you very much for your effort with the very constructive reviews.
|
@editorialbot generate pdf |
Hi @mikldk , I have now made a new stable release ( |
EDIT: Guess I do need to, updated the Zenodo record. |
@editorialbot set 10.5281/zenodo.6472583 as archive |
Done! Archive is now 10.5281/zenodo.6472583 |
@editorialbot set v1.0.0 as version |
Done! version is now v1.0.0 |
@editorialbot check references |
|
@editorialbot generate pdf |
@althonos Thanks. A few comments:
Please change and recompile (no need to make a new release, just update Zenodo meta data and the paper). |
Thanks, done. |
@editorialbot generate pdf |
@editorialbot recommend-accept |
|
👋 @openjournals/joss-eics, this paper is ready to be accepted and published. Check final proof 👉 openjournals/joss-papers#3171 If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3171, then you can now move forward with accepting the submission by compiling again with the command |
@editorialbot accept looks good! |
|
🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦 |
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨 Here's what you must now do:
Any issues? Notify your editorial technical team... |
Thank you all! This was really a pleasant process and I'll definitely consider JOSS again when I have something else suitable for publication. |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
This is how it will look in your documentation: We need your help! The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
|
Submitting author: @althonos (Martin Larralde)
Repository: https://github.com/althonos/pyrodigal/
Branch with paper.md (empty if default branch): paper
Version: v1.0.0
Editor: @mikldk
Reviewers: @Gab0, @standage
Archive: 10.5281/zenodo.6472583
Status
Status badge code:
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
@Gab0 & @standage, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mikldk 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 @standage
📝 Checklist for @Gab0
The text was updated successfully, but these errors were encountered: