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[REVIEW]: FGTpartitioner: A rapid method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets #2030

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @tkchafin (Tyler Chafin) Repository: https://github.com/tkchafin/FGTpartitioner Version: v1.0.1 Editor: @lpantano Reviewer: @dangeles, @YichaoOU Archive: 10.5281/zenodo.3635843

Status

status

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HTML: <a href="https://joss.theoj.org/papers/ea336b5f861c87d5a0321bc85f000985"><img src="https://joss.theoj.org/papers/ea336b5f861c87d5a0321bc85f000985/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ea336b5f861c87d5a0321bc85f000985/status.svg)](https://joss.theoj.org/papers/ea336b5f861c87d5a0321bc85f000985)

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

@dangeles & @YichaoOU, 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 @lpantano know.

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

Review checklist for @dangeles

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @YichaoOU

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. @dangeles, @YichaoOU it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1534/genetics.109.103010 is OK
- 10.1038/s41559-018-0611-6 is OK
- 10.1186/1479-7364-7-1 is OK
- 10.1126/sciadv.1501714 is OK
- 10.1145/1854776.1854788 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.3390/genes9030123 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

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

YichaoOU commented 4 years ago

The documentation and manuscript are well written. Installation and test cases are easy to follow.

In my case, ./FGTpartitioner.py -h does not work, but python FGTpartitioner.py -h works.

The GitHub repo provides examples but the documentation didn't specifically provide test commands such as, python FGTpartitioner.py -v examples/example_1.vcf.gz

Minor comments:

  1. What is the time complexity for your algorithm? Remember in the Wang 2010 paper, they claimed to have O(mn) and O(nm^2) in their proposed DP algorithms. It is OK that you don't write a formal algorithmic complexity analysis, but I think it is better to show the complexity of your algorithm.

  2. Did you use any publicly available data to verify your method?

Thanks, Yichao

dangeles commented 4 years ago

This is a neat algorithm that addresses an important problem for non-canonical model organism genomics. The README and paper are well-written, and in general the code is well-documented and nicely written.

Doc-strings are missing from all defined function in FGTpartitioner.py. It would improve the code significantly to add short doc-strings explaining the input, output and purpose of each function.

Two example datasets are provided, but to the best of my ability, it appears they give identical results, and no guidance is given to the user as to why two examples are provided. The example_noHet is included without a .tbi file (probably a good teaching moment). On the other hand, additional files are provided within the examples folder that could probably be ignored or documented somewhere.

Best, David

lpantano commented 4 years ago

Hey @tkchafin, do you think you could address the few comments of the editors?

tkchafin commented 4 years ago

@lpantano

lpantano commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

lpantano commented 4 years ago

@whedon check references

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1534/genetics.109.103010 is OK
- 10.1038/s41559-018-0611-6 is OK
- 10.1186/1479-7364-7-1 is OK
- 10.1126/sciadv.1501714 is OK
- 10.1145/1854776.1854788 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.3390/genes9030123 is OK

MISSING DOIs

- None

INVALID DOIs

- None
lpantano commented 4 years ago

@tkchafin, thank you! Then, last two steps: 1) is the version still v1.0.0, 2) can you create a zenodo DOI link where the title and the author match exactly the paper information and give it to us? Thanks!

tkchafin commented 4 years ago

@lpantano

lpantano commented 4 years ago

@whedon set v1.0.1 as version

whedon commented 4 years ago

OK. v1.0.1 is the version.

lpantano commented 4 years ago

@whedon set 10.5281/zenodo.3635843 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3635843 is the archive.

lpantano commented 4 years ago

@openjournals/joss-eics, we are ready here

kthyng commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

PDF failed to compile for issue #2030 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2030 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:73:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1534/genetics.109.103010 is OK
- 10.1038/s41559-018-0611-6 is OK
- 10.1186/1479-7364-7-1 is OK
- 10.1126/sciadv.1501714 is OK
- 10.1145/1854776.1854788 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.3390/genes9030123 is OK

MISSING DOIs

- None

INVALID DOIs

- None
kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

kthyng commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

PDF failed to compile for issue #2030 with the following error:

sh: 0: getcwd() failed: No such file or directory sh: 0: getcwd() failed: No such file or directory pandoc: 10.21105.joss.02030.pdf: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1534/genetics.109.103010 is OK
- 10.1038/s41559-018-0611-6 is OK
- 10.1186/1479-7364-7-1 is OK
- 10.1126/sciadv.1501714 is OK
- 10.1145/1854776.1854788 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.3390/genes9030123 is OK

MISSING DOIs

- None

INVALID DOIs

- None
kthyng commented 4 years ago

@openjournals/dev I'm not able to figure out what is going wrong with the paper here. Could you help?

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

PDF failed to compile for issue #2030 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2030 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:73:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1534/genetics.109.103010 is OK
- 10.1038/s41559-018-0611-6 is OK
- 10.1186/1479-7364-7-1 is OK
- 10.1126/sciadv.1501714 is OK
- 10.1145/1854776.1854788 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.3390/genes9030123 is OK

MISSING DOIs

- None

INVALID DOIs

- None
arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1534/genetics.109.103010 is OK
- 10.1038/s41559-018-0611-6 is OK
- 10.1186/1479-7364-7-1 is OK
- 10.1126/sciadv.1501714 is OK
- 10.1145/1854776.1854788 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.3390/genes9030123 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1273

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1273, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
arfon commented 4 years ago

@openjournals/dev I'm not able to figure out what is going wrong with the paper here. Could you help?

Apologies, I accidentally introduced a regression last night. This should be fixed now.

kthyng commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1276
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02030
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

kthyng commented 4 years ago

Ok it looks like everything is in order!

Congratulations to @tkchafin on your new publication! Thanks very much for your time and expertise to editor @lpantano and reviewers @dangeles and @YichaoOU!

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02030/status.svg)](https://doi.org/10.21105/joss.02030)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02030">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02030/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02030/status.svg
   :target: https://doi.org/10.21105/joss.02030

This is how it will look in your documentation:

DOI

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