[PRE REVIEW]: Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases

[editorialbot]

Submitting author: @Robaina (Dr. Semidán Robaina Estévez)
Repository: https://github.com/Robaina/Pynteny
Branch with paper.md (empty if default branch):
Version: v0.0.4
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6cccd58a757359187fdc4981bed38b75"><img src="https://joss.theoj.org/papers/6cccd58a757359187fdc4981bed38b75/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6cccd58a757359187fdc4981bed38b75/status.svg)](https://joss.theoj.org/papers/6cccd58a757359187fdc4981bed38b75)

Author instructions

Thanks for submitting your paper to JOSS @Robaina. Currently, there isn't a JOSS editor assigned to your paper.

@Robaina if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (504.6 files/s, 80379.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            355            492           2296
Markdown                         6            104              0            241
TeX                              1             12              0            182
Jupyter Notebook                 3              0           1135            117
CSS                              1             17              7             56
YAML                             2              1              4             37
JavaScript                       1              5              8             28
-------------------------------------------------------------------------------
SUM:                            32            494           1646           2957
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 759

[editorialbot]

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

OK DOIs

- 10.1093/nar/gkt263 is OK
- 10.1186/s12859-019-2996-x is OK
- 10.1186/1471-2105-11-431 is OK
- 10.1038/nbt1004-1315 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1093/nar/gkr1293 is OK
- 10.1101/2021.06.03.446950 is OK
- 10.1093/bioinformatics/btab007 is OK
- 10.1126/science.1153917 is OK
- 10.1093/bioinformatics/btq413 is OK
- 10.7554/eLife.78526 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[Robaina]

Based on the provided list of reviewers, vinisalazar and urmi-21 could fit well as reviewers, mouneem could also be a good fit.

[Kevin-Mattheus-Moerman]

@Robaina thanks for this submission. I am the AEiC on this track and will check this work for scope, with the help of the rest of the board if needed, and will do some initial checks before we proceed.

• JOSS requires an OSI approved open source licenses. You currently use the CC-BY-4.0 license license. I would personally regard the creative commons licenses most suitable for "content" such as text, images and related artistic/scholarly works, rather than software. In fact the Creative Commons organisation also recommends people not to use their licenses for software. So, to be considered for JOSS, please adopt an OSI approved open source software license.

[Kevin-Mattheus-Moerman]

@openjournals/dev ☝️ it looks like the editorial bot did not detect that an OSI license was not used. Is it currently only checking for a license in general or is it checking the license against the OSI list?

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@Robaina I have just assigned the quey-scope label for this submission. This means I am asking the editorial board to help decide if this work is in scope for JOSS or not. In particular, at first sight, the functionality contained in this submission seems to be somewhat limited, correct me if I am wrong but it seems to mostly facilitate a particular type of database search. So-called "single-function packages" are not in scope for JOSS. (see also: https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort), so we will now spend some time reviewing this work in terms of functionality to see if it in scope. The scope review should be concluded within about 2 weeks. If, beyond your README and the paper, you want to add any comments here, to further elaborate on functionality, feel free to do so.

[Robaina]

@Kevin-Mattheus-Moerman Thanks for managing our submission. I don't fully understand your comment. Do you mean that Pynteny would not qualify for consideration at JOSS because it is intended to search only prokaryotic sequence databases? This is, indeed, a particular type of database. However, it is not uncommon to focus only on prokaryotic or eukaryotic sequence data within bioinformatics due to the genome and gene organization differences between these two groups.

On the other hand, Pynteny provides, in my view, more than a single functionality. In summary:

1. Facilitates the construction of a sequence database labeled by gene position within the genome departing from 1.1) DNA assembly data or 1.2) GenBank files. This functionality is provided by Pynteny build subcommand

2. Allows searching predefined syntenic blocks of genes within unannotated protein or DNA sequence data through HMMs. To our knowledge, no other published tool provides this functionality. In addition, Pynteny allows syntenic blocks to be defined in a flexible (partial) way, to accommodate natural variability in syntenic structures among different taxa. This functionality is provided by Pynteny search subcommand.

3. Facilitates downloading and preprocessing of the largest profile HMM database (PGAP database), this functionality is optional and provided by Pynteny download subcommand

4. Provides a web graphical interface, which facilitates the use of this tool for education purposes. This functionality is provided by Pynteny app subcommand.

The repo contains more information in the wiki pages. There are also several Jupyter Notebooks which provide examples of Pyntenys functionality.

Should you have any questions regarding Pynteny's functionality that would help decide whether this tool is within JOSS scope, please do not hesitate to ask me.

[Robaina]

@Robaina thanks for this submission. I am the AEiC on this track and will check this work for scope, with the help of the rest of the boards if needed, and will do some initial checks before we proceed.

• JOSS requires an OSI approved open source licenses. You currently use the CC-BY-4.0 license license. I would personally regard the creative commons licenses most suitable for "content" such as text, images and related artistic/scholarly works, rather than software. In fact the Creative Commons organisation also recommends people not to use their licenses for software. So, to be considered for JOSS, please adopt an OSI approved open source software license.

Thank you for noticing. The license has been changed to an OSI-approved one.

[Robaina]

Hi @Kevin-Mattheus-Moerman ,

I recently submitted this package to pyOpenSci as well. Here is the open issue of the submission.

Thank you!

[NickleDave]

Thank you @Robaina for linking.

@Kevin-Mattheus-Moerman this does look in scope for us at pyOpenSci, although I need to do more detailed editorial checks later today.

If so, we would expect to follow the process we have with JOSS in the past, where we review first than pass on to you all. For example see pyOpenSci/software-submission#31 which corresponds to review #3248 at JOSS (fast-tracked after our review: #3248 (comment))

Just commenting here to avoid any confusion, @lwasser wanted to make sure everyone was in the loop.

[arfon]

@Kevin-Mattheus-Moerman – given this has been submitted to PyOpenSci, I think we should probably close this issue and pick up the (JOSS) scope query again once the package has been through the PyOpenSci review. What do you think?

[Kevin-Mattheus-Moerman]

@arfon sure. What method of closing do we use? E.g. @editorialbot withdraw? Feel free to process it too if you like.

[arfon]

@editorialbot withdraw

[editorialbot]

Paper withdrawn.

[arfon]

@arfon sure. What method of closing do we use? E.g. @editorialbot withdraw? Feel free to process it too if you like.

Yep, that's it!