Physcraper: Automated phylogenetic updating

[snacktavish]

Submitting Author: Emily Jane McTavish (@snacktavish)
All current maintainers: Emily Jane McTavish (@snacktavish), Luna L. Sanchez Reyes (@LunaSare)
Package Name: Physcraper
One-Line Description of Package: Automated phylogenetic updating
Repository Link: https://github.com/McTavishLab/physcraper
Version submitted: 0.55
Editor: @NickleDave
Reviewer 1: @bpucker
Reviewer 2: @leomrtns
Archive:
JOSS DOI: N/A
Version accepted: v 1.0
Date accepted (month/day/year): 09/14/2021

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Description

• Include a brief paragraph describing what your package does:

Physcraper is an open‐source, command-line Python program that automatizes the update of published
phylogenies by enriching underlying gene alignments with public DNA sequence data, and linking taxonomic information across databases.

Scope

• Please indicate which category or categories this package falls under:
  • Data retrieval
  • Data extraction
  • Data munging
  • Data deposition
  • Reproducibility
  • Geospatial
  • Education
  • Data visualization*

* Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see this section of our guidebook.

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences):

This package retrieves data from GenBank (https://www.ncbi.nlm.nih.gov/genbank/), the OpenTreeofLife (www.opentreeoflife.org), and TreeBase (www.treebase.org/), and links these datasets together to incorporate new sequence data into evolutionary estimates. Physcraper also provides a framework for comparison of published phylogenies with their updated versions, by using the conflict API of the Open Tree of Life project.

• Who is the target audience and what are scientific applications of this package?

Physcraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on already available expert phylogenetic knowledge.
Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?

The closest analogue in python is PyPhlawd https://fephyfofum.github.io/PyPHLAWD/.
This approach differs from other tools (PyPhlawd, Supersmart) automatize the assembly of DNA alignments from the GenBank database for phylogenetic reconstruction, in that Physcraper leverages existing homology statements in the form of alignments and existing phylogenetic trees to select appropriate loci and improve inference.
Another key feature of Physcraper is linking of taxonomic identifiers across databases including NCBI, GBIF and OpenTree of Life which provides easy interoperability with those resources, and the ability to easily compare relationships between new inferences and existing taxonomy and previously published studies.

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[snacktavish]

Edited to new release (0.55), with some minor updates.

[snacktavish]

Preprint posted at: https://www.biorxiv.org/content/10.1101/2020.09.15.299156v1

[lwasser]

hi there @snacktavish i'm so sorry we have been out of communication here. are you still interested in a review by pyopensci? i've been a bit overwhelemed by current events which has been a hit at work in productivity. We may have an editor for this however if you are still interested in a review.

[snacktavish]

Yes! We are still interested in a review by pyopensci, but we also understand if that isn't possible given the current situation. Thanks!

[NickleDave]

Hi @snacktavish !
I volunteered myself to be editor.

Currently I work in AI / neuro but my background is bio ... and one of the main reasons I made it into science is a really good prof who taught the first non-boring class I took, on bioinformatics where we worked on genome assembly, phylogenetics, and related things.

So I think I get at a high level what physcraper does and it definitely looks like a good fit for PyOpenSci.

One thing: since we are still relatively new, we don't have a huge pool of reviewers to draw from right now. I can think of some places to start asking, but do you by any chance have two people you could recommend as reviewers?

[lwasser]

thank you @NickleDave i'll list you as an editor here at the top!! and @snacktavish THANK YOU for your patience with us. Also you have the best GH handle ever :)

[NickleDave]

Hey @snacktavish just want to check back -- please let me know if you need me to start looking for reviewers

One thing: since we are still relatively new, we don't have a huge pool of reviewers to draw from right now. I can think of some places to start asking, but do you by any chance have two people you could recommend as reviewers?

and I agree with Leah that you have the best GitHub handle ever

[snacktavish]

Sorry for the delay! I started thinking about it, and then forgot to respond. Folks that I think would be good reviewers, or could potentially suggest others who would be include @blackrim @josephwb @jfwalker (Contributors to https://github.com/FePhyFoFum/PyPHLAWD) @rvosa @DomBennett (Contibutors to SuperSmart https://academic.oup.com/sysbio/article/66/2/152/2418028).

@LunaSare - any other suggestions?

Thanks for the username love! When I first joined GitHub I didn't fully realize how much it would be part of my professional identity and was just like, hey, I like snacks! And now 10ish years later, lots of folks call me @snacktavish and I love it. 🍜 🍕 🍟

[NickleDave]

Thank you @snacktavish that likes snacks!

The folks you tagged all sound like perfect reviewers.
I will give them a couple days to respond.
If we don't hear back and it's okay with you I will try reaching out to them by email. Please let me know if that's not ok.

I think I would also like to try and find a third reviewer from outside those you (very helpfully) suggested as @lwasser has asked me to do on other reviews.

[lwasser]

HI there all!! i think IF you can have one that @snacktavish suggests and one outside reviewer (for a total of 2 reviewers) that would be perfect :) thank you so much Dave !!!

[NickleDave]

Understood, thank you @lwasser

[NickleDave]

@snacktavish @lwasser adding initial editor checks.
Very swamped at work right now but I will reach out to reviewers by Thursday at the latest

Editor checks:

• Fit: The package meets criteria for fit and overlap.
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has an OSI accepted license
• Repository: The repository link resolves correctly

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Editor comments

• Looks like a perfect fit for pyOpenSci, within scope under categories of data retrieval and munging as maintainer has indicated.
• Package appears well-developed and maintained to me. I see no obvious issues at this time.
• Manuscript on biorxiv
• My impression is review would best address how the package meets its goal of usability by a non-specialist. Input from users and developers that have experience with related tools would be most helpful

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Reviewers: @bpucker @leomrtns
Due date: March 1, 2021