Closed gkanogiannis closed 1 year ago
Hi @gkanogiannis
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: metabinR
Type: Package
Title: Abundance and Compositional Based Binning of Metagenomes
Version: 0.99.0
biocViews: Classification, Clustering, Microbiome, Sequencing, Software
Authors@R:
c(person(given = "Anestis",
family = "Gkanogiannis",
role = c("aut", "cre"),
email = "anestis@gkanogiannis.com",
comment = c(ORCID = "0000-0002-6441-0688"))
)
Description: Provide functions for performing abundance and compositional based
binning on metagenomic samples, directly from FASTA or FASTQ files.
Functions are implemented in Java and called via rJava.
Parallel implementation that operates directly on input FASTA/FASTQ files
for fast execution.
License: GPL-3
Encoding: UTF-8
Language: en-US
LazyData: false
Depends:
R (>= 4.2)
Imports:
methods,
rJava,
utils
SystemRequirements: Java (>= 8)
RoxygenNote: 7.2.1
URL: https://github.com/gkanogiannis/metabinR
BugReports: https://github.com/gkanogiannis/metabinR/issues
Suggests:
BiocStyle,
cvms,
data.table,
ggplot2,
gridExtra,
knitr,
rmarkdown,
sabre,
spelling,
testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
reads.mapping <- fread(
system.file("extdata", "reads_mapping.tsv.gz",package = "metabinR")
)
reads.mapping$AB_id <- abundances$V3[
match(reads.mapping$genome_id,
abundances$V1)
]
reads.mapping <- reads.mapping[order(reads.mapping$anonymous_read_id),]
this is from vignette. Syntax and manipulations are complex. Can you define higher-level data structures and methods to make this easier for the user?
What if the abundances$V1 don't match any reads.mapping$genome_id ... ? Of course it works in your example but we want some defensive programming to help users deal with possible inconsistencies between independently managed resources. This is one of the motivations behind SummarizedExperiment, in which sample-level data and quantifications can have all kinds of identifiers, and we want to hand the user something that has some validity checking on construction.
is that really what we want in the vignette?
Why not just print the table?
Thanks for the submission, let us know your plans.
reads.mapping <- fread( system.file("extdata", "reads_mapping.tsv.gz",package = "metabinR") ) reads.mapping$AB_id <- abundances$V3[ match(reads.mapping$genome_id, abundances$V1) ] reads.mapping <- reads.mapping[order(reads.mapping$anonymous_read_id),]
this is from vignette. Syntax and manipulations are complex. Can you define higher-level data structures and methods to make this easier for the user?
I updated vignette to use dplyr-style operation for merging and ordering. I hope it looks better now.
What if the abundances$V1 don't match any reads.mapping$genome_id ... ? Of course it works in your example but we want some defensive programming to help users deal with possible inconsistencies between independently managed resources. This is one of the motivations behind SummarizedExperiment, in which sample-level data and quantifications can have all kinds of identifiers, and we want to hand the user something that has some validity checking on construction.
The purpose of metabinR
is to perform 3 types of binning (AB, CB and HC). It takes as input a set of fasta/fastq files and creates bins of reads.
The evaluation of the generated bins of reads is beyond the scope of this package and no mechanism or function is offered for this purpose.
For demonstration only, a simple way to perform evaluation of the bins is given in the vignette.
Example input fasta files are generated by reads simulator CAMISIM
and simple evaluation is done using the design files generated by it (for example the names of the fields of the produced distribution.txt and reads_mapping.tsv).
In the vignette example reads.mapping$genome_id always matches abundances$genome_id because it was fixed from the design.
Users of metabinR
are expected to use their own way of evaluation of the produced reads bins.
Why not just print the table?
Apologies for the ugliness. Changed it to plot it as table with knitr::kable
.
Dear @vjcitn , thank you for the pre-review comments. Please see my replies above. Pushed updated version 0.99.1 to github repo. Looking forward for the continuation of the review.
You've improved the aesthetics somewhat but I still think defensive programming and integrative datastructures like SummarizedExperiment or TreeSummarizedExperiment should be considered.
You've improved the aesthetics somewhat but I still think defensive programming and integrative datastructures like SummarizedExperiment or TreeSummarizedExperiment should be considered.
Dear @vjcitn it is something that I will for sure consider as improvement. Thank you.
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Dear @hpages salut. J'espere que tout va bien. I was wondering if we are on track here and if I am going to receive soon an initial review of metabinR
, in order to have some time until the deadline of 26 October for corrections and improvements based on your comments.
Looking forward to receiving your review, Anestis
Hi @gkanogiannis Tout va bien merci. Sorry for the slow response. I'm taking a look at metabinR and will come back with some feedback. Thanks for you patience.
Dear Hervé @hpages, thank you so much for your time and effort.
Dear @hpages, I was wondering if it will be possible to receive a review and feedback on this package. I am worried that it will not make it to the manifest of new release. Thank you again so much for tour efforts.
Thanks for your patience @gkanogiannis.
Package looks good. Only minor cosmetic issue is this:
> library(metabinR)
To cite metabinR in publications use:
A BibTeX entry for LaTeX users is
@Article{,
title = {A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes},
author = {Gkanogiannis Anestis and Thomas Bruls},
journal = {BMC Bioinformatics},
year = {2016},
volume = {Aug 19;17(1):311},
doi = {10.1186/s12859-016-1186-3},
url = {https://dx.doi.org/10.1186/s12859-016-1186-3},
}
This is not considered good practice. Please remove. Typical Bioconductor workflows will start by loading many packages, sometimes dozens or more. Bioconductor recommends packages to be as quiet as possible at load time.
Thanks
Received a valid push on git.bioconductor.org; starting a build for commit id: 6f76dd3e54be756409cc66839b4dc1807eb49461
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/metabinR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @hpages, citation message on package attach is removed and version bumped.
Thank you once again for your time and effort in reviewing metabinR
.
All looks good. Thanks!
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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Merci beaucoup, bonne soirée Hervé @hpages !
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