rSWeeP: Representations large biological sequences datasets in compact vectors on an R platform.

[DanrleyRF]

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• Repository: https://github.com/DanrleyRF/rSWeeP

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[bioc-issue-bot]

Hi @DanrleyRF

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: rSWeeP
Title: Functions to Make Vectorial Comparations on Amino Acid Sequence
Version: 0.99.0
Authors@R: 
    person(given = "Roberto",
 family = "Raittz",
 role = "aut",
 email = "raittz@ufpr.br")
    person(given = "Mariane",
 family = "G. Kulik",
 role = "aut")
    person(given = "Danrley R. Fernandes",
 role = c("com", "cre","aut"),
 email = "DanrleyRF@gmail.com")
Description: The SVect method was developed to favor the comparison between complete genomic sequences and to assist in phylogenetic analyzes. This method is based on the concept of sparse words, which are used to scan biological sequences and turn them into vectors, favoring the manipulation of the data.
biocViews: Software,StatisticalMethod,SupportVectorMachine,Technology,Sequencing,Genetics 
Depends: R (>= 3.6)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: 
    pracma,
    stats,
    ape,
    seqinr
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle
VignetteBuilder: knitr

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[mtmorgan]

please make sure that your package interoperates with standard Bioconductor data representations, especially DNAStringSet from the Biostrings package.

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[DanrleyRF]

@mtmorgan thank you for the attention. I believe that the package is package interoperational with standard Bioconductor data representations, as suggested

[mtmorgan]

15 January, 2020

Sorry for my delay. I don't see any interoperability with standard Bioconductor data structures. Please update, including in response to the following comments. When you've completed the updates please post a short comment summarizing your changes.

DESCRIPTION

• If the package primarily relies on seqinr, rather than Biostrings (e.g., the package imports seqinr, but does not depend, import, or suggest Biostrings, then really it belongs on CRAN; Biostrings is the standard pacakges for representing sequence data in Bioconductor, providing Bioconductor users with robust and interoperable concepts.

• can you provide a more descriptive Title: and more extensive Description: so that someone encountering these can tell precisely what functionality the package provides.

R

• The following specific comments should be applied to all code.

• Make sure the exposed functions of your package interoperate with standard Bioconductor objects. For instance SWeeP is written to accept a file name but should also accept a DNAString and / or DNAStringSet (maybe your method is really working on amino acid sequences? this needs to be clarified; the Biostrings representations are AAString / AAStringSet and readAAStringSet()). The natural way to do this is to use an S4 Generic and S4 methods, with the methods implementing a 'facade' pattern that do a little work and pass a consistent argument to a helper function that does the real lifting, along the lines of

  setGeneric(
      "SWeeP", 
      function(file, orthoBase) standardGeneric("SWeeP"),
      signature = "file"
  )
  
  setMethod("SWeeP", "character", function(file, orthoBase) {
      dna = readDNAStringSet(file)
      SWeeP(dna, orthoBase)
  })
  
  setMethod("SWeeP", "DNAStringSet", function(file, orthoBase) {
      ...
  })

• For robust code, start each user-facing function by validating user input. Thus check that orthoBase is a matrix (or can be coerced to a matrix, if that is appropriate) with, e.g.,

  stopifnot(is(orthoBase, "matrix"))

  Doing this at the start of the function so that the user finds out quickly and informatiely that they have used the wrong arugment; this also simplifies code further down, for instance there are three occurrence of as.matrix(orthoBase) in SWeeP(), but this operation only needs to be performed once.

• Carefuly consider the selection of package dependencies to re-use standard Bioconductor functionality. For isntance use Biostrings::readDNAStringSet for fasta input.

• use message(...) rather than print(paste(...)) to communciate with users. If there is an error (e.g. print("The amino acid sequences are too short ") use stop() making sure that the error tells the user what you have been checking, e.g., stop("'file' should reprsent a DNA sequence of more than 2001 nucleotides"). Actually, the message is printed when is.list(xfas) fails, and it is not clear why that condition would corresond to an amino acid sequence that is too short.

• SWeeP.R:42 revise

  for (i in c(1:(round(length(xfas)/block)))){

  to

  for (i in seq_len(length(xfas) / block))

  Note that the use of seq_len() avoids the use of 1:n, which is problematic when n == 0. Please also note that there is no need for c(), and that using additional spacing around operators such as / increases readability. Please review and revise all of your code for these types of issuse

• Please review the coding style guidelines (https://bioconductor.org/developers/how-to/coding-style/) and in particular consider using formatR or similar package for standardizing your code formating. Standard formatting makes it easier for others to read your code and hence contribute to your software.

• Please carefully review your code to remove operations taht have no effect. For example the use of c() above, the first line of

  projected <- list();
  projected <- (matrizid%*%as.matrix(orthBase))

  is

  projected <- matrizid %*% orthBase

  The call to Sys.time() in the next line is also redundant.

• consider adopting consistent, rather than 'cute', function and variable naming conventions, usually following a lowerCamelCase convention, e.g., sweep(), orthobase().

• aa2int() this code can be easily 'vectorized' (one R function call, rather than length(xfas) calls) with something like

  map <- c(A = 1L, a = 1L, R = 2L, r =2L, ...)
  xfas <- unnamed(map[xfas])

• consider adopting a more informative name for the data set datastring. Use standard R terminology to describe the object, e.g. 'A string vector with six strings' might be 'A character() vector of length 6.'

• fas2mat: use Biostrings functionality

vignette

• Instead of reading the R object datastring and writing it as a fasta file, include the fasta file directly in inst/extdata/exdna.fas and reference it in the ignette as

  path <- system.file(package = "rSWeeP", "extdata", "exdna.fas")

• please clarify the scale of the problem you are tackling. What size and number of sequences are you expecting your algorithm to work on? Can you generate a 'large' example that shows that it works at the scale you anticipate?

misc

• please remove non-R package source files from your git repository, e.g., the doc/ and Meta/ directories.

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Received a valid push; starting a build. Commits are:

5b877bc 99.4

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Your package has been built on Linux, Mac, and Windows.

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Received a valid push; starting a build. Commits are:

db40e70 99.6

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Your package has been built on Linux, Mac, and Windows.

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Received a valid push; starting a build. Commits are:

53d7c03 0.99.7

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Your package has been built on Linux, Mac, and Windows.

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Received a valid push; starting a build. Commits are:

b3dfdbf 99.8

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Your package has been built on Linux, Mac, and Windows.

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[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

9e84daa Update DESCRIPTION

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

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Received a valid push; starting a build. Commits are:

f583660 099.10

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

ad1ec12 99.11

[bioc-issue-bot]

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Your package has been built on Linux, Mac, and Windows.

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[DanrleyRF]

21 January 2020

Thank you for your comment @mtmorgan , your recommendations have been very useful in developing our package and improving our knowledge on the Bioconductor platform

DESCRIPTION

• The package no longer relies on seqinr, now operates only with Biostrings functions and variables
• The Title and the Description have been updated to be more precise in describing the package.

R

• Despcritional comments have been added to all codes.
• The sWeeP functions now accept AAStringset as well file names as a valid entry
• The sWeeP function now uses an S4 Generic and S4 methods
• The user input variable baseMatrix has now a validating step on the code
• The sWeeP function now uses Biostrings::readAAStringSet for FASTA input.
• All functions now only use message(...) to communicate with users.
• All 1:length(...) instances have been replaced with seq_len
• On all codes, the function tidy_source() from the formatR package has been used to standardizing code formating.
• All operations that do not affect have to the package working been removed.
• Some functions and variables naming has been changed aiming to follow the lowerCamelCase convention (the sWeeP function still as it's, due it is the method initials)
• aa2int() has been replaced by a vector inside the aa2num2()
• The data set datastring has been removed.
• fas2mat receives now an AAStringSet as entry

vignette

• Instead of reading the R object datastring and writing it as a FASTA file, a FASTA file has been included directly in inst/extdata/
• A bigger FASTA has been used in the "Quick Start" section, but still not 'larger' as the program can handle in max, due to the long time that would take to generate the example if the maximum where used

misc

• All non-R package source files have been removed from the git repository

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/DanrleyRF.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("rSWeeP"). The package 'landing page' will be created at

https://bioconductor.org/packages/rSWeeP

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.