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‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata

‎CONTRIBUTING.md

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# Welcome!
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Thank you for contributing to CDC's Open Source projects! If you have any
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questions or doubts, don't be afraid to send them our way. We appreciate all
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contributions, and we are looking forward to fostering an open, transparent, and
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collaborative environment.
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Before contributing, we encourage you to also read or [LICENSE](https://github.com/CDCgov/template/blob/master/LICENSE),
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[README](https://github.com/CDCgov/template/blob/master/README.md), and
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[code-of-conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md)
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files, also found in this repository. If you have any inquiries or questions not
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answered by the content of this repository, feel free to [contact us](mailto:[email protected]).
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## Public Domain
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This project is in the public domain within the United States, and copyright and
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related rights in the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).
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All contributions to this project will be released under the CC0 dedication. By
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submitting a pull request you are agreeing to comply with this waiver of
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copyright interest.
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## Requesting Changes
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Our pull request/merging process is designed to give the CDC Surveillance Team
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and other in our space an opportunity to consider and discuss any suggested
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changes. This policy affects all CDC spaces, both on-line and off, and all users
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are expected to abide by it.
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### Open an issue in the repository
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If you don't have specific language to submit but would like to suggest a change
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or have something addressed, you can open an issue in this repository. Team
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members will respond to the issue as soon as possible.
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### Submit a pull request
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If you would like to contribute, please submit a pull request. In order for us
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to merge a pull request, it must:
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* Be at least seven days old. Pull requests may be held longer if necessary
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to give people the opportunity to assess it.
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* Receive a +1 from a majority of team members associated with the request.
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If there is significant dissent between the team, a meeting will be held to
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discuss a plan of action for the pull request.

‎DESCRIPTION

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Package: SeqSpawnR
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Type: Package
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Title: Spawn Random DNA Sequences
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Version: 0.1.0
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Author: Tony Boyles <[email protected]>
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Maintainer: Tony Boyles <[email protected]>
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Description: This package simplifies the process of creating randomly mutated DNA sequences.
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License: file LICENSE
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Encoding: UTF-8
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LazyData: true
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Depends: R (>= 2.10.0)
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Imports:
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stringr,
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magrittr
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RoxygenNote: 6.1.1

‎DISCLAIMER.md

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# DISCLAIMER
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Use of this service is limited only to **non-sensitive and publicly available
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data**. Users must not use, share, or store any kind of sensitive data like
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health status, provision or payment of healthcare, Personally Identifiable
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Information (PII) and/or Protected Health Information (PHI), etc. under **ANY**
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circumstance.
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Administrators for this service reserve the right to moderate all information
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used, shared, or stored with this service at any time. Any user that cannot
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abide by this disclaimer and Code of Conduct may be subject to action, up to
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and including revoking access to services.
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The material embodied in this software is provided to you "as-is" and without
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warranty of any kind, express, implied or otherwise, including without
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limitation, any warranty of fitness for a particular purpose. In no event shall
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the Centers for Disease Control and Prevention (CDC) or the United States (U.S.)
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government be liable to you or anyone else for any direct, special, incidental,
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indirect or consequential damages of any kind, or any damages whatsoever,
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including without limitation, loss of profit, loss of use, savings or revenue,
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or the claims of third parties, whether or not CDC or the U.S. government has
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been advised of the possibility of such loss, however caused and on any theory
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of liability, arising out of or in connection with the possession, use or
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performance of this software.

‎LICENSE

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Apache License
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Version 2.0, January 2004
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‎NAMESPACE

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importFrom(magrittr,"%>%")
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importFrom(stringr,"str_replace")
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exportPattern("^[[:alpha:]]+")

‎R/SequenceSpawner.R

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#' spawn_sequences
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#'
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#' @param n The number of sequences to output
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#' @param snps The maximum number of snps in each mutant sequence
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#' @param seed The original DNA Sequence from which the outputs will be mutated
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#'
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#' @return A vector of mutant sequences
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#' @export
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spawn_sequences <- function(n = 20000, snps = 100, seed){
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if(missing(seed)){
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seed <- SeqSpawnR::HXB2
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}
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seednChar <- nchar(seed)
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SampleCodons <- c("GCA", "GCC", "GCG", "GCT", "AAC", "AAT", "GAC", "GAT", "TGC", "TGT", "GAC", "GAT", "GAA", "GAG", "TTC", "TTT", "GGA", "GGC", "GGG", "GGT", "CAC", "CAT", "ATA", "ATC", "ATT" ,"AAA", "AAG" ,"CTA", "CTC", "CTG", "CTT", "TTA", "TTG" , "ATG", "AAC", "AAT", "CCA", "CCC", "CCG", "CCT", "CAA", "CAG", "AGA", "AGG", "CGA", "CGC", "CGG", "CGT", "AGC", "AGT", "TCA", "TCC", "TCG", "TCT", "ACA", "ACC", "ACG", "ACT", "GTA", "GTC", "GTG", "GTT", "TGG", "TAC", "TAT", "CAA", "CAG", "GAA", "GAG" )
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SampleSNPs <- c("A", "C", "G", "T")
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# Set up the vector for the total number of seed variations
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sequences = vector(mode = "character", n)
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#Set up vectors to record the history of the Codon string to search for in the seed sequence, and the replacement
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# condon string
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RandomCodonSetHistory = vector(mode = "character", n)
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ReplacementCodonSetHistory = vector(mode = "character", n)
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#Initialize the seed vector with the initial seed sequence as a seed.
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sequences[1] <- seed
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x <- 1
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while(x < n){
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# The second value can be varied for the total number of possible codons that you want to be considered for consecutive
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# set of condons for variation
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NCodons <- sample(1:10, 1)
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# Of the entire set of codons that represent amino acids randomly select up to NCodons check for existence
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# of the codon string in the current seed under consideration.
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RandomCodonSet <- paste(sample(SampleCodons, NCodons, replace=TRUE), collapse="")
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RandomCodonSetHistory[x] <- RandomCodonSet
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# Do the same and select a codon set of the same length that will replace the searched set.
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ReplacementCodonSet <- paste(sample(SampleCodons, NCodons, replace=TRUE), collapse="")
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ReplacementCodonSetHistory[x] <- ReplacementCodonSet
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# If there is a match between the RandomCodonSet and the seed in processes, set the control flags,
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# and then replace the codon set, update the vector, and increment the count.
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if(RandomCodonSet %>% grep(sequences[x], fixed = TRUE) %>% length > 0){
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Newseed <- str_replace(sequences[sample(1:x, 1)], RandomCodonSet, ReplacementCodonSet)
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sequences[x+1] <- Newseed
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# Add more SNP substitutions randomly across the entire sequence to newly created variant. Replacement numbers are controlled by randomly
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# sampling the AddedSNP number, and randomly picking SNPs to replace.
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for (j in 1:(sample(1:snps, 1))){
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RandomSNP <- sample(SampleSNPs, 1);
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LocOfSNP <- sample(1:seednChar, 1);
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substr(sequences[x+1], LocOfSNP, LocOfSNP) = RandomSNP; # Location of selected SNP to be replaced.
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}
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x <- x+1
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}
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}
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return(sequences)
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}
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#' Pol Region of the HXB2 Strain of HIV
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#'
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#' @format A string with 1300 Characters
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"HXB2"
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#> [1] "HXB2"
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#' write_fasta
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#'
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#' @param sequences A Vector of Sequences
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#' @param filename A Filename
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#'
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#' @export
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write_fasta <- function(sequences, filename){
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if(missing(filename)){
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filename <- Sys.time() %>%
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gsub(" ", "-", .) %>%
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gsub(":","-", .) %>%
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paste(".fasta") %>%
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gsub(" ","",.)
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}
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time <- Sys.time()
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n <- length(sequences)
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for(i in 1:n){
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time %>%
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gsub(":", "_", .) %>%
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gsub(" ", "_", .) %>%
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paste(">", .) %>%
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gsub(" ", "", .) %>%
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paste(i) %>%
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gsub(" ", "-", .) %>%
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paste(sequences[i]) %>%
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gsub(" ", "\n", .) %>%
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write(file = filename, append = TRUE)
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}
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}

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