From 91d5857dbda5998839a002fbecae0f494dca960a Mon Sep 17 00:00:00 2001 From: Tony Boyles Date: Thu, 3 Jan 2019 12:23:26 -0500 Subject: [PATCH] Initial commit --- .Rbuildignore | 2 + .gitignore | 4 + CONTRIBUTING.md | 38 ++++++++ DESCRIPTION | 15 +++ DISCLAIMER.md | 23 +++++ LICENSE | 201 +++++++++++++++++++++++++++++++++++++++++ NAMESPACE | 4 + R/SequenceSpawner.R | 102 +++++++++++++++++++++ README.md | 91 +++++++++++++++++++ SeqSpawnR.Rproj | 21 +++++ code-of-conduct.md | 103 +++++++++++++++++++++ data/HXB2.rda | Bin 0 -> 486 bytes man/HXB2.Rd | 14 +++ man/spawn_sequences.Rd | 21 +++++ man/write_fasta.Rd | 16 ++++ 15 files changed, 655 insertions(+) create mode 100644 .Rbuildignore create mode 100644 .gitignore create mode 100644 CONTRIBUTING.md create mode 100644 DESCRIPTION create mode 100644 DISCLAIMER.md create mode 100644 LICENSE create mode 100644 NAMESPACE create mode 100644 R/SequenceSpawner.R create mode 100644 README.md create mode 100644 SeqSpawnR.Rproj create mode 100644 code-of-conduct.md create mode 100644 data/HXB2.rda create mode 100644 man/HXB2.Rd create mode 100644 man/spawn_sequences.Rd create mode 100644 man/write_fasta.Rd diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..91114bf --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..5b6a065 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..5ceaa70 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,38 @@ +# Welcome! +Thank you for contributing to CDC's Open Source projects! If you have any +questions or doubts, don't be afraid to send them our way. We appreciate all +contributions, and we are looking forward to fostering an open, transparent, and +collaborative environment. + +Before contributing, we encourage you to also read or [LICENSE](https://github.com/CDCgov/template/blob/master/LICENSE), +[README](https://github.com/CDCgov/template/blob/master/README.md), and +[code-of-conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md) +files, also found in this repository. If you have any inquiries or questions not +answered by the content of this repository, feel free to [contact us](mailto:surveillanceplatform@cdc.gov). + +## Public Domain +This project is in the public domain within the United States, and copyright and +related rights in the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/). +All contributions to this project will be released under the CC0 dedication. By +submitting a pull request you are agreeing to comply with this waiver of +copyright interest. + +## Requesting Changes +Our pull request/merging process is designed to give the CDC Surveillance Team +and other in our space an opportunity to consider and discuss any suggested +changes. This policy affects all CDC spaces, both on-line and off, and all users +are expected to abide by it. + +### Open an issue in the repository +If you don't have specific language to submit but would like to suggest a change +or have something addressed, you can open an issue in this repository. Team +members will respond to the issue as soon as possible. + +### Submit a pull request +If you would like to contribute, please submit a pull request. In order for us +to merge a pull request, it must: + * Be at least seven days old. Pull requests may be held longer if necessary + to give people the opportunity to assess it. + * Receive a +1 from a majority of team members associated with the request. + If there is significant dissent between the team, a meeting will be held to + discuss a plan of action for the pull request. diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..8eec2db --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,15 @@ +Package: SeqSpawnR +Type: Package +Title: Spawn Random DNA Sequences +Version: 0.1.0 +Author: Tony Boyles +Maintainer: Tony Boyles +Description: This package simplifies the process of creating randomly mutated DNA sequences. +License: file LICENSE +Encoding: UTF-8 +LazyData: true +Depends: R (>= 2.10.0) +Imports: + stringr, + magrittr +RoxygenNote: 6.1.1 diff --git a/DISCLAIMER.md b/DISCLAIMER.md new file mode 100644 index 0000000..63fa40c --- /dev/null +++ b/DISCLAIMER.md @@ -0,0 +1,23 @@ +# DISCLAIMER +Use of this service is limited only to **non-sensitive and publicly available +data**. 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Replacement numbers are controlled by randomly + # sampling the AddedSNP number, and randomly picking SNPs to replace. + for (j in 1:(sample(1:snps, 1))){ + RandomSNP <- sample(SampleSNPs, 1); + LocOfSNP <- sample(1:seednChar, 1); + substr(sequences[x+1], LocOfSNP, LocOfSNP) = RandomSNP; # Location of selected SNP to be replaced. + } + x <- x+1 + } + } + return(sequences) +} + +#' Pol Region of the HXB2 Strain of HIV +#' +#' @format A string with 1300 Characters +"HXB2" +#> [1] "HXB2" + +#' write_fasta +#' +#' @param sequences A Vector of Sequences +#' @param filename A Filename +#' +#' @export +write_fasta <- function(sequences, filename){ + if(missing(filename)){ + filename <- Sys.time() %>% + gsub(" ", "-", .) %>% + gsub(":","-", .) %>% + paste(".fasta") %>% + gsub(" ","",.) + } + + time <- Sys.time() + + n <- length(sequences) + + for(i in 1:n){ + time %>% + gsub(":", "_", .) %>% + gsub(" ", "_", .) %>% + paste(">", .) %>% + gsub(" ", "", .) %>% + paste(i) %>% + gsub(" ", "-", .) %>% + paste(sequences[i]) %>% + gsub(" ", "\n", .) %>% + write(file = filename, append = TRUE) + } +} diff --git a/README.md b/README.md new file mode 100644 index 0000000..f7ccec5 --- /dev/null +++ b/README.md @@ -0,0 +1,91 @@ +# SeqSpawnR + +Spawn Random DNA Sequences + +*This repository was created for use by CDC programs to collaborate on public health surveillance related projects in support of the CDC Surveillance Strategy. Github is not hosted by the CDC, but is used by CDC and its partners to share information and collaborate on software.* + +## Install + +```R +devtools::install_github('CDCgov/SeqSpawnR') +``` + +## Use + +```R +HIV_Samples <- SeqSpawnR::spawn_sequences(10) +``` + +`HIV_Samples` will be a vector of mutated HIV sequences. By default, it uses the *pol* region of the HXB2 strain of HIV as the DNA seed. To set the seed to a different DNA Sequence: + +```R +mySeed <- 'GATTACA' +HIV_Samples <- SeqSpawnR::spawn_sequences(10, seed = mySeed) +``` + +Where `mySeed` is a string containing the DNA Sequence you wish to use as your seed. + +If you'd like to write the samples into a fasta file... + +```R +filename <- 'HIV_Samples.fasta' +SeqSpawnR::write_fasta(HIV_Samples, filename) +``` + +## Public Domain +This repository constitutes a work of the United States Government and is not +subject to domestic copyright protection under 17 USC ยง 105. This repository is in +the public domain within the United States, and copyright and related rights in +the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/). +All contributions to this repository will be released under the CC0 dedication. By +submitting a pull request you are agreeing to comply with this waiver of +copyright interest. + +## License +The repository utilizes code licensed under the terms of the Apache Software +License and therefore is licensed under ASL v2 or later. + +This source code in this repository is free: you can redistribute it and/or modify it under +the terms of the Apache Software License version 2, or (at your option) any +later version. + +This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY +WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A +PARTICULAR PURPOSE. See the Apache Software License for more details. + +You should have received a copy of the Apache Software License along with this +program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html + +The source code forked from other open source projects will inherit its license. + + +## Privacy +This repository contains only non-sensitive, publicly available data and +information. All material and community participation is covered by the +Surveillance Platform [Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md) +and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md). +For more information about CDC's privacy policy, please visit [http://www.cdc.gov/privacy.html](http://www.cdc.gov/privacy.html). + +## Contributing +Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo) +and submitting a pull request. (If you are new to GitHub, you might start with a +[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing +to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, +non-exclusive, transferable license to all users under the terms of the +[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or +later. + +All comments, messages, pull requests, and other submissions received through +CDC including this GitHub page are subject to the [Presidential Records Act](http://www.archives.gov/about/laws/presidential-records.html) +and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html). + +## Records +This repository is not a source of government records, but is a copy to increase +collaboration and collaborative potential. All government records will be +published through the [CDC web site](http://www.cdc.gov). + +## Notices +Please refer to [CDC's Template Repository](https://github.com/CDCgov/template) +for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md), +[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md), +and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md). diff --git a/SeqSpawnR.Rproj b/SeqSpawnR.Rproj new file mode 100644 index 0000000..f0d6187 --- /dev/null +++ b/SeqSpawnR.Rproj @@ -0,0 +1,21 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace,vignette diff --git a/code-of-conduct.md b/code-of-conduct.md new file mode 100644 index 0000000..f657aae --- /dev/null +++ b/code-of-conduct.md @@ -0,0 +1,103 @@ +# Creating a Culture of Innovation +We aspire to create a culture where people work joyfully, communicate openly +about things that matter, and provide great services globally. We would like our +team and communities (both government and private sector) to reflect on +diversity of all kinds, not just the classes protected in law. Diversity fosters +innovation. Diverse teams are creative teams. We need a diversity of perspective +to create solutions for the challenges we face. + +This is our code of conduct (adapted from [18F's Code of Conduct](https://github.com/18F/code-of-conduct)). +We follow all Equal Employment Opportunity laws and we expect everyone we work +with to adhere to the [GSA Anti-harrasment Policy](http://www.gsa.gov/portal/directive/d0/content/512516), +even if they do not work for the Centers for Disease Control and Prevention or +GSA. We expect every user to follow this code of conduct and the laws and +policies mentioned above. + +## Be Empowering +Consider what you can do to encourage and support others. Make room for quieter +voices to contribute. Offer support and enthusiasm for great ideas. Leverage the +low cost of experimentation to support your colleagues' ideas, and take care to +acknowledge the original source. Look for ways to contribute and collaborate, +even in situations where you normally wouldn't. 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Consider + that calling attention to differences can feel alienating. + * Sustained disruption of meetings, talks, or discussions, including chatrooms. + * Patronizing language or behavior. + * Aggresive behavior, such as unconstructive criticism, providing correction + that do not improve the conversation (sometimes referred to as "well + actually's"), repeatedly interrupting or talking over someone else, feigning + surprise at someone's lack of knowledge or awareness about a topic, or subtle + prejudice. + * Referring to people in a way that misidentifies their gender and/or rejects + the validity of their gender identity; for instance by using incorrect + pronouns or forms of address (misgendering). + * Retaliating against anyone who files a formal complaint that someone has + violated these codes or laws. + +## Background +CDC Scientific Clearance is the process of obtaining approvals by appropriate +CDC officials before a CDC information product is released to the public or +CDC's external public health partners. Information products that require formal +clearance include print, electronic, or oral materials, that CDC employees +author or co-author, whether published by CDC or outside CDC. CDC contractors +developing content on behalf of CDC for the public or CDC's external public +health partners are also required to put their content through the formal +clearance process. The collaborative functions related to the projects include +blogs, wikis, forums, bug tracking sites, source control and +others deemed as necessary. + +For those individuals within the CDC, adherence to the following policies are +required: +* CDC ["Clearance of Information Products Disseminated Outside CDC for Public Use"](http://www.cdc.gov/maso/Policy/PublicUse.pdf) +* HHS ["Ensuring the Quality of Information Disseminated by HHS agencies"](http://aspe.hhs.gov/infoquality) + +All collaborative materials will be controlled by the rules contained within +this document. This will allow for the real-time collaboration opportunities +among CDC employees, CDC contractors and CDC public health partners. + +## Credit +This code of conduct was mainly adapted from [18F's Code of Conduct](https://github.com/18F/code-of-conduct) +and the [CDC's Informatics Innovation Unit R&D Lab's code of conduct.](http://www.phiresearchlab.org/?page_id=1715) + +## Relevant Legal Considerations +* [Laws enforced by the Equal Employment Opportunity Commission](http://www.eeoc.gov/laws/statutes/index.cfm) +* [Types of discrimination prohibited by law](http://www.eeoc.gov/laws/types) +* [New and proposed regulations](http://www.eeoc.gov/laws/regulations/index.cfm) diff --git a/data/HXB2.rda b/data/HXB2.rda new file mode 100644 index 0000000000000000000000000000000000000000..da3fa51efe04c953ef689d1ecacbb21efc001e5e GIT binary patch literal 486 zcmV6T4*^jL0KkKSy^7w?f?QE?g0KUL;w%~Jirt{00BS)8~^|SplP9zlMtY3 zp^=jiplP9zlMqUIDM(cHJwr#Nzdt^He!utM8RP8yF8>4lch~x!o(b*RC^2ZKpJwZ0n0?Ch8rL z*+!h1>ch&HGG^1()XKv7?@ZzENa@CTVW+OGkrNR*Nt0USS+-=|oT-g)lI=S#owaL~ z<r1rLslGS9Mt*qPL*~_aJ-zNdn9^HkjBjryJ+be5 zCx;qGe(&i#_=f%I$WzOGYdOlzuG?Cd24B6OKH9N4)u*&)0+i^|vyl*D$sf(eJq%5ibfa3L-3(4K~D>ulN16srAJKnOs-6PIQDH*mu6W(En^*Gk6zbnP) zjO5xKudheXifuI)(