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Merge pull request #109 from rrohwer/master
Minor Edits to Reflect mSphere publication
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| These are scripts for reformatting the ARB output of the Freshwater Training Set | ||
| # README arb-scripts | ||
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| Robin's in the process of pulling them together into a repeatable workflow. | ||
| That's gonna be in this repo soon. | ||
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| The .pl script is the one Trina uses already. | ||
| The ones Robin's adding are to address bugs she's encountered while working on 16STaxAss. | ||
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| When Robin is not writing code, she enjoys referring to herself in the 3rd person. | ||
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| RRR 2-8-16 | ||
| These are scripts for reformatting the ARB output of the Freshwater Training Set. | ||
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| This folder also includes the scripts and files used for the TaxAss manuscript's Marathonas Validation (fig 1 in paper). These are located inside the `Marathonas_test` folder. |
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| # README figure-scripts | ||
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| These scripts generate the final versions of figures and tables for the paper. | ||
| Many of the figures and tables are already generated in the workflow, but this is | ||
| the version of the script where I tweak colors, dimensions, resolution, etc. | ||
| For tables, a csv with the data is generated that msphere later formatted pretty. | ||
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| Also included are figures generated for my ISME16 poster, figures that didn't make | ||
| the final cut, and a script for finding all the stats listed in the text. | ||
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| The folder structure for reproducing the manuscript's data is `TaxAss-BatchFiles.zip`. | ||
| This folder pairs with the directions in `README-TaxAss-BatchFiles.html`. | ||
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| The Marathonas validation batch files and directions are inside the `arb-scripts` folder. | ||
| The directions are in the file `arb-scripts/Marathonas_test/README_marathonas_validation.html` | ||
| and all necessary files are also in that folder. |
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| Scripts for 16S Taxonomy Assignment Workflow | ||
| README tax-scripts | ||
| === | ||
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| This folder contains the scripts used for OTU assignment. Detailed descriptions of them are in the `Clean Workflow.txt` document. | ||
| This folder contains the TaxAss scripts. Detailed descriptions of them are in `TaxAss_Directions.html`. You can read the directions online here: [tax-scripts/TaxAss_Directions.html](https://htmlpreview.github.io/?https://github.com/McMahonLab/TaxAss/blob/master/tax-scripts/TaxAss_Directions.html) | ||
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| To use TaxAss, download this folder, add your data and databases, and use it as your working directory. |
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| # RRR 2018-7-20 | ||
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| # dada2 has an internal implementation of the Wang classifier/ RDP classifier / mothur default / TaxAss choice | ||
| # BUT, just keep using mothur with TaxAss because formatting is painful. | ||
| # this script takes the dada2 output file (seqtab_nochim) and cretes otus.fasta and otus.abund | ||
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| # command line syntax: | ||
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| # Rscript reformat.dada2.seqtabs.R seqtab_nochim.rds otus.fasta otus.abund | ||
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| # ---- Accept Arguments from Terminal Command Line ---- | ||
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| userprefs <- commandArgs(trailingOnly = TRUE) | ||
| path.to.seqtab <- userprefs[1] | ||
| fasta.output <- userprefs[2] | ||
| abund.output <- userprefs[3] | ||
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| cat("fuck you forgot to comment out the file paths in reformat_dada2_seqtabs.R!") | ||
| path.to.seqtab <- "/Users/athena/Desktop/dada2-meV45/dada2/seqtab_nochim.rds" | ||
| fasta.output <- "~/Desktop/otus.fasta" | ||
| abund.output <- "~/Desktop/otus.abund" | ||
| count.output <- "/Users/athena/Desktop/dada2-meV45/taxass_gg/data/otus.count" | ||
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| # ---- define functions ---- | ||
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| import.dada2.file <- function(path){ | ||
| is.rds <- grepl(pattern = "*.rds", x = path) | ||
| if (is.rds){ | ||
| seqtab_nochim <- readRDS(file = path) | ||
| return(seqtab_nochim) | ||
| }else{ | ||
| cat("input must be rds file ending in \".rds\"\nSave it in this format at the end of dada2 pipeline using\nsaveRDS(object = seqtab_nochim, file = \"filename\")") | ||
| } | ||
| } | ||
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| make.fasta.file <- function(dadatable, fasta.path){ | ||
| fasta.seqs <- colnames(dadatable) | ||
| otu.names <- paste("otu", 1:length(fasta.seqs), sep = "_") | ||
| fasta.names <- paste(">", otu.names, sep = "") | ||
| fasta.file <- paste(fasta.names, fasta.seqs, sep = "\n") | ||
| write.table(x = fasta.file, file = fasta.path, quote = F, row.names = F, sep = "\n", col.names = F) | ||
| cat("Made file: ", fasta.path, "\n") | ||
| return(otu.names) | ||
| } | ||
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| find.zero.samples <- function(tot.reads, otu.table){ | ||
| read.stats <- boxplot(x = tot.reads, plot = F) | ||
| cat("These samples have outlier read counts. Samples with zero reads are being removed.\n",paste(names(read.stats$out), " : ", read.stats$out, sep = "", "\n")) | ||
| index <- which(tot.reads == 0) | ||
| return(index) | ||
| } | ||
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| convert.to.rel.abund <- function(OTUs){ | ||
| sample.totals <- rowSums(OTUs) | ||
| # vectors are applied to matrices by stepping down rows in a column | ||
| norm.otus <- OTUs / sample.totals * 100 | ||
| return(norm.otus) | ||
| } | ||
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| reformat.for.taxass <- function(OTUs){ | ||
| # rows = OTUs, cols = samples, col 1 = seqIDs | ||
| otu.table <- t(OTUs) | ||
| otu.table <- cbind(row.names(otu.table), otu.table) | ||
| colnames(otu.table)[1] <- "seqID" | ||
| return(otu.table) | ||
| } | ||
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| make.abund.file <- function(OTUs, FilePath){ | ||
| write.table(x = OTUs, file = FilePath, quote = FALSE, sep = "\t", row.names = FALSE) | ||
| cat("Made file: ", FilePath, "\n") | ||
| } | ||
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| make.count.file <- function(Count, FilePath){ | ||
| Count <- cbind(names(Count), Count) | ||
| colnames(Count) <- c("Sample.Name", "Total.Reads") | ||
| write.table(x = Count, file = FilePath, quote = F, sep = "\t", row.names = F) | ||
| cat("Made file: ", FilePath, "\n") | ||
| } | ||
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| # ---- use functions ---- | ||
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| seqtab_nochim <- import.dada2.file(path = path.to.seqtab) | ||
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| seqIDs <- make.fasta.file(dadatable = seqtab_nochim, fasta.path = fasta.output) | ||
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| colnames(seqtab_nochim) <- seqIDs | ||
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| read.count <- rowSums(seqtab_nochim) | ||
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| index <- find.zero.samples(tot.reads = read.count, otu.table = seqtab_nochim) | ||
| if(length(index) > 0){ | ||
| read.count <- read.count[-index] | ||
| seqtab_nochim <- seqtab_nochim[-index, ] | ||
| } | ||
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| seqtab_nochim <- convert.to.rel.abund(OTUs = seqtab_nochim) | ||
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| seqtab_nochim <- reformat.for.taxass(OTUs = seqtab_nochim) | ||
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| make.abund.file(OTUs = seqtab_nochim, FilePath = abund.output) | ||
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| make.count.file(Count = read.count, FilePath = count.output) | ||
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