add filter script

bin/filter_and_trim.R

@@ -0,0 +1,55 @@
+#!/usr/bin/env Rscript
+packages <- c('dada2', 'optparse', 'yaml')
+
+suppressPackageStartupMessages({
+    lapply(packages, require, character.only = TRUE)
+    })
+
+## https://stackoverflow.com/questions/9129673/passing-list-of-named-parameters-to-function
+option_list = list(
+    make_option(c("--id"), type="character", default=NULL, help="Sample ID"),
+    make_option(c("--fwd"), type="character", default=NULL, help="Forward/Read 1"),
+    make_option(c("--rev"), type="character", default=NULL, help="Rev/Read 2"),
+    make_option(c("--cpus"), type="numeric", , default=1, help="cpus"),
+    make_option(c("--trimFor"), type="numeric", , help="trim from 5' for R1"),
+    make_option(c("--trimRev"), type="numeric", , help="trim from 5' for R2"),
+    make_option(c("--truncFor"), type="numeric", , help="truncate R1 to this"),
+    make_option(c("--truncRev"), type="numeric", , help="trucate R2 to this"),
+    make_option(c("--maxEEFor"), type="numeric", , help="maxEE for R1"),
+    make_option(c("--maxEERev"), type="numeric", , help="maxEE for R2"),
+    make_option(c("--truncQ"), type="numeric", , help="Quality score to truncate to"),
+    make_option(c("--maxN"), type="numeric", help="Maximum Ns allowed"),
+    make_option(c("--maxLen"), type="numeric", help="Max length"),
+    make_option(c("--minLen"), type="numeric", help="Min length"),
+    make_option(c("--rmPhiX"), default=TRUE, action="store_true", help="Remove possible PhiX sequences")
+)
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+print(opt)
+
+tmpFunc <- function(...) {
+    print(as.list(match.call()))
+    filterAndTrim(...)
+}
+
+out <- filterAndTrim(fwd        = opt$fwd,
+                    filt        = paste0(opt$id, ".R1.filtered.fastq.gz"),
+                    rev         = opt$rev,
+                    filt.rev    = paste0(opt$id, ".R2.filtered.fastq.gz"),
+                    trimLeft    = c(opt$trimFor,  opt$trimRev),
+                    truncLen    = c(opt$truncFor, opt$truncRev),
+                    maxEE       = c(opt$maxEEFor, opt$maxEERev),
+                    truncQ      = opt$truncQ,
+                    maxN        = opt$maxN,
+                    rm.phix     = opt$rmPhiX,
+                    maxLen      = opt$maxLen,
+                    minLen      = opt$minLen,
+                    compress    = TRUE,
+                    verbose     = TRUE,
+                    multithread = opt$cpus
+                    )
+
+colnames(out) <- c('input', 'filtered')
+
+write.csv(out, paste0(opt$id, ".trimmed.txt"))