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| #' QC Raw Sequence Metadata | ||
| #' | ||
| #' Performs basic QC checks and reports potential issues with downstream processing. | ||
| #' | ||
| #' @param metadata The output of downloadSequenceMetadata(). Must be provided as either the data.frame returned by downloadSequenceMetadata() or as a filepath to the csv file produced by downloadSequenceMetadata() when dir is specified. | ||
| #' @param outdir_sequence Default file.path(PRESET_OUTDIR, PRESET_OUTDIR_SEQUENCE). Directory where raw sequence files can be found before reorganizing. | ||
| #' | ||
| #' @return Report file of potential quality issues with metadata records | ||
| qcMetadata <- function(metadata, outdir = file.path(PRESET_OUTDIR, PRESET_OUTDIR_SEQMETA)) { | ||
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| metadata_load_err <- FALSE | ||
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| if(class(metadata) == "data.frame") { | ||
| metadata <- metadata | ||
| } else if(class(metadata) == "character") { | ||
| if(file.exists(metadata)) { | ||
| metadata <- read.csv(metadata) | ||
| } else { | ||
| metadata_load_err <- TRUE | ||
| } | ||
| } else { | ||
| metadata_load_err <- TRUE | ||
| } | ||
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| if(metadata_load_err) { | ||
| stop("'metadata' must be the data.frame output from downloadSequenceMetadata() or a filepath to the local copy of the output from downloadSequenceMetadata()") | ||
| } | ||
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| # QC check #1: completeness | ||
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| # Using metadata, look up the sequencing run ID and target gene for each file | ||
| match_fn_to_meta <- match(basename(fn), metadata$rawDataFileName) | ||
| runIDs <- metadata$sequencerRunID[match_fn_to_meta] | ||
| targetGenes <- as.character(metadata$targetGene[match_fn_to_meta]) | ||
| targetGenes[grep("16S", targetGenes, ignore.case=TRUE)] <- "16S" | ||
| targetGenes[grep("ITS", targetGenes, ignore.case=TRUE)] <- "ITS" | ||
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| if(all(is.na(runIDs))) stop("All sequencer run ID values are NA. Cannot proceed with reorganizing this download batch. | ||
| Try a different `fn` or `metadata`.") | ||
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| files_organized <- c() | ||
| for(i in 1:length(fn)) { | ||
| # get run ID associated with the zip file | ||
| runID <- runIDs[i] | ||
| if(is.na(runID)) { | ||
| warning("No recorded sequencer run ID in metadata for file: ", fn[i], ". Skipping this file.") | ||
| next | ||
| } | ||
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| # get target gene associated with the zip file | ||
| targetGene <- targetGenes[i] | ||
| if(is.na(runID)) { | ||
| warning("No recorded target gene in metadata for file: ", fn[i], ". Skipping this file.") | ||
| next | ||
| } | ||
| if(!(targetGene %in% c("16S", "ITS"))) { | ||
| warning("Recorded target gene in metadata for file does not clearly indicate '16S' or 'ITS': ", fn[i], | ||
| ". Skipping this file.") | ||
| next | ||
| } | ||
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| # If the file is a tar file (unusual case) | ||
| if(grepl("tar.gz", fn[i])) { | ||
| tar_filenames <- untar(fn[i], list=TRUE) | ||
| untarred_dir <- file.path(outdir_sequence, "untarred") | ||
| untar_dir <- if(!dir.exists(untarred_dir)) dir.create(untarred_dir) | ||
| untar(fn[i], list=FALSE, exdir = untarred_dir) | ||
| file.remove(fn[i]) | ||
| untarred <- file.path(untarred_dir, tar_filenames) | ||
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| # rename untarred files by appending sequencer run ID and moving to target gene-specific subdirectory | ||
| untarred_rename_to <- file.path(outdir_sequence, targetGene, "0_raw", paste0("run", runID, "_", basename(untarred))) | ||
| if(length(untarred) > 0) { | ||
| untarred_rename_to <- file.path(outdir_sequence, targetGene, "0_raw", paste0("run", runID, "_", basename(untarred))) | ||
| renamed <- file.rename(untarred, untarred_rename_to) | ||
| if(!all(renamed)) { | ||
| warning(sum(!renamed), " untarred file(s) in sequencer run ", runID, "were not successfully reorganized") | ||
| } | ||
| files_organized <- c(files_organized, untarred_rename_to[renamed]) | ||
| } | ||
| message("Extracted files from ", basename(fn[i]), " and reorganized its contents.") | ||
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| # If the file is not tarred (typical case) | ||
| } else { | ||
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| # rename file by appending sequencer run ID and moving to target gene-specific subdirectory | ||
| rename_to <- file.path(outdir_sequence, targetGene, "0_raw", paste0("run", runID, "_", basename(fn[i]))) | ||
| renamed <- file.rename(fn[i], rename_to) | ||
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| if(!renamed) { | ||
| warning(fn[i], " was not successfully reorganized") | ||
| } else { | ||
| files_organized <- c(files_organized, rename_to) | ||
| } | ||
| message("Reorganized ", basename(fn[i])) | ||
| } | ||
| } | ||
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| # Gzip all non-gzipped fastq files | ||
| for(i in 1:length(files_organized)) { | ||
| if(!grepl(".gz$", files_organized[i])) { | ||
| gzip(files_organized[i]) | ||
| } | ||
| } | ||
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| if(length(files_organized) > 0) { | ||
| message(length(files_organized), " out of ", length(fn), " files in sequencer run ", runID, " were successfully reorganized.") | ||
| message("Reorganized files can be found in ", file.path(outdir_sequence, "ITS", "0_raw"), " and ", file.path(outdir_sequence, "16S", "0_raw"), ".") | ||
| return(files_organized) | ||
| } else { | ||
| warning("No files were successfully reorganized") | ||
| return(NULL) | ||
| } | ||
| } |
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