--- title: "ena parser" author: "Simeon Lim Rossmann" date: "2024-10-23" output: html_document --- ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) library(tidyverse) ``` ```{r fill tbl} template <- "fastq2_template_1729686589164.tsv" header <- scan(template, nlines = 1, what = character()) tbl <- readr::read_tsv(template, skip = 1) %>% dplyr::right_join(tibble( instrument_model= "Illumina MiSeq", library_source= "METAGENOMIC", library_selection = "PCR", library_strategy= "AMPLICON", library_layout= "PAIRED") ) file_reader <- function(marker){ fs <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21", marker, "raw_data"), pattern = "R1_001.fastq.gz") fs_full <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21", marker, "raw_data"), pattern = "R1_001.fastq.gz", full.names = TRUE) rs <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21", marker, "raw_data"), pattern = "R2_001.fastq.gz") rs_full <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21", marker, "raw_data"), pattern = "R2_001.fastq.gz", full.names = TRUE) md5_f <- sapply(fs_full, tools::md5sum) md5_r <- sapply(rs_full, tools::md5sum) samp <- stringr::str_replace(fs, ".*_S", "S") %>% stringr::str_remove("_L001.*") lib_name <- paste0("NIBIO_mpt_", marker) stud <- "ENA_acc" tibble(sample = samp, study = stud, instrument_model= "Illumina MiSeq", library_name = lib_name, library_source= "METAGENOMIC", library_selection = "PCR", library_strategy= "AMPLICON", library_layout= "PAIRED", forward_file_name = fs, forward_file_md5 = md5_f, reverse_file_name = rs, reverse_file_md5 = md5_r ) } markers <- c("Nems", "16S", "FITS1", "FITS2", "OITS", "Trich") tb <- lapply(markers, file_reader) %>% bind_rows() ```