From 08ee62b65402d761e5fc04ec44b48cccb83d2e07 Mon Sep 17 00:00:00 2001
From: simeon <simeon.rossmann@nibio.no>
Date: Fri, 25 Oct 2024 14:49:56 +0200
Subject: [PATCH] ENA parser
---
ENA submission/ena_parser.Rmd | 69 +++++++++++++++++++
.../fastq2_template_1729686589164.tsv | 2 +
2 files changed, 71 insertions(+)
create mode 100644 ENA submission/ena_parser.Rmd
create mode 100644 ENA submission/fastq2_template_1729686589164.tsv
diff --git a/ENA submission/ena_parser.Rmd b/ENA submission/ena_parser.Rmd
new file mode 100644
index 0000000..243a876
--- /dev/null
+++ b/ENA submission/ena_parser.Rmd
@@ -0,0 +1,69 @@
+---
+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()
+```
\ No newline at end of file
diff --git a/ENA submission/fastq2_template_1729686589164.tsv b/ENA submission/fastq2_template_1729686589164.tsv
new file mode 100644
index 0000000..da3b31c
--- /dev/null
+++ b/ENA submission/fastq2_template_1729686589164.tsv
@@ -0,0 +1,2 @@
+FileType fastq Read submission file type
+sample study instrument_model library_name library_source library_selection library_strategy library_layout forward_file_name forward_file_md5 reverse_file_name reverse_file_md5
--
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