From a9bca3ea476d75191a71a86415139752ff506866 Mon Sep 17 00:00:00 2001
From: Simeon <51403284+simeross@users.noreply.github.com>
Date: Fri, 22 Nov 2024 11:30:20 +0100
Subject: [PATCH] sra parser
---
.../SRA_metadata.txt | 0
SRA submission/SRA_submission.tsv | 1 +
SRA submission/sra_parser.Rmd | 91 +++++++++++++++++++
3 files changed, 92 insertions(+)
rename SRA_metadata.txt => SRA submission/SRA_metadata.txt (100%)
create mode 100644 SRA submission/SRA_submission.tsv
create mode 100644 SRA submission/sra_parser.Rmd
diff --git a/SRA_metadata.txt b/SRA submission/SRA_metadata.txt
similarity index 100%
rename from SRA_metadata.txt
rename to SRA submission/SRA_metadata.txt
diff --git a/SRA submission/SRA_submission.tsv b/SRA submission/SRA_submission.tsv
new file mode 100644
index 0000000..9eaa882
--- /dev/null
+++ b/SRA submission/SRA_submission.tsv
@@ -0,0 +1 @@
+sample_name library_ID title library_strategy library_source library_selection library_layout platform instrument_model design_description filetype filename filename2 filename3 filename4 assembly fasta_file sample
diff --git a/SRA submission/sra_parser.Rmd b/SRA submission/sra_parser.Rmd
new file mode 100644
index 0000000..bb4977f
--- /dev/null
+++ b/SRA submission/sra_parser.Rmd
@@ -0,0 +1,91 @@
+---
+title: "sra parser"
+author: "Simeon Lim Rossmann"
+date: "2024-11-22"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+library(tidyverse)
+```
+
+```{r fill tbl}
+template <- "SRA_metadata.txt"
+tbl <- readr::read_tsv(template) %>%
+ dplyr::right_join(tibble(
+ instrument_model= "Illumina MiSeq",
+ platform = 'ILLUMINA',
+ library_source= "METAGENOMIC",
+ library_selection = "PCR",
+ library_strategy= "AMPLICON",
+ library_layout= "PAIRED",
+ filetype = 'fastq'
+ )
+ )
+
+file_reader <- function(marker){
+ fs <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21",
+ marker[1], "raw_data"),
+ pattern = "R1_001.fastq.gz")
+ fs_full <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21",
+ marker[1], "raw_data"),
+ pattern = "R1_001.fastq.gz",
+ full.names = TRUE)
+ rs <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21",
+ marker[1], "raw_data"),
+ pattern = "R2_001.fastq.gz")
+ rs_full <- list.files(file.path("~/Documents/Marte_Metabarcoding/Run_August21",
+ marker[1], "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[1],
+ '_', samp)
+
+ out <- tibble(sample = samp,
+ library_ID = lib_name,
+ instrument_model= "Illumina MiSeq",
+ platform = 'ILLUMINA',
+ library_source= "METAGENOMIC",
+ library_selection = "PCR",
+ library_strategy= "AMPLICON",
+ library_layout= "PAIRED",
+ filetype = 'fastq',
+ design_description = paste0('Total DNA was extracted from 45 mL soil samples. ',
+ 'Each soil sample and DNA from the appropriate ',
+ 'mock control was amplified with "', marker[1],
+ '" PCR primers targeting the amplification ',
+ 'of ', marker[2], ' sequences. Samples were ',
+ 'indexed in the amplification PCR (1-step) ',
+ 'and demultiplexed by the MiSeq.'),
+ filename=fs,
+ filename2=rs
+ )
+
+ return(out)
+
+}
+
+markers <- list(c("Nems",'nematode 18S'),
+ c("16S",'bacterial 16S'),
+ c("FITS1", 'fungal ITS1'),
+ c("FITS2", 'fungal ITS2'),
+ c("OITS", 'oomycete ITS1'),
+ c("Trich", 'Trichodoridae 18S'))
+
+tb <- lapply(markers, file_reader) %>%
+ bind_rows()
+
+### Fuse back to template to make sure all column names are identical
+tbl <- right_join(tbl, tb)
+all.equal(as.data.frame(tbl), as.data.frame(tb))
+
+write_tsv(tbl, "SRA_submission.tsv", col_names = TRUE)
+```
\ No newline at end of file
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