GEO Helper Script

This script generates GEO high-throughput sequencing submission v2.1 template compliant annotations for fastq and fastq.gz files.

Requirements

macOS or Linux bases system with gzip and head utilities available.

Usage

With R inside the directory containing all the fastq files:

source("https://github.com/Shians/GeoHelper/raw/master/geo_helper.R")
cat(get_raw_files_info(), "\n")

or from the shell

Rscript -e 'source("https://github.com/Shians/GeoHelper/raw/master/geo_helper.R"); cat(get_raw_files_info(), "\n")'

The printed output should be suitable for copy-pasting into the GEO template spreadsheet.

macOS users can use

source("https://github.com/Shians/GeoHelper/raw/master/geo_helper.R")
cat(get_raw_files_info(), file = pipe("pbcopy"))

or

Rscript -e 'source("https://github.com/Shians/GeoHelper/raw/master/geo_helper.R"); cat(get_raw_files_info(), file = pipe("pbcopy"))'

to directly output into the clipboard for immediate pasting into excel.