Skip to content

Instantly share code, notes, and snippets.

@muppetjones
Forked from danielecook/FastQC_aggregate.sh
Last active August 29, 2015 14:26
Show Gist options
  • Save muppetjones/98d85c8ad40d3325961d to your computer and use it in GitHub Desktop.
Save muppetjones/98d85c8ad40d3325961d to your computer and use it in GitHub Desktop.
Examine Fastqc reports in aggregate; brings images, statistics, and summaries together. #fastq
#!/bin/bash
# Run this script in project root--expected structure: `./fastqc/<sample>/*.zip`
# This script aggregates images of each type in individual folders
# o looking across data is quick.
zips=`ls fastqc/*/*.zip`
for i in $zips; do
unzip -oq -d "$(dirname "$i")" $i;
done
fastq_folders=${zips/.zip/}
aggregate_folder=fastqc/aggregated
rm -rf "$aggregate_folder" # Remove aggregate folder if present
mkdir "$aggregate_folder"
# Rename Files within each using folder name.
for folder in $fastq_folders; do
folder=${folder%.*}
img_files=`ls ${folder}/Images/*png`;
for img in $img_files; do
img_name=$(basename "$img");
img_name=${img_name%.*}
new_name=${folder};
new_name="$(basename "${folder/_fastqc/}")"
mkdir -p "${aggregate_folder}"/${img_name};
mv $img "${aggregate_folder}"/${img_name}/${new_name}.png;
done;
done;
# Concatenate Summaries
for folder in $fastq_folders; do
folder=${folder%.*}
cat ${folder}/summary.txt >> "${aggregate_folder}"/summary.txt
done;
# Concatenate Statistics
for folder in $fastq_folders; do
folder=${folder%.*}
head -n 10 ${folder}/fastqc_data.txt | tail -n 7 | awk -v f=${folder/_fastqc/} '{ print $0 "\t" f }' >> "${aggregate_folder}"/statistics.txt
rm -rf ${folder}
done
@muppetjones
Copy link
Author

Modified for different directory structure and DRY aggregate folder

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment