renameFQGZ_keeplane.bash

#!/bin/bash

# bash script to rename raw fq.gz files from NovoGene with TAMUCC sample name decode file

enable_lmod
module load parallel

if [[ -z "$1" ]]; then
        echo "please specify the name of the decode file"
        echo "bash renameFQGZ.bash NameOfDecodeFile.tsv"
        exit 1
else
        echo "decode file read into memory"
fi

if [[ -z "$2" ]]; then
        echo "rename not specified, original and new file names will be printed to screen"
        echo "bash renameFQGZ.bash $1"
        echo; echo "if you want to rename then bash renameFQGZ.bash $1 rename"; echo
        MODE="test"
elif [[ "$2" == rename ]]; then
        echo "rename specified, files will be renamed"
        read -p "Are you sure? " -n 1 -r
        if [[ $REPLY =~ ^[Yy]$ ]]; then
                echo
                echo "bash renameFQGZ.bash $1 rename"
                MODE="rename"
        else
                echo
                echo "rename aborted, original and new file names will be printed to screen"
                echo "bash renameFQGZ.bash $1"
                MODE="test"
        fi
else
        echo "rename not specified, original and new file names will be printed to screen"
        echo "bash renameFQGZ.bash $1 $2"
        echo; echo "if you want to rename then bash renameFQGZ.bash $1 rename"; echo
        MODE="test"
fi

echo "writing original file names to file, origFileNames.txt..."
ls *_1.fq.gz | \
        sed 's/1\.fq\.gz//' | \
        sort > \
        origFileNames.txt

echo "writing newFileNames.txt..."
sed 's/_.*_L/-L/1' origFileNames.txt > newFileNames.txt
sed -i 's/.$/-/' newFileNames.txt
sed $'s/\t/\//' $1 > decode_sedlist.txt
sed -i 's/^/s\//' decode_sedlist.txt
sed -i 's/$/\//' decode_sedlist.txt

echo "editing newFileNames.txt..."
sed -i -f decode_sedlist.txt newFileNames.txt

reportOldNewFILENAMES(){
        echo "preview of orig and new R1 file names..."
        parallel --no-notice -k --link "echo {1}1.fq.gz {2}1.fq.gz" :::: origFileNames.txt :::: newFileNames.txt

        echo "preview of orig and new R2 file names..."
        parallel --no-notice -k --link "echo {1}2.fq.gz {2}2.fq.gz" :::: origFileNames.txt :::: newFileNames.txt
}
reportOldNewFILENAMES

if [[ $MODE == rename ]]; then
        echo; echo "Last chance to back out. If the original and new file names look ok, then proceed."
        read -p "Are you sure you want to rename the files? " -n 1 -r
        if [[ $REPLY =~ ^[Yy]$ ]]; then
                echo; echo "saving relationship between old and new names..."
                reportOldNewFILENAMES > old_new_filenames.log
                
                echo; echo "renaming R1 files..."
                parallel --no-notice -k --link "mv {1}1.fq.gz {2}1.fq.gz" :::: origFileNames.txt :::: newFileNames.txt

                echo "renaming R2 files..."
                parallel --no-notice -k --link "mv {1}2.fq.gz {2}2.fq.gz" :::: origFileNames.txt :::: newFileNames.txt
        else
                echo
                echo "rename aborted, exiting..."
                exit 1
        fi
fi