CNV files don't have the name as the actual ID, this extracts the id from the file and lists the filename and id next to eachother. A couple of other functions are in here as well.

cnv_filename

#list all files, make folder for each


ls * | grep .idat | awk 'BEGIN{FS="_"}{print $1}' | sort -u > folderlist.txt

for folders in $(cat folderlist.txt)
do
 mkdir $folders
done

for files in $(ls * | grep .idat )
do
 fmove=$(echo $files | awk 'BEGIN{FS="_"}{print $1}' )
 echo "moving $files to $fmove"
 mv $files "$fmove"/$files
done


for files in $(ls /oasis/scratch/comet/amaihofer/temp_project/psy2/intensities/ | grep psy2_4)
do
 fname=$(cat /oasis/scratch/comet/amaihofer/temp_project/psy2/intensities//$files | awk 'NR==15 {print $2}')
 echo $files $fname >> psy2_files.txt
 fname=""
done

for files in $(ls /cygdrive/g/broad_download/CVB_PTSD_Roberts_GUTS_PsychChip/idats)
do
 f2=$(echo $files | awk 'BEGIN{FS="_"}{print $1}')
 #echo "Looking for $files plate in missing plate list "
 if grep -q $f2 /cygdrive/g/psy2_3/platelist.txt.txt;
 then 
 echo $f2 found will move
 mv /cygdrive/g/broad_download/CVB_PTSD_Roberts_GUTS_PsychChip/idats/$files /cygdrive/g/broad_download/psy2/CVB_PTSD_GUTS_NHS_Idat/idat/g4/.
 fi
done