split_big_final_report

##Part 1: If final report is not split into 1 subject per file, this will split it up. Otherwise don't run this part!

#User: List name of final report file here
final_report=Akesogen_Cohen_FC_CNV_V.1_FinalReport.txt

#Creates a header
head -n10 $final_report > header.txt

#Column $1 is the default here, but the number should correspond to whatever number the subjects are named in
awk  'NR>10{print >$1}' $final_report


for file in $(ls | grep -v $final_report | grep -v header.txt | grep -v temp)
do
 echo $file
 cat header.txt $file > temp && mv temp $file
done


## Part 2:

#Get sample name from the final report text file
#Column $1 is the default here, but the number should correspond to whatever number the subjects are named in


for files in $(ls | grep -v $final_report | grep -v header.txt | grep -v temp)
do
 samplename=$(awk 'NR==12{print $1}' $files)
 echo $files $samplename >> sample_ids.txt
 samplename=""
done