Sort command not working as expected
- by user964689
If anybody can help me to write a loop to iterate over files in a folder it would save me a huge amount of time. I think it must be quite a simple solution ,but I currently don't know how to nest a loop within a loop. So far I have this script:
cd /folderlocation/
for i in `</textfile_containing_lines_to_iterate_through`
do
#size=`echo $i | perl -nE '/:([\d-]+)/ && say abs(eval $1)'`
#echo "$size"
zcat dataset | head -n 18 > temp"$i".vcf
tabix dataset $i >> temp"$i".vcf
vcftools --window-pi 1000000 --vcf temp10individuals"$i".vcf >> run_summary.txt
cat out.windowed.pi >> outputfile_2
#rm temp*
done
grep -v "PI" outputfile_2 > outputfile
rm outputfile_2
I need to expand this so that the script will run multiple times, through all of the 'textfiles_containing_lines_to_iterate_through'. Currently I change the name of the textfile manually each time and re-run the script. So I'd need a loop that does this for file in folder, and also that uses the name of the file as part of the outputfile name so that I can match an output file to an inputfile.
Any help would be really useful and greatly appreciated!
Many thanks in advance.
