truncation scripts

Make a lists of files you want to process, and call it all.txt.

Then run following in bash:
while read fna;
do read qual;
echo "Running $fna";
time truncate_fasta_qual_files.py -f $fna -q $qual -b 220 -o filtered/;
echo "";
done < all.txt

I hope this works.

quality scores script

In a terminal, cd to folder with all the converted .qual files.
Get a list of all .qual files in that folder by running:
ls *.qual > quallist.txt

Analyse the quality of every .qual file in that list by running:
while read line;
do time quality_scores_plot.py -q $line -o quality_histograms/$line/;
done < quallist.txt