Commit dc5319f7 authored by Denis Jacob Machado's avatar Denis Jacob Machado

Bash script to execute awa-trim.py and awa-map.py for different k-mers using the example data.

parent 5b6c5e77
#!/bin/bash
set -o errexit
function part1 {
for k in 13 15 17 19 21 23 25 27 29 31 ; do
python3 awa-trim.py -s consensus.fa -w ${k} -l 15000 -o example_${k}mer.fa
done
}
function part2 {
for f in example_*mer.fa ; do
k=$(echo ${f} | grep -o -E "[0-9]+")
python3 awa-map.py -i index_${k}mer -f example_${k}mer.fa -r reads.fq -s alignment_${k}mer.sam -p 4 -v &> log_${k}mer.log
done
}
part1 # Clip putative circular sequences from within the given scaffold
part2 # Get stats for each putative fragment
exit
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