temp.sh

grep -B 1 GCCGTAAACGGTGGGCGCTAGGTGTGAGGGTCTTTTCACGACTTTCGTGCCGTAGCTAACGCATT peerj-7636-Long-Read.fasta --color | grep -v '^--$' > test.fa
muscle -in test.fa > test-aligned.fa
facount test-aligned.fa
    446
fasta2oneline test-aligned.fa -o test-oneline.fa
o-smart-trim test-oneline.fa --from-start -o test-good-starts.fa
o-smart-trim test-good-starts.fa --from-end -o test-good-ends.fa
o-trim-uninformative-columns-from-alignment test-good-ends.fa
mv test-good-ends.fa-TRIMMED test-final.fa
facount test-final.fa
    403
entropy-analysis test-final.fa --quick # gives me this: https://imgur.com/yWsYXjg
fastaunique test-final.fa -o test-final-unique.fa
facount test-final-unique.fa
    94
grep '>' test-final-unique.fa | awk 'BEGIN{FS="|"}{print $2}' | head -n 10
    frequency:190
    frequency:70
    frequency:12
    frequency:11
    frequency:9
    frequency:7
    frequency:4
    frequency:4
    frequency:3
    frequency:3
entropy-analysis test-final-unique.fa --quick # gives me this: http://i.imgur.com/dBDGdx5.png