notes: mmseqs2 example call

notes/mmseqs2.sh

@@ -20,10 +20,14 @@ mmseqs createdb ${asm2} ${db2}
 mmseqs createindex ${db1} tmp
 mmseqs createindex ${db2} tmp
 
-# search
+# search: query target
 mmseqs search ${db1} ${db2} ${out12} tmp --start-sens 1 --sens-steps 3 -s 7 --threads 5 -v 3
 mmseqs search ${db2} ${db1} ${out21} tmp --start-sens 1 --sens-steps 3 -s 7 --threads 5 -v 3
 
 # tables
 mmseqs convertalis ${db1} ${db2} ${out12} ${out12}.tsv --format-output "query,target,qcov,tcov,evalue,pident,nident,gapopen,mismatch,alnlen,qstart,qend,qlen,tstart,tend,tlen"
 mmseqs convertalis ${db2} ${db1} ${out21} ${out21}.tsv --format-output "query,target,qcov,tcov,evalue,pident,nident,gapopen,mismatch,alnlen,qstart,qend,qlen,tstart,tend,tlen"
+
+# stats
+awk -F'\t' '$3 >= 0.9 && $4 >= 0.9 && $6 >= 0.9 {print $0}' ${out12}.tsv | cut -f1 | sort | uniq | wc -l
+awk -F'\t' '{printf "%.1f\n", $4}' ${out21}.tsv | sort | uniq -c | sed 's/^\s\+//' | sort -k2,2 -n
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