#!/bin/bash

# Blast All against All

# Fail on unbound variables. E.g. when arguents are not given
set -u

# Takes 1 argument - the input FASTA file
fasta_in=$1

formatdb -pT -i $fasta_in
blastall -m 8 -p blastp -i $fasta_in -d $fasta_in -o $fasta_in.blastm8.tab

# Output description
##  1. Query (The query sequence id)
##  2. Subject (The matching subject sequence id)
##  3. % id
##  4. alignment length
##  5. mistmatches
##  6. gap openings
##  7. q.start
##  8. q.end
##  9. s.start
## 10. s.end
## 11. e-value
## 12. bit score