#!/bin/bash
# 1. Create the list_org_157.txt by saving it from the main-www-page 
# 2. Change the -ipwd to you directory of sequences.
# 3. Change the -opwd to where you want the profiles to be


# Naive model for penta-mers
~/bin/classifier -crr -f_f lista_org_157.txt -ipf .fna -ipwd /local/dalevi/data -opwd /local/dalevi/profiles -osf n4_ -k 4 -frac 0.1 -m 2 -s 222

# Markov model for penta-mers
~/bin/classifier -crr -f_f lista_org_157.txt -ipf .fna -ipwd /local/dalevi/data -opwd /local/dalevi/profiles -osf m4_ -k 4 -frac 0.1 -m 0 -s 222 -nofna

# Variable length Markov model
~/bin/classifier -crr -f_f lista_org_157.txt -ipf .fna -ipwd /local/dalevi/data -opwd /local/dalevi/profiles -pseudo -osf 768_ -npar 768 -minc 5 -kmax 9 -frac 0.1 -s 2
22 -nofna