#!/bin/bash

echo "Removing files to which MSA does not produce an optimal alignment ..."

cd ref1/test2
pwd
rm 1bbt3*
rm 1havA*
rm 1sbp*
rm 1uky*
rm 2cba*
rm 2hsdA*
rm 2pia*
rm 3grs*
rm kinase*
cd -

cd ref1/test3
pwd
rm 1ac5*
rm 1ajsA*
rm 1bgl*
rm 1cpt*
rm 1dlc*
rm 1eft*
rm 1gowA*
rm 1lvl*
rm 1ped*
rm 1pkm*
rm 1taq*
rm 2ack*
rm 2myr*
rm 4enl*
rm arp*
rm gal4*
rm glg*
cd -

cd ref2/test
pwd
rm 1ajsA*
rm 1havA*
rm 1idy*
rm 1lvl*
rm 1pamA*
rm 1ped*
rm 1r69*
rm 1tgxA*
rm 1uky*
rm 1wit*
rm 2hsdA*
rm 2trx*
cd -

cd ref3/test
pwd
rm 1ajsA*
rm 1idy*
rm 1pamA*
rm 1ped*
rm 1r69*
rm 1ubi*
rm 1uky*
rm 1wit*
rm 2myr*
rm 4enl*
rm kinase*
cd -

cd ref4/test
pwd
rm 1ckaA*
rm 1csp*
rm 1lkl*
rm 1mfa*
rm 1pysA*
rm 2abk*
cd -

cd ref5/test
pwd
rm 1ivy*
rm 1qpg*
rm kinase3*
cd -

cd ref6/test
pwd
rm *.msf
cd -

cd ref6/test_1a
pwd
rm *.msf
cd -

cd ref6/test_1b
pwd
rm *.msf
cd -

cd ref6/test_2a
pwd
rm apo_*
rm kringle_*
rm myb_*
rm sh3_*
cd -

cd ref6/test_2b
pwd
rm *.msf
cd -

cd ref6/test_2c
pwd
rm *.msf
cd -

cd ref6/test_3
pwd
rm *.msf
cd -

cd ref6/test_4
pwd
rm ank_1_*
rm ank_2_ref6.*
rm lrr_2_ref6.*
rm lrr_3_ref6.*
rm sh3_1*
rm sh3_2_ref6.*
rm sushi_1_ref6.*
rm sushi_2_ref6.*
rm zf_1_ref6.*
rm zf_2_ref6.*
cd -

cd ref7/test
pwd
rm *.msf
cd -

cd ref8/test
pwd
rm *.msf
cd -

echo "done."
