Shell Programming and Scripting

ma <<EOF
H_X.fas
auto
n
/home/multalign/dna.tab

n
msf
y
aligned
l
100.90
EOF

[host@localhost temp]$ ma <<EOF
H_X.fas
auto
n
/home/multalign/dna.tab

n
msf
y
aligned
l
100.90
EOF

Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890

Sequence file:  
Input format (gcg, mul, embl, genbank, auto): (def = auto)  
Other Input parameters (y/n) ?: (def=n) 
Symbol comparison table: (def = blosum62.tab) 
Gap value ? (def = value in Symbol comparison file):   
Other Alignment parameters (y/n) ?: (def=n) 
Output format (msf, mul, doc): (def = msf) 
Other Output parameters (y/n) ?: (def=n) 
Ouput order as (aligned, input)) ?: (def=aligned) 
Save cluster as a drawing or as a list (d/l) ?: (def = l) 
 Consensus levels (default = 90 and 50) ? :  Reading H_X.fas
Sequence #  26
Reading /home/multalign/dna.tab
Saving Configuration.
Clustering with fast
Action successful                                                              
Saving H_X.clu
Aligning
gnl|hbvcds|AB059659_ ..................with gnl|hbvcds|EF157291_ Position #    gnl|hbvcds|AB059659_ ...................with gnl|hbvcds|EU498228_ Position #   gnl|hbvcds|AB059659_ ....................with gnl|hbvcds|FJ356715_ Position #  gnl|hbvcds|AB059659_ .....................with gnl|hbvcds|FJ356716_ Position # gnl|hbvcds|AB059659_ ......................with gnl|hbvcds|HM066946_ Position #gnl|hbvcds|AB059659_ .......................with gnl|hbvcds|HM117850_ Position gnl|hbvcds|AB059659_ ........................with gnl|hbvcds|HM117851_ Positiongnl|hbvcds|AB179747_ ................with gnl|hbvcds|AB059660_ ..Position #    gnl|hbvcds|AB059660_ ...................with gnl|hbvcds|AB059659_ Position #   gnl|hbvcds|AB059659_ ....................with gnl|hbvcds|AB205010_ Position #  gnl|hbvcds|AB059659_ .....................with gnl|hbvcds|HM117851_ Position # gnl|hbvcds|AB059659_ ......................with gnl|hbvcds|AB064315_ Position #gnl|hbvcds|AB059659_ .......................with gnl|hbvcds|AY090454_ .PositionAction successful  2 iteration(s)                                              
Saving H_X.cl2
Saving H_X.msf
[host@localhost temp]$

ma -c:/home/multalign/dna.tab -k:100.90 H_X.fas

#!/bin/bash                                                                                                   

for x in H #This has more variable which i will loop like {A..H}
do
    echo $x
    for y in PreS1 PreS2 S X
    do
        /home/multalign/tab/ma -c:/home/multalign/dna.tab -k:100.90 ${x}_${y}.fas
        echo
        echo Done: ${x}_${y}.msf
        echo
    done

done