Shell Programming and Scripting

awk -F'[^A-Z0-9_]+' 'FNR==NR{a[$1]=$2;next}{for(n=1;n<=NF;n++)if($n in a)gsub($n,a[$n])}1' table text.txt > result.txt

awk 'FILENAME=="table" {arr[$1]=$2}
       FILENAME=="bigfile { for(i=1; i< NF; i++) {if($i in arr) {$i=arr[$i]}}
                                    print $0;
                                  } ' table bigfile > newbigfile

import fileinput
table={}
for line in open("table"):
    line=line.strip().split()
    table[line[0]] = line[-1]
for line in fileinput.FileInput("file",inplace=1,backup=".txt"):
    line=line.strip()
    for i,j in table.iteritems():
        if i in line: line=line.replace(i,j)
    print line

$ 
$ cat config.txt
VIFIS1_1_PE1836 VIBRIO_FISCHERI
VIPAR1_1_PE1662 VIBRIO_PARAHAEMOLYTICUS
VIPAR1_1_PE2235 VIBRIO_PARAHAEMOLYTICUS
VIPAR1_2_PE1355 VIBRIO_PARAHAEMOLYTICUS
VIVUL1_1_PE1801 VIBRIO_VULNIFICUS      
$                                      
$ cat bigfile.txt                      
blah blah blah VIFIS1_1_PE1836 blah blah
blah blah blah                          
blah blah VIVUL1_1_PE1801 blah blah VIPAR1_1_PE2235
blah blah                                          
$                                                  
$
$ perl -ne 'BEGIN { open(CF,"config.txt");
>                   while (<CF>) {split; $x{$_[0]}=$_[1]}
>                   close(CF)
>                 }
> { chomp; @y=split/ /; $buf="";
>   foreach $i (@y) {$buf .= (defined($x{$i}) ? $x{$i} : $i)." "};
>   $buf=~s/ $//; print "$buf\n";
> }' bigfile.txt
blah blah blah VIBRIO_FISCHERI blah blah
blah blah blah
blah blah VIBRIO_VULNIFICUS blah blah VIBRIO_PARAHAEMOLYTICUS
blah blah
$
$