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string replacement using a lookup table

 
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# 1  
Old 08-19-2010
string replacement using a lookup table
Dear all thanks for helping in advance.. Know this should be fairly simple but I failed in searching for an answer.

I have a file (replacement table) containing two columns, e.g.:
Code:
ACICJ ACIDIPHILIUM
ACIF2 ACIDITHIOBACILLUS
ACIF5 ACIDITHIOBACILLUS
ACIC5 ACIDOBACTERIUM
ACIC1 ACIDOTHERMUS
ACIAC ACIDOVORAX

which are tab or space delimited (which can be changed easily)

And need to use this table to replace in another file all occurances of strings from the first column by their counterpart strings. Can this be done easily in bash shell?

Thankx again
Last edited by Franklin52; 08-19-2010 at 03:58 PM.. Reason: Please use code tags
# 2  
Old 08-19-2010
Post an example of the other file and the desired output with the given replacement table.
# 3  
Old 08-19-2010
Quote:
Originally Posted by Franklin52
Post an example of the other file and the desired output with the given replacement table.
Example input and output would be like the attached. The table would be used to identify and replace the strings..
input.txt (180 Bytes) 
output.txt (246 Bytes) 
# 4  
Old 08-19-2010
MySQL
Code:
# sed 's/F5\|F2/DITHIOBACILLUS/g;s/CJ/DIPHILIUM/;s/C5/DOBACTERIUM/' infile
(PARDP_1_PE905,(ACIDITHIOBACILLUS_1_PE2435,ACIDITHIOBACILLUS_1_PE2737)100)80)88;
(ACIDIPHILIUM_2_PE3051,METRJ_9_PE1586)95;
(ACIDOBACTERIUM_1_PE2202,ACIBL_1_PE895)96;
(ACIDITHIOBACILLUS_1_PE2306,ACIDITHIOBACILLUS_1_PE2606)100,MAGSM_1_PE17)92,

# 5  
Old 08-19-2010
Quote:
Originally Posted by ygemici
Code:
# sed 's/F5\|F2/DITHIOBACILLUS/g;s/CJ/DIPHILIUM/;s/C5/DOBACTERIUM/' infile
(PARDP_1_PE905,(ACIDITHIOBACILLUS_1_PE2435,ACIDITHIOBACILLUS_1_PE2737)100)80)88;
(ACIDIPHILIUM_2_PE3051,METRJ_9_PE1586)95;
(ACIDOBACTERIUM_1_PE2202,ACIBL_1_PE895)96;
(ACIDITHIOBACILLUS_1_PE2306,ACIDITHIOBACILLUS_1_PE2606)100,MAGSM_1_PE17)92,

I guess this is an ad hoc suggestion, which will not do ( as the replacement table is hundreds and the input file - thousands of lines.
# 6  
Old 08-19-2010
Quote:
Originally Posted by roussine
I guess this is an ad hoc suggestion, which will not do ( as the replacement table is hundreds and the input file - thousands of lines.
i cant know your file how many lines and line lenghths..

you can check this Smilie
sed, a stream editor

if you cant success try this..
Code:
 
# perl -pe 's/F5/DITHIOBACILLUS/g;s/F2/DITHIOBACILLUS/;s/CJ/DIPHILIUM/;s/C5/DOBACTERIUM/' infile

# 7  
Old 08-19-2010
Quote:
Originally Posted by ygemici
i cant know your file how many lines and line lenghths..

you can check this Smilie
sed, a stream editor

if you cant success try this..
Code:
 
# perl -pe 's/F5/DITHIOBACILLUS/g;s/F2/DITHIOBACILLUS/;s/CJ/DIPHILIUM/;s/C5/DOBACTERIUM/' infile

sed is a powerful thing, i have this page in bookmarks Smilie, thanks
But still my lines to replace are many more..
 
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