grep multiple rows from file.

Shell Programming and Scripting
1

Hi, I have file1 that contains many columns as show the first three below:

"At1g29930"     198     2105
"At5g46430"     5569     9576
"At1g64740"     1908     2505
"At5g46430"     6717     11317
"At1g64740"     453     655
"At1g12470"     33     18
"At1g80680"     149     262
"At1g23040"     6351     2620
"At1g31390"     -18     87
"At5g19860"     -30     68
"At1g80470"     -49     85
"IC-At1g29930-1 um"     2203     1713
"IC-At1g29930-5 um"     4873     3668
"At5g19860.1"     90     132
"At5g20520"     6     81
"At1g80680.1"     123     186

What I want is to extract the rows from file1 by the first column that contains my following list in file2:

At5g46430
At1g64740
At1g12470
At1g80680
At1g23040
At1g31390
At5g19860
At1g80470
At1g29930
At5g20520

Members in file2 are unique but in file1 they may have multiple copies or iso-forms, like At1g80680 and At1g80680.1. My challenge is to get the rows in file1 that matches exactly by

grep -wf file2 file1 > file3;

If there is multiple match, get one (or the first one?) and ignore the rest (eg At1g29930, not IC-At1g29930-1 um or IC-At1g29930-5 um), but it did not work. Any help is highly appreciated!

2

something like this,

$sed -n 's/\"\(At[^ \.]\)\" ./\1/gp' input | sort -u
At1g12470
At1g23040
At1g29930
At1g31390
At1g64740
At1g80470
At1g80680
At5g19860
At5g20520
At5g46430

3 
 
awk -v t="\"" '/^\"?At/&&NR==FNR{gsub(t,"",$1);a[$1]=1;next}
 {if(a[$1]) print}' file1 file2
4

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