Insert blank line if grep not found

Shell Programming and Scripting
1

Hi all,

I've googling around forum regarding my prob, the nearest would same as thread tittled Insert blank line if grep not found, but she/he did not mention the solution, so I would like to request your help

I've this task, to search in file2 based on pattern in file1 and output it to file3. If the pattern is not found I want it to put it as blank line in file3.

file1

ACGTGCAT
ACGGTACG
CGTGATGC
GTAGCAGT
GGCATGCT
GTGACGTA

file2

ACGTGCAT      34
GGCATGCT      54
GTGACGTA      24

output (file3)

ACGTGCAT     34
<blank line>
<blank line>
<blank line>
GGCATGCT     54
GTGACGTA     24

I've been trying using this command

for f in `cat file1` ; do grep "$f" file >> file3 ; done

but it dont keep blank space. I want to have result as file3 (shown above) so I can paste back to file1 and it show the same sequence position.

thanks in advance

2 
while read line1
do
    line2=`grep "$line1" file2`
    if [ ! -z "$line2" ] ; then
        echo "$line2" >> file3
    else
        echo "" >> file3
    fi
done < file1
2 Likes
3

Hi Rohon,

Superb!! :b::b: Exactly as i want.

Thanks, you saved my day

1 Like
4 
 
awk 'NR==FNR{a[$1]=$0;next;}{if(a[$1]) print a[$1];else print "";}' file2 file1 > file3
5

wrong message