Question: how to extract/grep lines containing specific word?
0
gravatar for arsilan324
3 months ago by
arsilan32450
arsilan32450 wrote:

Hi all,

I am trying to extract lines containing specific word from tabular file! I am using this command

grep "[Sorghum bicolor]" file.txt

Here [Sorghum bicolor] is the word (desired string) for the line which i want to retain. But this comamnd print everything as it is and doesn't filter. I have used -E and -i as well. Also, I want to do the reverse, print lines without this word. Can you please comment? Thanks in advance

awk sed grep • 197 views
ADD COMMENTlink modified 3 months ago by Kevin Blighe21k • written 3 months ago by arsilan32450
0
gravatar for Kevin Blighe
3 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

Just do:

grep -w "Sorghum bicolor" file.txt

...and the inverse:

grep -w "Sorghum bicolor" -v file.txt
ADD COMMENTlink written 3 months ago by Kevin Blighe21k

For some reason, the output file is still empty. Can you comment on it? Here is the link to the file

ADD REPLYlink written 3 months ago by arsilan32450

You'll probably need

grep -w "[Sorghum bicolor]" file.txt
ADD REPLYlink written 3 months ago by WouterDeCoster29k
1

Thanks! - some things about your file: the formatting is 'all over the place' and it does not look to be in the proper encoding. It looks like you ported it from Excel or something? I cannot confirm because, perhaps, DropBox has modified something.

Look at the file in VIM an you will see many ^M characters, and also run wc -l on the file an you'll get 0 lines. Ensure that the encoding is correct first. Try functions like dos2unix, etc ( take a look here: https://kb.iu.edu/d/acux ).

ADD REPLYlink written 3 months ago by Kevin Blighe21k
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