Shell Programming and Scripting

Code:

 
grep -f genes.txt refseq_exons.txt 
grep -wFf genes.txt refseq_exons.txt > output.txt
awk 'FNR==NR {a[$1]; next} $1 in a' genes.txt refseq_exons.txt > output.txt

The above seem to match the records but not all of them and I'm not sure why., I am just trying to match the gene name in genes.txt to all entries with that name in refseq_exons.txt. Thank you .

Your genes.txt contains trailing spaces.
grep then requires that the trailing spaces are in refseq_exons.txt, too!
The awk command, by using $1, while reading the first file (where FNR is NR), strips off the spaces. ($0 would retain the spaces).
But in the second file it does the match in the 1st field $1, you obviously want the last field $NF! (NF is the number of fields, $NF is the last field, and $(NF-1) is the second last field).

Code:

awk 'FNR==NR {a[$1]; next} ($NF in a)' genes.txt refseq_exons.txt

Looks like the field you need to match on is in the last column of refseq_exons.txt so your awk should read:

Code:

awk 'FNR==NR {a[$1]; next} $NF in a' genes.txt refseq_exons.txt > output.txt

Edit: Too slow MadeInGermany replied while I was typing - Hey post 3000 .

Congratulations Chubler_XL on completing 3000 posts . I too have dream to help people as much as I can and learn from people as I can which is only possible only by useful posting. Congratulations again !!


Thanks,
R. Singh