How to grep the outputs of awk, line by line? - awk

Question

Let's say I have the following text file:
$ cat file1.txt outputs
MarkerName Allele1 Allele2 Freq1 FreqSE P-value Chr Pos
rs2326918 a g 0.8510 0.0001 0.5255 6 130881784
rs2439906 c g 0.0316 0.0039 0.8997 10 6870306
rs10760160 a c 0.5289 0.0191 0.8107 9 123043147
rs977590 a g 0.9354 0.0023 0.8757 7 34415290
rs17278013 t g 0.7498 0.0067 0.3595 14 24783304
rs7852050 a g 0.8814 0.0006 0.7671 9 9151167
rs7323548 a g 0.0432 0.0032 0.4555 13 112320879
rs12364336 a g 0.8720 0.0015 0.4542 11 99515186
rs12562373 a g 0.7548 0.0020 0.6151 1 164634379
Here is an awk command which prints MarkerName if Pos >= 11000000
$ awk '{ if($8 >= 11000000) { print $1 }}' file1.txt
This command outputs the following:
MarkerName
rs2326918
rs10760160
rs977590
rs17278013
rs7323548
rs12364336
rs12562373
Question: I would like to feed this into a grep statement to parse another text file, textfile2.txt. Somehow, one pipes the output from the previous awk command into grep AWKOUTPUT textfile2.txt
I would like each row of the awk command above to be grepped against textfile2.txt, i.e.
grep "rs2326918" textfile2.txt
## and then
grep "rs10760160" textfile2.txt
### and then
...
Naturally, I would save all resulting rows from textfile2.txt into a final file, i.e.
$ awk '{ if($8 >= 11000000) { print $1 }}' file1.txt | grep PIPE_OUTPUT_BY_ROW textfile2.txt > final.txt
How does one grep from a pipe line by line?
EDIT: To clarify, the one constraint I have is that file1.txt is actually the output of a previous pipe. (I'm trying to simplify the question somewhat.) How would that change the answer?

Answer 1

awk + grep solution:
grep -f <(awk '$8 >= 11000000{ print $1 }' file1.txt) textfile2.txt > final.txt
-f file - obtain patterns from file, one per line

Answer 2

You can use bash to do this:
bash-3.1$ echo "rs2326918" > filename2.txt
bash-3.1$ (for i in `awk '{ if($8 >= 11000000) { print $1 }}' file1.txt |
grep -v MarkerName`; do grep $i filename2.txt; done) > final.txt
bash-3.1$ cat final.txt
rs2326918
Alternatively,
bash-3.1$ cat file1.txt | (for i in `awk '{ if($8 >= 11000000) { print $1 }}' |
grep -v MarkerName`; do grep $i filename2.txt; done) > final.txt
The switch grep -v tells grep to reverse its usual activity and print all lines that do not match the pattern. This switch "inVerts" the match.

Answer 3

only using awk can do this for you:
$ awk 'NR>1 && NR==FNR {if ($8 >= 110000000) a[$1]++;next} \
{ for(i in a){if($0~i) print}}' file1.txt file2.txt> final.txt