I am trying to use a .txt file with around 5000 patterns (spaced with a line) to search through another file of 18000 lines for any matches. So far I've tried every form of grep and awk I can find on the internet and it's still not working, so I am completely stumped.

Here's some text from each file.



There's no extra spaces or anything.


snpid hg18chr bp a1 a2 zscore pval CEUmaf
rs3131972       1       742584  A       G       0.289   0.7726  .
rs3131969       1       744045  A       G       0.393   0.6946  .
rs3131967       1       744197  T       C       0.443   0.658   .
rs1048488       1       750775  T       C       -0.289  0.7726  .
rs12562034      1       758311  A       G       -1.552  0.1207  0.09167
rs4040617       1       769185  A       G       -0.414  0.6786  0.875
rs4970383       1       828418  A       C       0.214   0.8303  .
rs4475691       1       836671  T       C       -0.604  0.5461  .
rs1806509       1       843817  A       C       -0.262  0.7933  .

The file.txt was downloaded directly from a med directory.

I'm pretty new to UNIX so any help would be amazing!

This is copied from stackoverflow. I have tried every single thing that's been recommended but the output is still blank. Am I maybe missing a syntax issue or something in my text files?

P.S. Things I've tried:

grep -Fw -f Pattern.txt File.txt
fgrep -f Pattern.txt File.txt

awk '{kount++;print   $0}' $FILENAME | fgrep -f - Pattern.txt

awk 'NR==FNR{pats[$0]; next} $2 in pats' Pattern.txt File.txt

closed as off-topic by jasonwryan, Bernhard, Anthon, Michael Homer, garethTheRed Nov 27 '14 at 8:20

This question appears to be off-topic. The users who voted to close gave this specific reason:

  • "This question has been posted on multiple sites. Cross-posting is strongly discouraged; see the help center and community FAQ for more information." – jasonwryan, Bernhard, Anthon, Michael Homer, garethTheRed

  • 2
    Please show us what you have tried. – cuonglm Nov 27 '14 at 6:12
  • Crossposted stackoverflow.com/questions/27163970/… – jasonwryan Nov 27 '14 at 6:30
  • @BananaMannock Why your output is blank? Because you don't have a same pattern inside Pattern.txt file from your File.txt. For testing, add rs12562034 in your Pattern.txt file and try the commands given for you and you will luck ;) – αғsнιη Nov 27 '14 at 16:55

Try this with GNU grep:

grep -f Pattern.txt File.txt

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