Pull out multiple lines with grep patternfile


 
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# 1  
Pull out multiple lines with grep patternfile

Hi,
I'm trying to get lines from a file using identifiers in the first two columns. I have used:

cat MasterFile.txt | grep -f Pattern.txt

and the lines I want display on screen. If I try to put them in a file the file is created but stays empty:

cat MasterFile.txt | grep -f Pattern.txt > output.txt

Also: If I use the whole pattern file (tested with 12 top lines from my pattern file to start) it doesn't even display on screen.....

Any ideas how I can do this? Very frustrating that the process seems to work but then hit the brick wall!!!
# 2  
u can try cat MasterFile.txt | grep -f - Pattern.txt

this should work
# 3  
Please use CODE tags!

If you don't show us the contents of MasterFile.txt and Pattern.txt, there isn't much we can do to figure out why your pipelines aren't working (although they could easily be made faster and more efficient by getting rid of the unneeded cat commands).

What system are you using. (Are you by any chance using any files produced on a Windows system with carriage return and newline characters at the end of each line instead of just a newline?)
# 4  
I have a file1 as
>NC_0123
>NC_0124
>NC_0125

and file 2
>NC_0123
ACGTGCGTC
>NC_0125
ACTGCGTCGTCG
>NC_0126
ACTGCGTGCGTCG

i want the output as
>NC_0123
ACGTGCGTC
>NC_0125
ACTGCGTCGTCG

i am using cat file1 | grep -A 1 -wf - file2 but its not working

P.S. have used the same command n number of times with the same type of files nad it works! God knws y its nt working here!

---------- Post updated at 04:48 AM ---------- Previous update was at 04:47 AM ----------

I am sry fr nt using code tags!
# 5  
Hw abt wrt n pln Nglsh?

Nd, dnt hijack oths' threads!
# 6  
I am sorry If I offended someone in any way! I am really new to this forum and yes I am learning the rules now. I never meant to hijack any threads!! It's just that I was in a difficult situation and found a similar post in this thread so posted a reply.

Any solution to the above problem will be highly appreciated thanks! Smilie
# 7  
I'd suggest you open a new thread and give FGPonce a chance to have his/her request worked upon and answered.
You might even want to delete / edit-to-nil your posts in this thread.
 

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