I am a biologist who is new to linux and am having difficulty generating a script to do what I want it to do! I have tried basic grep commands, but even that does not give me back the data I want.
I have many files that are all currently in .xslx and I'm not sure if they need to be .csv or .txt for this to work... Each of these files has ~90,000 lines.
Basically I want a script that will ask me what I am looking for:
Then I want to look through all of the lines in all of my files (~200) and see if $GeneName is present in field 13 (it may be present multiple times in the one file, or not at all).
If it is present in field 13, I want the entire line/s it is in, plus the file name/s it is found in to be printed to a .txt file.
I have tried using grep command and it just gives me back all lines from the file, not the lines containing $GeneName. I apologise I do not have a better unix background, but I have been trying for days and I just cannot generate it!!! I would appreciate any help.
There is a heading line at the top of each file, and each subsequent line starts with chr. For this example, I would be wanting to identify the lines containing WASH7P in file1.txt and file2.txt (or if this would work with .csv files?)
file1.txt
file2.txt
I would like be asked to type in GeneName (i.e. WASH7P) and the output in a .txt file to be something like:
Many thanks,
Kelly
Last edited by Franklin52; 09-14-2011 at 04:00 AM..
Reason: Please use code tags for code and data samples, thank you
Hi Kelly,
Go through this and let me know if there's any problem. Use tags while posting your queries. The code below is working fine for me and giving the expected output.
Thank you so so much Chubler_XL, this is what happened when I ran your script:
Any clue why?
Something I forgot to mention, I would like the output file to be $GeneName_date.txt please
Thank you so much again for your help,
Kelly
---------- Post updated at 09:22 PM ---------- Previous update was at 09:16 PM ----------
Dear Mayur,
Thank you so much for providing me with this script, but I am having the same problem as I have had before
When I ran your script
All it did was concatenate the 6 .txt files I have in that directory? I just want single lines from these files that contain $GeneName.
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