Row extraction problems

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7.3 years ago

Janey ▴ 30

Hi At first I thought that this work is so simple for me. I have File1 (ID list) and File2 (reference file). I want to extract some full rows by ID list from File2. I am not familiar to R and Python. I used "grep -f File1 File2" and some other commands but i got errors. Can anyone show me a simple solution to solve this problem.

RNA-Seq • 1.5k views

ADD COMMENT • link 7.3 years ago by Janey ▴ 30

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man join / http://superuser.com/questions/25302

ADD REPLY • link 7.3 years ago by Pierre Lindenbaum 161k

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What errors did you get? grep -f is a pretty standard approach.

ADD REPLY • link 7.3 years ago by Alex Reynolds 35k

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Hi Alex I run this command "grep -f File1.txt (IDs) File2.txt(Ref) > output" several times for avoiding error but I output file containing the entire of file 2.

ADD REPLY • link 7.3 years ago by Janey ▴ 30

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Maybe you need a literal string search, if you need exact matches: $ grep -Ff file1.txt file2.txt > output

ADD REPLY • link 7.3 years ago by Alex Reynolds 35k

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I thank you very much Alex, your command solved my problem.

ADD REPLY • link 7.3 years ago by Janey ▴ 30

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when I extracted the columns, folowing command was pretty good: cut -f 1,2,3 File_name | sed 's/[\t]/,/g' > output

ADD REPLY • link 7.3 years ago by Janey ▴ 30

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