1

I have a big file of fasta sequence and a list of IDs. I need to grep some sequences with header using their IDs from another file. Here, is the files examples.

File 1:

>AB1234
ACGTAGATA
>AB3456
ACGATAGAT
>AB4567
ACGTGTGA

File 2

>AB1234
>AB3456
  • Generic programming questions are better suited for stackexchange.com – user692175 Nov 14 '17 at 18:11
  • @MichaelBay Is this a generic programming question? – George Udosen Nov 14 '17 at 18:14
  • Which is the id file here? – George Udosen Nov 14 '17 at 18:16
  • @George I think it is and the OP's other question as well. So, a pattern is being shown. But if you want to answer it I'm not stopping you ;) – user692175 Nov 14 '17 at 18:18
  • @George So far the OP asked two questions. So, when I say "OP's other question" it must be askubuntu.com/questions/974459/… Now, how are both questions related to Ubuntu? Answers for both are applicable to pretty much any Linux distro and beyond therefore better suited to main SE. – user692175 Nov 14 '17 at 18:45
1

You can have grep read patterns from a file, one pattern per line, with the -f option:

grep -x -F -A 1 -f 'File 2' 'File 1'

Additionally,

  • -F interprets patterns literally and not as regular expressions,

  • -x only matches entire lines,

  • -A N prints N lines following each match.

0

I got this to work:

for i in $(cut -d" " -f1- file2); do grep -o "$i" file1 | tee -a result.txt; done

Assumption file1 == id file, and file2 == file to be greped

Result.txt:

AB1234
AB3456
  • Please edit your question and show us the id file and the expected outcome – George Udosen Nov 15 '17 at 4:45

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