Sorting BLAST file

Question

[stan.aanhane]

Hi everyone,

I have some blast files which I want to filter. Because I am only interested in the blast results with an E-value of 0.0.

The results are in a .txt file and the E-value is located in column number 10. How can I filter the unwanted results away with bash?

Thank you in advance!

[Gio12]

If selecting for evalues below, let's say 0.001 and assuming your file is tab delimited,

awk -F '\t' '{if ($10 <= 0.001) print $0}' blast_file.txt > Filtered_blast_file.txt

[stan.aanhane]

I'm not sure it's working, because it's taking quite a while for just a test run(50 results)

My file looks like this:

lclav   scf7180005140699        99.970  60186   10      6       1       60181   66205   6023    0.0     1.110e+05

And that for all the blast results

Answer 1

[Gio12]

Ah, is your file space delimited? If so, try this

 awk -F ' ' '{if ($10 <= 0.001) print $0}' blast_file.txt > Filtered_blast_file.txt

[stan.aanhane]

Yes the file is space delimited, but its still not working... When using this command there is no error, but the new txt file empty, and I'm not sure why

[Gio12]

Are you sure your e-value is in column 10?

[stan.aanhane]

Well stupid me... Cant count, it was column eleven. Thank you!

[GenoMax]

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