extracting Genus abundance info from Kraken 2 output file
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8 weeks ago
arshad1292 ▴ 40

Hello

I have a kraken 2 output (k2report.txt file that looks like this:

enter image description here

What I want to do is to extract only number of reads for example for Genus i.e. G with taxid 2316020, 2719313, 207244 and 572511 and so on. I am not interested in D, O or R etc.

I have a large file with many hundred Genuses. Does anyone has any shell/python script that I could use to extract only Genus abundance (number of reads) for sample1, sample2 and sample3?

I would really appreciate your help.

Many thanks,

kraken2 • 284 views
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Do you mean you want to subset your matrix where lvl_type == "G"?

If yes then you can use grep "\tG\t" input-file.

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Yes that's correct that I want a subset of matrix that contains only "G".

I tried your script but it produced nothing...

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Actually, I assumed tab (\t) as the field separator.

If it is the filed separator and is still not working, you should probably add -P to the grep command. Something like this.

grep -P "\tG\t" input-file-name
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Ok this one works. Thanks a lot!

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