This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to extract organisms name from the headers in a multi-fasta file?

Hi, I am trying to extract organisms' names from the headers in a multi-fasta file named input.fa shown below:

>KZR5864_Org_name_nam_strain.11
GHTKKLACWQRTTAAFFGYYWOPPEEDSSSSLKKDDIIPFTQWENMAATGGFDMLLAAPP
>OIA4716.3_Org_other_name_bla_bla
AHHTTIPLNCCWWETRQKLLSSNNNMTIPAHGFSSLLKANCDSM
>SMAR_08120_Other_org_name_bla
AGTHHKKLAMNCWTQEREYPPILLSSDFMNCCVTTQQLAK

what I want is to obtain is the organism name in the header. I have tried the following sed command but I am unable to check for the alphanumerics, therefore, I am also getting the digits after the first underscore like in third header.

sed -eT -e 's|_|&\n|;D' input.fa > out.txt

Expected results:

Org_name_nam_strain.11
Org_other_name_bla_bla
Other_org_name_bla

Please tell me how to obtain org names only. Thanks!

fasta regex sed header
• 3,851 views • link
updated by finswimmer finswimmer • written by MB • MB

Are these all of the possible formats for your FASTA headers? I ask because the regex from either sed, Perl, or awk won't really matter if there is more variety than what you show in your example FASTA headers. The regex using any of these programs has to be exactly tailored to the input, which if I had to guess is more diverse than what you show here.

• 0 views • link
written by jean.elbers jean.elbers

Yes, these are all the possible formats for fasta headers in the input file.

• 0 views • link
written by MB • MB

This works with your example. I can't guarantee it will work with all of the lines.

grep ">" input.fa |perl -pe "s/>\w+\.\d+\_(.+)/\1/"|perl -pe "s/>[A-Za-z0-9]+_(.+)/\1/"|perl -pe "s/[0-9]+_(.+)/\1/"
• 0 views • link
written by jean.elbers jean.elbers

Thanks, it worked! It is giving all the organisms names.

• 0 views • link
written by MB • MB

Or:

grep '>' input.fa | sed 's/.*[0-9]_//'

Grep picks lines starting with '>' and sed removes everything before "[0-9]_" (including match).

• 0 views • link
written by ahaswer ahaswer

It worked too! Thanks!

• 0 views • link
written by MB • MB

with sed:

$ sed -rn 's/.*(org\.*)/\1/pgi' test.txt  (or)
$ sed -n '/>/ s/.*[0-9]_//p' test.txt

Org_name_nam_strain.11
Org_other_name_bla_bla
org_name_bla

with awk:

$ awk '/>/ {sub(".*[0-9]_","",$0);print}' test.txt

Org_name_nam_strain.11
Org_other_name_bla_bla
Other_org_name_bla
• 0 views • link
written by cpad0112 cpad0112

1 answer

So the organism name is everything which follows after a number and an underscore.

$ grep -oP '(?<=[0-9]_).*' input.fa
  • -o forces grep to return only the match and not the whole line
  • -P activate perl regular expression which is needed for the positive look behind
• 0 views • link
written by finswimmer finswimmer

Log in to answer this question.

More posts like this