How to Grep the complete sequences containing a specific motif in a fasta file using shell command? Also, I want to include the lines beginning with a > before these target sequences.
I found this post :about Grep the complete sequences containing a specific motif in a fasta file similar to my problem but I'm looking for different motif:
My motifs look like that :
SXXXX(F/S)XXXL
All my fasta file in one line and I have more than 300 sequences:
for example:
my sequence :
>sp|Q9H257.2|CARD9_HUMAN RecName: Full=Caspase recruitment domain-containing protein 9; Short=hCARD9
MSDYENDDECWSVLEGSRVTLTSVIDRSRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQKKVQDLTALLSSK
>sp|Q9H37.2|CTYU_HUMAN
HHHSVLEGFRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQKKVQDLTALLSSK
>sp|Q9re7.2|CARer_HUMAN RecName
BKLSVLEGWRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQKKVQDLTALLSSK
The result should be only the first two sequences because they have the motifs SXXXX(F/S)XXXL
>sp|Q9H257.2|CARD9_HUMAN RecName: Full=Caspase recruitment domain-containing protein 9; Short=hCARD9
MSDYENDDECWSVLEGSRVTLTSVIDRSRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQKKVQDLTALLSSK
>sp|Q9H37.2|CTYU_HUMAN
HHHSVLEGFRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQKKVQDLTALLSSK
I tried these command but that returned all three sequences
grep 'S...F\|S\|L.\(.\)\1\{4\}' jara3.fasta -B 1 > jara4.fasta
•
written
by
Jason •
3 answers
using seqkit, for sequences with regex (input from OP):
$ seqkit grep -srip 'S.{4}[FS].{3}L' test.fa
>sp|Q9H257.2|CARD9_HUMAN RecName: Full=Caspase recruitment domain-containing protein 9; Short=hCARD9
MSDYENDDECWSVLEGSRVTLTSVIDRSRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRK
VGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLM
TEVMKLQKKVQDLTALLSSK
>sp|Q9H37.2|CTYU_HUMAN
HHHSVLEGFRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDIL
QRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQK
KVQDLTALLSSK
For sequences without regex:
$ seqkit grep -svrip 'S.{4}[FS].{3}L' test.fa
>sp|Q9re7.2|CARer_HUMAN RecName
BKLSVLEGWRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDIL
QRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQK
KVQDLTALLSSK
Note: I used . in sequence assuming that only alphabets (AA) are present in sequence.
if you happen to have MEME-Suite installed, you also have a very nice fasta-grep which
- knows about IUPAC codes
- ignores newlines and treats sequence
- can emit positions or matches - your pick
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What about if I want to keep only sequences that don’t have the motif” SXXXX (F/S)XXXL” and save that in new fasta file:
The result in that case should be only this sequence:
sp|Q9re7.2|CARer_HUMAN RecName BKLSVLEGWRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQKKVQDLTALLSSK
Read
man grepand particularly read about the-voption, and think about how you would use that with the accepted answer.