how to remove description from header?
2
1
Entering edit mode
14 months ago
Sapphire ▴ 10

I have a header like this-

>sp|A0A0H2Z7X0|TPBB_PSEAB Diguanylate cyclase TpbB OS=Pseudomonas aeruginosa (strain UCBPP-PA14) OX=208963 GN=tpbB PE=1 SV=1
MNRRRRYTGSNPSLRRVLYRAHLGVALVAVFTAGLAVTLVGLLTLRAYADPNQQLIARSI
SYTVEAAVVFGDAQAAEESLALIASSEEVSSAIVYDRQGQPLASWHRESTGPLHLLEQQL

And I want my header like this

>A0A0H2Z7X0 
MNRRRRYTGSNPSLRRVLYRAHLGVALVAVFTAGLAVTLVGLLTLRAYADPNQQLIARSI
SYTVEAAVVFGDAQAAEESLALIASSEEVSSAIVYDRQGQPLASWHRESTGPLHLLEQQL

Thank you!

fasta • 651 views
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3
Entering edit mode
14 months ago
biofalconch ★ 1.3k

Under the assumption that everything starts with sp:

sed 's/>sp|/>/;s/|.*//' YourSequences.fa > YourNewSequences.fa
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0
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Thanks a lot

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2
Entering edit mode
14 months ago
bk11 ★ 3.0k

You can use awk too for this propose-

cat yourdata.fasta

>sp|A0A0H2Z7X0|TPBB_PSEAB Diguanylate cyclase TpbB OS=Pseudomonas aeruginosa (strain UCBPP-PA14) OX=208963 GN=tpbB PE=1 SV=1
MNRRRRYTGSNPSLRRVLYRAHLGVALVAVFTAGLAVTLVGLLTLRAYADPNQQLIARSI
SYTVEAAVVFGDAQAAEESLALIASSEEVSSAIVYDRQGQPLASWHRESTGPLHLLEQQL

cat yourdata.fasta |awk 'BEGIN { FS=OFS="|" } /^>/ { print ">" $2; next }1'
>A0A0H2Z7X0
MNRRRRYTGSNPSLRRVLYRAHLGVALVAVFTAGLAVTLVGLLTLRAYADPNQQLIARSI
SYTVEAAVVFGDAQAAEESLALIASSEEVSSAIVYDRQGQPLASWHRESTGPLHLLEQQL
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