Protein fasta file header shorten
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5 weeks ago

Dear all,

I want to short my fasta file header, which is like below, I listed two sequences. At the same time I want to keep all the sequences exactly the way they are.

>lcl|VSMA01000001.1_prot_KAB5584702.1_1 [locus_tag=GE09DRAFT_1165795] [db_xref=InterPro:IPR002198,JGIDB:Conioc1_1165795] [protein=tetrahydroxynaphthalene reductase] [protein_id=KAB5584702.1] [location=join(1826..1931,1988..2458,2736..2863,2927..3064)] [gbkey=CDS] 
MPGLTTNTGKYDQIPGPLGLASASLEGKVALVTGAGRGIGREMAQELGRRGAKVIVNYANSQESAEEVVQAIKKSGSDAA SIKANVSDVDQIVRMFDEAVKVFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFNINTRGQFFVAREAYKHLEVGGRLILM GSITGQAKGVPKHAVYSGSKGTIETFVRCMAIDFGDKKITVNAVAPGGIKTDMYHAVCREYIPNGINLTDDEVDEYACTW SPLHRVGLPIDIARVVCFLASQDGEWINGKVLGIDGAACM 

>lcl|VSMA01000001.1_prot_KAB5584703.1_2 [locus_tag=GE09DRAFT_1165796] [db_xref=InterPro:IPR021840,JGIDB:Conioc1_1165796] [protein=hypothetical protein] [protein_id=KAB5584703.1] [location=complement(join(3193..3215,3871..4374,4440..5628,5725..5886,5941..5989,6050..6066,6130..6234,6286..6495,6547..6561,6622..6728,6843..7103,7155..7719))] [gbkey=CDS] 
MFHPSRRRAEQTAYEYNIQATEDHEHDHGVVNLSAEKRRRPRGKRPNYKPTALKWPFIVAQILVLVIAMGLIIWAEKAMP DSDSTAIIDPLPSKGLPERSVKPEFGKHFRRDNTSGVVETATSQLDVQETTLTGGDGLITPGLGSTNGPADNVKTAVTDD

And I only want to keep the header like this:

>GE09DRAFT_1165795 
MPGLTTNTGKYDQIPGPLGLASASLEGKVALVTGAGRGIGREMAQELGRRGAKVIVNYANSQESAEEVVQAIKKSGSDAA SIKANVSDVDQIVRMFDEAVKVFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFNINTRGQFFVAREAYKHLEVGGRLILM GSITGQAKGVPKHAVYSGSKGTIETFVRCMAIDFGDKKITVNAVAPGGIKTDMYHAVCREYIPNGINLTDDEVDEYACTW SPLHRVGLPIDIARVVCFLASQDGEWINGKVLGIDGAACM
>GE09DRAFT_1165796
MFHPSRRRAEQTAYEYNIQATEDHEHDHGVVNLSAEKRRRPRGKRPNYKPTALKWPFIVAQILVLVIAMGLIIWAEKAMP DSDSTAIIDPLPSKGLPERSVKPEFGKHFRRDNTSGVVETATSQLDVQETTLTGGDGLITPGLGSTNGPADNVKTAVTDD

I would be super greatful for any help.

Thanks, Yanfang

header shorten fasta • 279 views
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See if this works:

$ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < id | awk ' {if ($0 ~ /^>/) {split($0,a,"="); split(a[2],b,"]"); print ">"b[1]} {print $9} }' | tr "\t" "\n"  | fold -w 80
>GE09DRAFT_1165795
MPGLTTNTGKYDQIPGPLGLASASLEGKVALVTGAGRGIGREMAQELGRRGAKVIVNYANSQESAEEVVQAIKKSGSDAA
SIKANVSDVDQIVRMFDEAVKVFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFNINTRGQFFVAREAYKHLEVGGRLILM
GSITGQAKGVPKHAVYSGSKGTIETFVRCMAIDFGDKKITVNAVAPGGIKTDMYHAVCREYIPNGINLTDDEVDEYACTW
SPLHRVGLPIDIARVVCFLASQDGEWINGKVLGIDGAACM
>GE09DRAFT_1165796
MFHPSRRRAEQTAYEYNIQATEDHEHDHGVVNLSAEKRRRPRGKRPNYKPTALKWPFIVAQILVLVIAMGLIIWAEKAMP
DSDSTAIIDPLPSKGLPERSVKPEFGKHFRRDNTSGVVETATSQLDVQETTLTGGDGLITPGLGSTNGPADNVKTAVTDD
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Entering edit mode

Hey GenoMax,

Thanks you so much. I managed to do this, and I adapted your code with a code I read somewhere else.

awk 'BEGIN{FS=" "}{if(NF>1) {split($2,a,"="); split(a[2],b,"]"); printf(">%s\n",b[1])}else{print $0}}' in.fasta > out.fasta

I posted it here, hope it can be useful for others.

Thanks so much for your help. Yanfang

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Entering edit mode
5 weeks ago

input (works with flattened fasta):

$ cat test.fa 
>lcl|VSMA01000001.1_prot_KAB5584702.1_1 [locus_tag=GE09DRAFT_1165795] [db_xref=InterPro:IPR002198,JGIDB:Conioc1_1165795] [protein=tetrahydroxynaphthalene reductase] [protein_id=KAB5584702.1] [location=join(1826..1931,1988..2458,2736..2863,2927..3064)] [gbkey=CDS] i
atgc
>lcl|VSMA01000001.1_prot_KAB5584703.1_2 [locus_tag=GE09DRAFT_1165796] [db_xref=InterPro:IPR021840,JGIDB:Conioc1_1165796] [protein=hypothetical protein] [protein_id=KAB5584703.1] [location=complement(join(3193..3215,3871..4374,4440..5628,5725..5886,5941..5989,6050..6066,6130..6234,6286..6495,6547..6561,6622..6728,6843..7103,7155..7719))] [gbkey=CDS]
cagt

output:

$ awk -F 'locus_tag=|]' 'NR %2 == 1 {print ">"$2 }; NR % 2 == 0 {print}' test.fa

>GE09DRAFT_1165795
atgc
>GE09DRAFT_1165796
cagt

$ sed -r '/^>/ s/.*locus_tag=(.*_[0-9]+)\]\s\[db_xref.*/>\1/' test.fa
>GE09DRAFT_1165795
atgc
>GE09DRAFT_1165796
cagt
  • sed function here expects locus tag and db_xref in each header
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Entering edit mode
5 weeks ago
Dunois ▴ 970

Here's something way more succinct in sed:

sed -E 's/^.*locus_tag\=([A-Za-z0-9_]+).*$/>\1/g' test.fa 
>GE09DRAFT_1165795
MPGLTTNTGKYDQIPGPLGLASASLEGKVALVTGAGRGIGREMAQELGRRGAKVIVNYANSQESAEEVVQAIKKSGSDAA SIKANVSDVDQIVRMFDEAVKVFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFNINTRGQFFVAREAYKHLEVGGRLILM GSITGQAKGVPKHAVYSGSKGTIETFVRCMAIDFGDKKITVNAVAPGGIKTDMYHAVCREYIPNGINLTDDEVDEYACTW SPLHRVGLPIDIARVVCFLASQDGEWINGKVLGIDGAACM 

>GE09DRAFT_1165796
MFHPSRRRAEQTAYEYNIQATEDHEHDHGVVNLSAEKRRRPRGKRPNYKPTALKWPFIVAQILVLVIAMGLIIWAEKAMP DSDSTAIIDPLPSKGLPERSVKPEFGKHFRRDNTSGVVETATSQLDVQETTLTGGDGLITPGLGSTNGPADNVKTAVTDD
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$ sed -r '/^>/ s/.*locus_tag=([[:alnum:]]+).*$/>\1/' test.fa
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