Hi,
I'm a newbie so please be patient.
I have a fasta file like this:
>gi|820716087|gb|AKG62099.1| eIF-2 alpha kinase [Leishmania donovani]
MAKKKNECHSCRLVQAYNTCENDEIKDEIDIIVNTYENVRVSGKSAAHYRVLVPLTSESHPSRRVTLEIR
VVPGYPYVVPAINLLFPPGLQPGCEGTLSEYEVKQMAKEVLNNIQPCLPSGMPCMMQIVSTVASIVECSI
DPPSQQQNGKAQGEPKVLSAGQSSSLTPVPLKAKEALKLSLFAFHLLKKCCHMKNPESNEEAASNFDWLV
KYLLDSVRIFPEAARSFFPWNGISSSRAFAANIESALALPPDQQGLPKWLWEDEGRNPRIQQGSEGRYRN
>gi|820957452|pdb|4WZH|B Chain B, Dihydroorotate Dehydrogenase From Leishmania Viannia Braziliensis
MGSSHHHHHHSSGLVPRGSHMASMTGGGQMGRGSMSLQVGILGNTFANPFMNAAGVMCSTEEELAAMTES
TSGSLITKSCTPALREGNPAPRYYTLPLGSINSMGLPNKGFDFYLAYSARHHDYSRKPLFISISGFSAEE
NAEMCKRLAPVAAEKGVILELNLSCPNVPGKPQVAYDFDAMRRYLAAISEAYPHPFGVKMPPYFDFAHFD
AAAEILNQFPKVQFITCINSIGNGLVIDVETESVVIKPKQGFGGLGGRYVFPTALANVNAFYRRCPGKLI
FGCGGVYTGEDAFLHVLAGASMVQVGTALHEEGAAIFERLTAELLDVMAKKGYKALDEFRGKVKAMD
How do I transform the names to have something like this:
>gb_AKG62099.1
MAKKKNECHSCRLVQAYNTCENDEIKDEIDIIVNTYENVRVSGKSAAHYRVLVPLTSESHPSRRVTLEIR
VVPGYPYVVPAINLLFPPGLQPGCEGTLSEYEVKQMAKEVLNNIQPCLPSGMPCMMQIVSTVASIVECSI
DPPSQQQNGKAQGEPKVLSAGQSSSLTPVPLKAKEALKLSLFAFHLLKKCCHMKNPESNEEAASNFDWLV
KYLLDSVRIFPEAARSFFPWNGISSSRAFAANIESALALPPDQQGLPKWLWEDEGRNPRIQQGSEGRYRN
>pdb_4WZH
MGSSHHHHHHSSGLVPRGSHMASMTGGGQMGRGSMSLQVGILGNTFANPFMNAAGVMCSTEEELAAMTES
TSGSLITKSCTPALREGNPAPRYYTLPLGSINSMGLPNKGFDFYLAYSARHHDYSRKPLFISISGFSAEE
NAEMCKRLAPVAAEKGVILELNLSCPNVPGKPQVAYDFDAMRRYLAAISEAYPHPFGVKMPPYFDFAHFD
AAAEILNQFPKVQFITCINSIGNGLVIDVETESVVIKPKQGFGGLGGRYVFPTALANVNAFYRRCPGKLI
FGCGGVYTGEDAFLHVLAGASMVQVGTALHEEGAAIFERLTAELLDVMAKKGYKALDEFRGKVKAMD
The idea is to have just the genebank id, or, if it's not in the name, one of the ids and where is it from
Saludos :)
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radha.jg •
awk 'BEGIN{FS="|"}{if(NF>1) {printf(">%s_%s\n", $3, $4)}else{print $0}}' foo.fa > fixed.fa
Excellent. Thank you very much. I seriously need to learn how to program in awk.
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radha.jg •
In case of sp_, how do I use an unique identifier like gi? I assume that $1 and $2 will do
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radha.jg •
You could check the number of fields (NF) in a more elaborate way and use $1 and $2 as needed.
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Devon Ryan
Hey Devon Ryan,
Could you please help me with some modification of your code for my problem?
I also want to shorten the fasta file sequence header, which looks like this:
>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_KAB5584705.1_4 [locus_tag=GE09DRAFT_52] [db_xref=InterPro:IPR010730,JGIDB:Conioc1_52] [protein=heterokaryon incompatibility protein-domain-containing protein] [protein_id=KAB5584705.1] [location=10796..11233] [gbkey=CDS]
MPTRLLEIDPQANSRHIRLVSDTGILLKERYAALSHCWGKSPTNTTTKAVFVSHTQGIDILSLSKTFQHTIFVTRELGIR
YLWIDSLCIIQDDEDDWKREAENMADVFANAFVTIAASASTDGDGGLFYPRALETERSGTVRWTI
And I want the header to be this:
>GE09DRAFT_1165795
>GE09DRAFT_52
And I tried your code with
awk 'BEGIN{FS=" "}{if(NF>1) {printf(">%s\n", $2)}else{print $0}}' in.fasta > out.fasta
It gave me the results:
>[locus_tag=GE09DRAFT_1165795]
..
SO How can I cut the [locus_tag= and ]?
I would be really appreciated for any help.
Thanks!
Yanfang
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wang-yanfang •
I think I figured this out by adapting two codes together.
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
Thanks all the help!
Yanfang
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wang-yanfang •
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