replace the NP* accession in header of the fasta file with gene name using GFF file

Question

[najibveto]

hello, I would like to know if it is possible replace the NP* accession in header of the fasta file with gene name using GFF file. the fasta file of protein is a fellow:

>NP_037582.1 NADH dehydrogenase subunit 1 (mitochondrion) [Paralichthys olivaceus] 
MISTLITHIINPLALIVPVLLAVAFLTLLERKVLGYMQLRKGPNIVGPYGLLQPIADGIKLFIKEPVRPSTASPVLFLLA PMLALTLALTLWAPMPLPYSTVDLNLGILFVLALSSLAVYSILGSGWASNSKYALVGALRAVAQTISYEVSLGLILLNII ILTGGFTLQTFNTAQEAVWLVLPAWPLAAMWYISTLAETNRAPFDLTEGESELVSGFNVEYAGGPFALFFLAEYSNILLM NTLSAVLFLGASHIPTIATLTAINLMTKAALLSVVFLWVRASYPRFRYDQLMHLIWKNFLPLTLALIIWHLALPTALAGL PPQL

>NP_037583.1 NADH dehydrogenase subunit 2 (mitochondrion) [Paralichthys olivaceus] 
MNPFILTTLLLGLGLGTTITFASSHWLLAWMGLEINTLAIIPLMAQHHHPRAVEATTKYFLTQATAAATLLFASMTNAWL TGQWDIQQMTHPLATTMIIIALALKIGLAPMHSWLPEVLQGLDLTTGLILSTWQKLAPFALLMQIQLDNPTPLIILGLTS TLVGGWGGLNQTQLRKILAYSSIAHLGWMMLILQFSPLLTLLALITYLIMTSSVFLIFKMNKATTINALAISWTKTPILT ALIPLVLLSLGGLPPLTGFMPKWFILQELTKQDLATLATLAALTALLSLYFYLRLSYAMTLTMAPNNLTGTTPWRFSSPQ LTLPLAISSTTATLLLPLAPATLALLTT

>NP_037584.1 cytochrome c oxidase subunit I (mitochondrion) [Paralichthys olivaceus] 
MAITRWFFSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGALLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGN WLIPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSGVEAGAGTGWTVYPPLASNLAHAGASVDLTIFSLHLAGISSILG AINFITTIINMKPTTVTMYQIPLFVWAVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGH PEVYILILPGFGMISHIVAYYSGKKEPFGYMGMVWAMMAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKV FSWLATLHGGNIKWETPLLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIVAAFVHWFPLF TGYTLHSTWTKVHFGVMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYALWNTVSSIGSLMSLVAVIMFLFIIWEAFSAKR EVLSVLMTATNVEWLHGCPPPYHTFEEPAFVRAPLN

>NP_037585.1 cytochrome c oxidase subunit II (mitochondrion) [Paralichthys olivaceus] 
MAHPSQLGFQDAASPLMEELLHFHDHALMIVILISTMVLYIIVAMVTAKLTDKLVLDSQEIEIIWTVLPAIILILIALPS LRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYEDLGFDSYMTPTQDLTPGQFRLLEADHRMVTPVESPIRVLISAEDVL HSWAIPALGVKVDAVPGRLNQTTFIISRPGVFFGQCSEICGANHSFMPIVVEAVPLQHFENWSSLMIEEA

>NP_037586.1 ATP synthase F0 subunit 8 (mitochondrion) [Paralichthys olivaceus] 
MPQLNPAPWFMILVFSWMVFLTIIPPKVLAHTFPNEPTPQSTQKPKTESWNWPWY

>NP_037587.1 ATP synthase F0 subunit 6 (mitochondrion) [Paralichthys olivaceus] 
MMLSFFDQFMSPVYLGIPLIALAIILPWALFPTPSSRWMNNRLLTLQGWFINRFTSQLLLPLNLGGHKWATLFASLMIFL LSINMLGLLPYTFTPTTQLSLNMGLAVPLWLATVIIGMRNQPTHALGHLLPEGTPTALIPVLIIIETISLFIRPLALGVR LTANLTAGHLLIQLIATAAFVLLPIMPMIAISTATLLFLLTLLEVAVAMIQAYVFVLLLSLYLQENV

>NP_037588.1 cytochrome c oxidase subunit III (mitochondrion) [Paralichthys olivaceus] 
MAHQAHPYHMVDPSPWPLTGAIAALLMTSGLAIWFHFHSTTLMTLGTILLILTIFQWWRDVVREATFQGHHTPPVQKGLR YGMILFITSEVLFFLGFFWAFYHASLAPTPELGGFWPPAGITPLDPFEVPLLNTAVLLASGVTVTWAHHSIMEGKRKQAI HSLFLTILLGGYFTFLQALEYHEAPFTIADGVYGATFFVATGFHGLHVLIGSTFLAVCLLRQILHHFTANHHFGFEAAAW YWHFVDVVWLFLYISIYWWGS

>NP_037589.1 NADH dehydrogenase subunit 3 (mitochondrion) [Paralichthys olivaceus] 
MSLLMTIITITALLSTILAIVSFWLPQISPDHEKLSPYECGFDPMGSARLPFSLRFFLIAILFLLFDLEIALLLPLPWGD QLPTPLLTFTWATAVLFLLTLGLIYEWIQGGLEWAE

>NP_037590.1 NADH dehydrogenase subunit 4L (mitochondrion) [Paralichthys olivaceus] 
MTPTHFAFSSAFLLGLTGLAFHRFHLLSALLCLEGMMLSLFIALSLWTLQLDSTNFSASPMLLLAFSACEASAGLALLVA TARTHGTDRLQSLNLLQC

>NP_037591.1 NADH dehydrogenase subunit 4 (mitochondrion) [Paralichthys olivaceus] 
MLKILIPTLMLIPTAWLVKPNWLWPTTLTHSFCISLASLSWLKNLSETGWSSLNLCMATDALSTPLLVLTCWLLPLMILA SQNHTASEPINRQRMYITLLTSLQFFLILAFGATEIIMFYVMFEATLIPTLIIITRWGNQTERLNAGTYFLFYTLAGSLP LLVALLLLQNSAGTLSLLTLHYTDPTHMTSYGDKLWWAGCLLAFLVKMPLYGVHLWLPKAHVEAPIAGSMILAAVLLKLG GYGMIRMMTMLEPLTKELSYPFIIFALWGVVMTGSICLRQTDLKSLIAYSSVSHMGLVAGGVLIQSPWGLTGSLILMIAH GLTSSALFCLANTNYERTHSRTMVLARGLQMALPLMATWWFIASLANLALPPLPNLMGELMIIISLFNWSWWTLALTGTG TLITAGYSLYMFLMTQRGPLPTHILALEPSHTREHLLIALHLLPLILLVLKPELIWGWTA

based on the gff file:

> gff-version 3 !gff-spec-version 1.21 !processor NCBI annotwriter
> !genome-build Flounder_ref_guided_V1.0 !genome-build-accession
> NCBI_Assembly:GCF_001970005.1 !annotation-source NCBI Paralichthys
> olivaceus Annotation Release 100 sequence-region NW_017859641.1 1
> 23627241 species
> https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8255
> NW_017859641.1 RefSeq region 1 23627241 . + .
> ID=NW_017859641.1:1..23627241;Dbxref=taxon:8255;Name=Unknown;breed=gynogenesis;chromosome=Unknown;dev-stage=adult;gbkey=Src;genome=genomic;mol_type=genomic
> DNA;sex=female;tissue-type=blood NW_017859641.1 Gnomon gene 39370
> 44846 . + .
> ID=gene-LOC109628151;Dbxref=GeneID:109628151;Name=LOC109628151;gbkey=Gene;gene=LOC109628151;gene_biotype=protein_coding NW_017859641.1 Gnomon mRNA 39370 44846 . + .
> ID=rna-XM_020085119.1;Parent=gene-LOC109628151;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;Name=XM_020085119.1;gbkey=mRNA;gene=LOC109628151;model_evidence=Supporting evidence includes similarity to: 1 EST%2C 17 Proteins%2C and 100%25
> coverage of the annotated genomic feature by RNAseq alignments%2C
> including 14 samples with support for all annotated
> introns;product=WD40 repeat-containing protein
> SMU1;transcript_id=XM_020085119.1 NW_017859641.1 Gnomon exon 39370
> 39492 . + .
> ID=exon-XM_020085119.1-1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 40402 40612 . + .
> ID=exon-XM_020085119.1-2;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 40851 41003 . + .
> ID=exon-XM_020085119.1-3;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 41172 41282 . + .
> ID=exon-XM_020085119.1-4;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 41412 41540 . + .
> ID=exon-XM_020085119.1-5;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 41692 41811 . + .
> ID=exon-XM_020085119.1-6;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 41922 42038 . + .
> ID=exon-XM_020085119.1-7;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 42250 42377 . + .
> ID=exon-XM_020085119.1-8;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 42511 42637 . + .
> ID=exon-XM_020085119.1-9;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 42717 42884 . + .
> ID=exon-XM_020085119.1-10;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 43227 43379 . + .
> ID=exon-XM_020085119.1-11;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon exon 43829 44846 . + .
> ID=exon-XM_020085119.1-12;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XM_020085119.1;gbkey=mRNA;gene=LOC109628151;product=WD40
> repeat-containing protein SMU1;transcript_id=XM_020085119.1
> NW_017859641.1 Gnomon CDS 39467 39492 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 40402 40612 . + 1
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 40851 41003 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 41172 41282 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 41412 41540 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 41692 41811 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 41922 42038 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 42250 42377 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 42511 42637 . + 1
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 42717 42884 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 43227 43379 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon CDS 43829 43927 . + 0
> ID=cds-XP_019940678.1;Parent=rna-XM_020085119.1;Dbxref=GeneID:109628151,Genbank:XP_019940678.1;Name=XP_019940678.1;gbkey=CDS;gene=LOC109628151;product=WD40 repeat-containing protein SMU1;protein_id=XP_019940678.1
> NW_017859641.1 Gnomon gene 45747 54972 . + .
> ID=gene-LOC109633196;Dbxref=GeneID:109633196;Name=LOC109633196;gbkey=Gene;gene=LOC109633196;gene_biotype=protein_coding

how is it possible to change the protein id into gene name? thank you for your help.

Answer 1

[lieven.sterck]

Not possible I'm afraid. At least not given those two files. Main reason being that those NP* accession numbers do not appear in the GFF file.

You might be able to achieve this after all, if you extract the gene/protein sequences based on the GFF file and compare the sequences to your input file.

[najibveto]

thank you for the reply, the GFF contains other accession numbers for NP, just i put a small part of the fasta file and GFF file. I put the link for both GFF and faa: olive founder protein fasta

the gff file for olive flounder