i want to replace accession number with gene name?

Question

[Neel]

Hi i have fasta file of sequence where i want to replace CP077971.1_494> MexR respectively in that fasta file for all the genes were there, Is there anyway to do that?

  >CP077971.1_494 P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpMexR
MNYPVNPDLMPALMAVFQHVRTRIQSELDCQRLDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSRVHDELFAPLTPVEQATLVHLLDQCLAAQPLEDI
    >CP077971.1_1265 P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpnalC
    MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIEEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG
    >CP077971.1_1470 P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpnalD
    MRRTKEDSEKTRTAILLAAEELFLEKGVSHTSLEQIARAAGVTRGAVYWHFQNKAHLFNEMLNQVRLPPEQLTERLSGCDGSDPLRSLYDLCLEAVQSLLTQEKKRRILTILMQRCEFTEELREAQERNNAFVQMFIELCEQLFARDECRVRLHPGMTPRIASRALHALILGLFNDWLRDPRLFDPDTDAEHLLEPMFRGLVRDWGQASSAP
    >CP077971.1_2660 P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpMexT
    MNRNDLRRVDLNLLIVFETLMHERSVTRAAEKLFLGQPAISAALSRLRTLFDDPLFVRTGRSMEPTARAQEIFAHLSPALDSISTAMSRASEFDPATSTAVFRIGLSDDVEFGLLPPLLRRLRAEAPGIVLVVRRANYLLMPNLLASGEISVGVSYTDELPANAKRKTVRRSKPKILRADSAPGQLTLDDYCARPHALVSFAGDLSGFVDEELEKFGRKRKVVLAVPQFNGLGTLLAGTDIIATVPDYAAQALIAAGGLRAEDPPFETRAFELSMAWRGAQDNDPAERWLRSRISMFIGDPDSL

Thank you!

Answer 1

[rpolicastro]

You can use seqkit replace

seqkit replace -p "^(\S+)(.*\s)(\S+)$" -r "\$3\$2\$3" input.fasta

>pumpMexR P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpMexR
MNYPVNPDLMPALMAVFQHVRTRIQS
>pumpnalC P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpnalC
MNDASPRLTERGRQRRRAMLDAATQA

If it's always 'pump' before the gene name you can further clean it up.

seqkit replace -p "^(\S+)(.*\spump)(\S+)$" -r "\$3\$2" input.fasta

>MexR P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pump
MNYPVNPDLMPALMAVFQHVRTRIQS
>nalC P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pump
MNDASPRLTERGRQRRRAMLDAATQA

If it's not always pump you'll need to create a tab delimited key-value file such as.

CP077971.1_494  MexA
CP077971.1_1265 nalC

And use that key-value file (which I will call replacements.tsv below) for replacement.

seqkit replace -p "^(\S+)(.*)" -r "{kv}\$2" -Kk replacements.tsv input.fasta

>MexA P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpMexR
MNYPVNPDLMPALMAVFQHVRTRIQS
>nalC P_aeruginosa_ZPPH33resistance-nodulation-cell division (RND) antibiotic efflux pumpnalC
MNDASPRLTERGRQRRRAMLDAATQA

[Neel]

Thank you Sir for your reply. Now its done.