Add text to fasta header based in a list

Question

[cabraham03]

hi, I have a fasta files of a genome, something like:

Strain-01.faa

>IMEHDJCA_03186 Serine/threonine-protein phosphatase 2
MEFKHRFIDGSRYQRIFVIGDIHGKLALLQDTLKRVDFHGERDLLISVGDLIDRGPDSVG
VLDYYQTHDWFEAVMGNHEWMMVNALDAQNKLERSEKEAYFIKIWHRNGCEWSQNL
>IMEHDJCA_03187 Serine transporter
MKESRETLNFSDTLPTETWTKHDTHWVLSLFGTAVGAGILFLPINLGIGGFWPLVLLALL
AFPMTFWGHRALARFVLSSKQADADFTDVVEEHFGAKAGRLISLLYFLSIFPILLIYGVG
>IMEHDJCA_03189 hypothetical protein
MNNQRHGITFGIERIGSQTILVFKATGTLTHQDYQAIAPVLEAALAGINRQQMNMLADIS
EFSGWEPRAAWDDFQLGLKIGFSVNKVAVYGDKNWQELAAKVGSWFISGEMKSFGD

so I want to add an extra ID based in a list within a Genes_file.txt file.

Genes_file.txt

ID      Gene        Strain-01       Strain-02       Strain-03
ID_01   pphB        IMEHDJCA_03186  DIBHEKPI_01648  LLMDBGDK_00598
ID_02   group_1001  IMEHDJCA_03187  DIBHEKPI_01635  LLMDBGDK_00611
ID_03   group_1002  IMEHDJCA_03189  DIBHEKPI_01628  LLMDBGDK_00616

for example for the fasta Strain-01.faa file has the IMEHDJCA_03186 id corresponding to the Strain-01, so I want to add the ID_01 number of the column ID in Genes_file.txt to the header of the sequence, something like, for ID_01 correspond to IMEHDJCA_03186, ID_02 to IMEHDJCA_03187, ID_03 to IMEHDJCA_03189, and the result will be like:

Strain-01_edited.faa

>ID_01 IMEHDJCA_03186 Serine/threonine-protein phosphatase 2
MEFKHRFIDGSRYQRIFVIGDIHGKLALLQDTLKRVDFHGERDLLISVGDLIDRGPDSVG
VLDYYQTHDWFEAVMGNHEWMMVNALDAQNKLERSEKEAYFIKIWHRNGCEWSQNL
>ID_02 IMEHDJCA_03187 Serine transporter
MKESRETLNFSDTLPTETWTKHDTHWVLSLFGTAVGAGILFLPINLGIGGFWPLVLLALL
AFPMTFWGHRALARFVLSSKQADADFTDVVEEHFGAKAGRLISLLYFLSIFPILLIYGVG
>ID_03 IMEHDJCA_03189 hypothetical protein
MNNQRHGITFGIERIGSQTILVFKATGTLTHQDYQAIAPVLEAALAGINRQQMNMLADIS
EFSGWEPRAAWDDFQLGLKIGFSVNKVAVYGDKNWQELAAKVGSWFISGEMKSFGD

I just want to add a ID code of the Genes_file.txt to the header of the fasta file of each strain file.

Any idea to do this ? in bash or R, or any other way ?

Thanks so much

[cpad0112]

with seqkit:

$ seqkit -w 0 --quiet replace -K -p '^(\w+)( .+)$' -r '{kv} ${1} ${2}' -k <(awk -v OFS="\t" 'NR > 1 {print $3,$1}' test.txt) test.fa


>ID_01 IMEHDJCA_03186  Serine/threonine-protein phosphatase 2
MEFKHRFIDGSRYQRIFVIGDIHGKLALLQDTLKRVDFHGERDLLISVGDLIDRGPDSVGVLDYYQTHDWFEAVMGNHEWMMVNALDAQNKLERSEKEAYFIKIWHRNGCEWSQNL
>ID_02 IMEHDJCA_03187  Serine transporter
MKESRETLNFSDTLPTETWTKHDTHWVLSLFGTAVGAGILFLPINLGIGGFWPLVLLALLAFPMTFWGHRALARFVLSSKQADADFTDVVEEHFGAKAGRLISLLYFLSIFPILLIYGVG
>ID_03 IMEHDJCA_03189  hypothetical protein
MNNQRHGITFGIERIGSQTILVFKATGTLTHQDYQAIAPVLEAALAGINRQQMNMLADISEFSGWEPRAAWDDFQLGLKIGFSVNKVAVYGDKNWQELAAKVGSWFISGEMKSFGD  

Answer 1

[Pierre Lindenbaum]

sed -f <(awk '{printf("s/^>%s/>%s %s/\n",$3,$1,$3);}' Genes_file.txt) Strain-01.faa