Edit FASTA header to add organism name after the accession number using perl or sed.

Question

[MB]

I have multiple FASTA files consisting of more than a thousand FASTA sequences with FASTA header as follows:

>KXL50728 pep supercontig:ASM157207v1:5WFSArich_Contig_00366:153:473:1 gene:FE78DRAFT_27124 transcript:KXL50728 gene_biotype:protein_coding transcript_biotype:protein_coding description:hypothetical protein
>KXL50729 pep supercontig:ASM157207v1:5WFSArich_Contig_00366:642:809:1 gene:FE78DRAFT_126205 transcript:KXL50729 gene_biotype:protein_coding transcript_biotype:protein_coding description:hypothetical protein

I want to edit these headers as follows:

>KXL50728Acidomycesrichmondensis
>KXL50729Acidomycesrichmondensis

Could anybody please tell me how to do it using Perl or using sed command (most preferable)?

[MB]

Thanks to all, it worked!

[finswimmer]

You're welcome.

Please be so kind to mark all answers as accepted. Doing so everyone can see that this solve your problem.

fin swimmer

[WouterDeCoster]

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Answer 1

[finswimmer]

Hello MB,

try this:

$ sed 's/^\(>\S*\).*/\1Acidomycesrichmondensis/' your.fasta > new.fasta

What we are asking sed to do is: In every line which startet with > keep any character until the first non-whitespace character and replace the rest of the line with Acidomycesrichmondensis.

In the regex:

• ^ matches for the line start
• (...) build a group, so we can output it later
• \S* matches for as many non-whitespace characters as possible
• .* matches for any other character

In the substition:

• \1 print the first group we defined in the regex
• replaces the rest of line with Acidomycesrichmondensis

Another way is to use awk:

$ awk -F " " '{if($0 ~ "^>") {print $1"Acidomycesrichmondensis"} else {print $0}}' your.fasta > new.fasta

fin swimmer

Answer 2

[cpad0112]

$ sed  '/>/ s/\s.*/Acidomycesrichmondensis/' test.fa 
$ awk '/>/ {gsub (" .*","Acidomycesrichmondensis", $0)}1' test.fa

input:

$ cat test.fa 
>KXL50728 pep supercontig:ASM157207v1:5WFSArich_Contig_00366:153:473:1 gene:FE78DRAFT_27124 transcript:KXL50728 gene_biotype:protein_coding transcript_biotype:protein_coding description:hypothetical protein
atgc
>KXL50729 pep supercontig:ASM157207v1:5WFSArich_Contig_00366:642:809:1 gene:FE78DRAFT_126205 transcript:KXL50729 gene_biotype:protein_coding transcript_biotype:protein_coding description:hypothetical protein
atgc

output:

$ awk '/>/ {gsub (" .*","Acidomycesrichmondensis", $0)}1' test.fa 
>KXL50728Acidomycesrichmondensis
atgc
>KXL50729Acidomycesrichmondensis
atgc
$ sed  '/>/ s/\s.*/Acidomycesrichmondensis/' test.fa 
>KXL50728Acidomycesrichmondensis
atgc
>KXL50729Acidomycesrichmondensis
atgc