Edit FASTA header to add organism name after the accession number using perl or sed.
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)?
2 answers
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:
\1print 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 $0}}' your.fasta > new.fasta
fin swimmer
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$ 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
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Thanks to all, it worked!
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
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