Split multifasta file using awk command

Question

[fec2]

Hi,

I have a FASTA file and need to split the file into multiple FASTAs, one gene per file. Refer to the post Splitting A Fasta File, I have tried below

awk -F "|" '/^>/ {close(F) ; F = $1".fasta"} {print >> F}' yourfile.fa

However, every output file name contain symbol ">", for example ">my_contig_name.fasta".

May I know how to avoid to have ">" in the output file name? Thanks.

[ATpoint]

Please use the search function, this has been asked many times before:

Split multifasta file in individual sequence file

How to split a multi fasta file into individual chromosomes

splitting multifasta-file in python

Split the multiple sequences file into a separate files

[fec2]

Hi,

Actually I have tried several command from these posts, but only the above command work for me. However, this command has created ">" in the output name.

Answer 1

[AK]

Try changing the command to:

awk -F "|" '/^>/ {close(F); ID=$1; gsub("^>", "", ID); F=ID".fasta"} {print >> F}' yourfile.fa

If not limited to awk, you can use: seqkit split --by-id yourfile.fa.

[fec2]

Thank you very much!

Answer 2

[Jean-Karim Heriche]

Try

awk -F "|" '/^>/ {close(F) ; F = substr($1,2,length($1)-1)".fasta"} {print >> F}' yourfile.fa

[fec2]

Thank you very much!