Split multifasta file using awk command
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.
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Jean-Karim Heriche
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fec2 •
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fec2 •
2 answers
Try
awk -F "|" '/^>/ {close(F) ; F = substr($1,2,length($1)-1)".fasta"} {print >> F}' yourfile.fa
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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
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.