How to linearize a FASTA sequence using awk.

README.md

Linearize a fasta sequence

awk -f linearizefasta.awk < input.fa

or

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa

Format back to fasta

tr "\t" "\n" < linearized.tsv

if you know your fasta header have a length < 60

tr "\t" "\n" < linearized.tsv | fold -w 60

linearizefasta.awk

/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;}
     {printf("%s",$0);}
END  {printf("\n");}

Thanks. I find it quite useful