bioinformatics Linearizing a FASTA sequence. Linearize a FASTA sequence with AWK
Example
Reading line by line
awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa
one can read this awk script as:
- if the current line (
$0) starts like a fasta header (^>). Then we print a carriage return if this is not the first sequence.(N>0?"\n":"")followed with the line itself ($0), followed with a tabulation (\t). And we look for the next line (next;) - if the current line (
$0) does not start like a fasta header, this is the default awk pattern. We just print the whole line without carriage return. - At the end (
END) we only print a carriage return for the last sequence.
