I came across this one-liner script fu for getting rid of newline characters in a fixed width text file. The idea is to change a file full of entries like:
>IGHV1-18*01
CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAG
GTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGC
TGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTAC
AATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACA
GACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCC
GTGTATTACTGTGCGAGAGA
to
>IGHV1-18*01
CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA
I am not very experienced with AWK so I figured it would be a good learning experience to try and decipher it. However, I am having difficulties. Specifically about multiple blocks coming after each other, is the first block an implicit for-loop?
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa