Converting FASTQ to FASTA with SED/AWK

Question

I have a data in that always comes in block of four in the following format (called FASTQ):

@SRR018006.2016 GA2:6:1:20:650 length=36
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN
+SRR018006.2016 GA2:6:1:20:650 length=36
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!+!
@SRR018006.19405469 GA2:6:100:1793:611 length=36
ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+SRR018006.19405469 GA2:6:100:1793:611 length=36
7);;).;);;/;*.2>/@@7;@77<..;)58)5/>/

Is there a simple sed/awk/bash way to convert them into this format (called FASTA):

>SRR018006.2016 GA2:6:1:20:650 length=36
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN
>SRR018006.19405469 GA2:6:100:1793:611 length=36
ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

In principle, we want to extract the first two lines in each block-of-4 and replace @ with >.

user_8344060 · Answer

You might be interested in bioawk, it is an adapted version of awk which is tuned to process fasta files

bioawk -c fastx '{ print ">"$name ORS $seq }' file.fastq

Note: BioAwk is based on Brian Kernighan's awk which is documented in "The AWK Programming Language", by Al Aho, Brian Kernighan, and Peter Weinberger (Addison-Wesley, 1988, ISBN 0-201-07981-X) . I'm not sure if this version is compatible with POSIX.

Converting FASTQ to FASTA with SED/AWK

13 Answers