Converting FASTQ to FASTA with SED/AWK

Posted by neversaint on Stack Overflow See other posts from Stack Overflow or by neversaint
Published on 2009-10-09T07:22:51Z Indexed on 2010/05/09 20:08 UTC
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sed

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awk

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unix

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bash

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linux

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 >.

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