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Converting FASTQ to FASTA with SED/AWK

Asked 2009-10-09T07:22:51.063
19

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 >.

awk sed bioinformatics fasta fastq
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4 Answers

7

just awk , no need other tools

# awk '/^@SR/{gsub(/^@/,">",$1);print;getline;print}' file
>SRR018006.2016 GA2:6:1:20:650 length=36
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN
>SRR018006.19405469 GA2:6:100:1793:611 length=36
ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
answered 2009-10-09T11:57:09.287
3

I'd write

awk '
    NR%4 == 1 {print ">" substr($0, 2)}
    NR%4 == 2 {print}
' fastq > fasta
answered 2011-06-30T22:33:48.867
2

This is the fastest I've got, and I stuck it in my .bashrc file:

alias fq2fa="awk '{print \">\" substr(\$0,2);getline;print;getline;getline}'"

It doesn't fail on the infrequent but not impossible quality lines that start with @... but does fail on wrapped FASTQ, if that's even legal (it exists though).

answered 2011-10-27T23:06:31.307
1

Here's the solution to the "skip every other line" part of the problem that I just learned from SO:

while read line
do
    # print two lines
    echo "$line"
    read line_to_print
    echo "$line_to_print"

    # and skip two lines
    read line_to_skip
    read line_to_skip
done

If all that needs to be done is change one @ to >, then I reckon

while read line
do
    echo "$line" | sed 's/@/>/'
    read line
    echo "$line"

    read line_to_skip
    read line_to_skip
done

will do the job.

answered 2009-10-09T07:39:06.273

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