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I have an output from vcfutils.pl vcf2fq with specified minimal depth, and it means that nucleotides with not enough depth are lowercase. I would like to change them to gaps. I could do it in higher language but I would like to know the solution in bash. I have found simple solution to replace all lowercase to uppercase:

awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' in.fna > out.fna

but I would like to replace lowercase with -. The first row need to be omitted. Could you help me? Thanks

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3 Answers 3

Reset to default
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The following sed command will do the trick.

sed -e '/^[^>]/ s/[a-z]/\-/g' in.fna > out.fna

Lines starting with > will be escaped and the lowercase characters will be replaced with - .

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  • $\begingroup$ Thaks. I did try to do it without making new copy, but this works. $\endgroup$
    – robinj
    Nov 7, 2018 at 12:48
  • $\begingroup$ you can pipe this to vcfutils.pl vcf2fq output. $\endgroup$
    – arup
    Nov 9, 2018 at 5:31
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You could try it with sed.
Replace all lower-case chars with - in lines not starting with >:

sed -e '/^>/!s/[a-z]/-/g' in.fa
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You can also use this solution where tr command from linux can solve your problem:

tail -n +2 in.fna | tr '[:lower:]' '-'

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