Hello, I’m trying to find a way to replace a string of exactly 100 Ns in a fasta sequence with some other character, ex Z.
It’s a multi line fasta too long to be converted to a single line, so sed won’t work.
Text editing tools will replace any string of 100 Ns. If the string is 99 or 101 Ns it shouldn’t be changed.
I’m stumped. Any suggestions will be appreciated.
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Anibesa •
A seqkit solution.
Here's some example data.
>seq_1
ATGNNNNNNNNNNTCGA
>seq_2
ATGNNGCGAGGCCCTTT
>seq_3
NNNNNNNNNNCCCCTGA
>seq_4
NNNGGTATTGCGTTATG
>seq_5
NNNNNNNNNNNNTTTAA
>seq_6
ATGNNNNNNNNNNNNGG
>seq_7
ATGTCCGNNNNNNNNNN
>seq_8
AAAGTCTAANNNNNNNN
Replacing Ns with Zs only if there are just 10 Ns.
EDIT: Correction courtesy of shenwei356
seqkit replace -s -p "([^N]|^)N{10}([^N]|$)" -r $(echo -e '${1}'$(printf 'Z%.0s' {1..10})'${2}') test.fasta
And the result.
>seq_1
ATGZZZZZZZZZZTCGA
>seq_2
ATGNNGCGAGGCCCTTT
>seq_3
ZZZZZZZZZZCCCCTGA
>seq_4
NNNGGTATTGCGTTATG
>seq_5
NNNNNNNNNNNNTTTAA
>seq_6
ATGNNNNNNNNNNNNGG
>seq_7
ATGTCCGZZZZZZZZZZ
>seq_8
AAAGTCTAANNNNNNNN
The two flanking non-N bases are missing (G and T for seq_1).
$ seqkit replace -s -p "([^N]|^)N{10}([^N]|$)" -r $(printf 'Z%.0s' {1..10}) test.fasta
>seq_1
ATZZZZZZZZZZCGA
$ seqkit replace -s -p "([^N]|^)N{10}([^N]|$)" -r $(echo -e '${1}'$(printf 'Z%.0s' {1..10})'${2}') test.fasta
>seq_1
ATGZZZZZZZZZZTCGA
Thank you for the correction to my (obvious) mistake! I've edited the post with the correct answer.
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Perfect! Thank you.
Please check the comment below.