Replacing a character in multiple fasta files within a folder

Question

[alexis.diaz]

How can I replace a character in multiple fasta files within a folder? More specific, I want to replace the character "?" by "N" through multiple fasta files.

Thanks in advance for your advice.

Answer 1

[Mensur Dlakic]

Assuming that your files all end in .fasta, go to that directory and type:

find . -name "*.fasta" | xargs -i sed -i 's/\?/N/g' {}

Yet another approach:

for f in *.fasta ; do sed -i 's/\?/N/g' $f ; done

[alexis.diaz]

Hi Mensur Dlakic,

Thanks so much! It worked. I also found another way: sed -i -se 's/?/N/g' *.fasta.

Answer 2

[Pierre Lindenbaum]

look at find /path/to/dir -exec and Remove unwanted characters from FASTA file

[alexis.diaz]

Thanks for your prompt response, however I do not want to remove the character "?", I want to replace it by "N". I tried sed -i 's/?/N/g' *, but with no success.

The fact that all of my files end with the letter "A" before the format denomination seems to be an issue for the command.

Do you have an idea how to solve this?