Adding special character in fasta headers

Question

[vahapel]

Dear all,

I want to add a special character "/1" to eacf of fasta header (at the end of fasta header) in a 8.5 GB fasta file. I used following command;

perl -p -e 's/^(>.*)$/$1-New_Header_info/g' input.fasta > output.fasta

This code is ok when we put any character in place of "New_Header_info", unfortunately when I typing "/1", i could not get the result.

Is there any solution for this ?

Thanks for all reply,

Answer 1

[Ram]

Pretty sure bioawk can help you :)

bioawk -c fastx '{ print $name"\1\n"$seq; }' <inFile.fasta

If you face an error with \1, try \\1 - this is just in case awk recognizes \1 as a capture pattern - this may also be the reason you face the problem in your code.

[vahapel]

Dear RamRS, thank you introducing "bioawk" to me!. It looks like very useful for my project

[Ram]

You're welcome. It changed my life too :)

Answer 2

[iraun]

Try this:

perl -p -e 's/^(>.*)$/$1\/1/g' input.fasta

[vahapel]

Dear airan,

Your code works perfectly, thank you for your support!

[iraun]

Glad to help :).