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Adding special character in fasta headers

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,

sequencing
• 4,122 views • link
updated by Ram Ram • written by vahapel vahapel

2 answers

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.

• 0 views • link
written by Ram Ram

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

• 0 views • link
written by vahapel vahapel

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

• 0 views • link
written by Ram Ram

Try this:

perl -p -e 's/^(>.*)$/$1\/1/g' input.fasta
• 0 views • link
updated by Ram Ram • written by iraun iraun

Dear airan,

Your code works perfectly, thank you for your support!

• 0 views • link
updated by Ram Ram • written by vahapel vahapel

Glad to help :).

• 0 views • link
updated by Ram Ram • written by iraun iraun

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