How to add characters to start of fasta header

Zapages · 01-13-2015, 06:12 AM

Hi Everyone,

I have small question. How do we add characters to a start of a fasta header?

I know we can add it to the end of Fasta header using this.

Code:

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

Although I could use Galaxy, but I am trying to avoid it for this and learn a bit of perl at the same time.

Thank you in advance.

-Zapages

ajk · 01-13-2015, 08:01 AM

You're almost all the way there: just move the $1 to the end of the replacement string. Also, it'll be a little easier if you take the greater than (>) out of the match.

Code:

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

For this, you really don't need the /g at the end since you're matching the whole line and, because the .* is greedy, the $ at the end of the match string is unnecessary as well.

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01-13-2015, 06:12 AM	#1
Zapages Member Location: NJ Join Date: Oct 2012 Posts: 97	How to add characters to start of fasta header Hi Everyone, I have small question. How do we add characters to a start of a fasta header? I know we can add it to the end of Fasta header using this. Code: perl -p -e 's/^(>.*)$/$1-New_Header_info/g' input.fasta > output.fasta Although I could use Galaxy, but I am trying to avoid it for this and learn a bit of perl at the same time. Thank you in advance. -Zapages

01-13-2015, 08:01 AM	#2
ajk Junior Member Location: Massachusetts Join Date: Feb 2009 Posts: 1	You're almost all the way there: just move the $1 to the end of the replacement string. Also, it'll be a little easier if you take the greater than (>) out of the match. Code: perl -p -e 's/^>(.)/>New_Header_Info $1/' input.fasta > output.fasta For this, you really don't need the /g at the end since you're matching the whole line and, because the . is greedy, the $ at the end of the match string is unnecessary as well.