How To Add Specific Word To Fasta Header

Question

[Palu]

I have more than 5000 fasta sequence in a file and want to add a word , for instance phosphate, to header of all sequence. please tell me a PERL solution for that.

Answer 1

[brentp]

inplace:

    perl -pi -e "s/^>/>phosphate-/g" your.fasta

or new file:

    perl -p -e "s/^>/>phosphate-/g" your.fasta > phosphate.fasta

to add it to the end, use this regexp

    's/^(>.*)$/$1-phosphate/g'

[Palu]

THANKS brentp, but i want to in the last of my header..is there any trick

[brentp]

@palu I edited my answer, see the last line.

[Palu]

thank you very much sir. for any layman person like me. final code will be like that

perl -p -e "s/^(>.*)$/$1-phosphate/g" your.fasta > phosphate.fasta

[brentp]

except you should use single quotes: perl -p -e 's/^(>.*)$/$1-phosphate/g' in.fasta > out.fasta

[Neilfws]

palu, if you like Brent's answer the best, you should select it as such (hover over the votes to do that).

[Palu]

@newlife thanks i do that

Answer 2

[Daniel]

An easy way with sed:

sed 's/>.*/&_phosphate/' foo.in >bar.out

Answer 3

[Brian Bushnell]

A faster option, from the BBMap package:

bbrename.sh in=file.fasta out=renamed.fasta prefix=phosphate addprefix=t

[O.rka]

Is there a way to get this to work with protein fasta?

Answer 4

[arnstrm]

I know there are lots of option and it can be easily done with many unix one liners, but here is another alternative (my favorite).

bioawk -c fastx '{ print ">PREFIX"$name; $seq }' input.fasta
bioawk -c fastx '{ print ">"$name"|SUFFIX"; $seq }' input.fasta

[al-ash]

Hi, I'm not sure I understand the (bio)awk syntax, but your command was not working for me (did not print sequences)...I put there a new line instead of a semicolon:

 bioawk -c fastx '{ print ">PREFIX" $name "\n" $seq }' input.txt >outupt.txt

which seems to work. Anyway thanks for pointing me towards the solution.