Perl Script 5 : How to add specific word to fasta header

Question : 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.

Convert Multi Fasta file into a Single line FASTA File

Store Multi Fasta Header into a Separate File

Answer : So you have a file with multiline fasta file with several hundreads of sequence like this

>Cryptococcus gattii

MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKK

>Daphnia pulex

MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKM

and want to make them look like this

>Cryptococcus gattii - phosphate

MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKK

>Daphnia pulex - phosphate

MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKM

this PERL one liner can help you

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

where

phosphate - word you want to add

input.fasta - file where sequences are stored at present

out.fasta - file where your result will be stored

Sanjay Singh

Perl Script 5 : How to add specific word to fasta header

Comments

Post a Comment