Question: Changing fasta headers in multifasta file
0
gravatar for James
7 months ago by
James10
APHA Weybridge, UK
James10 wrote:

Hi, Please can anyone help me with this. I have a multifasta file that I want to make a blast database but the header of each sequence is not quite in the correct format. The multifasta has several 100000 sequences in it so really dont want to start again.

correct format should be

>unique-id|my sequence name|etc|etc

I currently have

>notunique___|unique-id|my sequence name|etc|etc

Im pretty sure this should be doable with the sed command but no clue how to do this myself. I want too either just delete 'notunique___|' or replace '>notunique___|' with a new >

notunique is a mix of letters and numbers that are not always the same length of characters.

Any help would be much appreciated

Thank you James

sed • 412 views
ADD COMMENTlink modified 7 months ago by genomax55k • written 7 months ago by James10

Renaming Entries In A Fasta File

ADD REPLYlink written 7 months ago by Sej Modha3.6k

Dear James, you may also be interested in SEDA (http://www.sing-group.org/seda/), a desktop software that incorporates a lot of functions for processing FASTA files. One of that functions is the "Rename header", which allows you changing headers in different ways. Regards.

ADD REPLYlink written 7 months ago by Hugo130
2
gravatar for lieven.sterck
7 months ago by
lieven.sterck2.2k
Belgium, Ghent, VIB
lieven.sterck2.2k wrote:

you can use this perl oneliner:

cat <yourFile> | perl -pi -e 's/>.+?\|/>/g'

on the other hand there should be many other solutions already posted on biostars ;-)

ADD COMMENTlink written 7 months ago by lieven.sterck2.2k

Thank you so much lieven.sterck, that worked perfectly.

While there seem to be lots of posts about this stuff I couldn't work out how to change other answers to my exact problem. I really have no experience with these things.

Thanks again James

ADD REPLYlink written 7 months ago by James10
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