Question: Change Fasta Id'S
0
gravatar for rowe
6.4 years ago by
rowe0
United Kingdom
rowe0 wrote:

Hello,

I've got multiple blast hits in a fasta file. But I want the description, instead of accessions. So when I make a tree, I get nice names.

For example:

>gi|255587543|ref|XM_002534260.1| Ricinus communis Protein kinase APK1B, chloroplast precursor, putative, mRNA

To:

>Ricinus_communis_APK1B

I know this can be done by hand, but there's just too many of them!

Hope you can help me.

fasta identifiers • 2.3k views
ADD COMMENTlink modified 6.4 years ago by Daniel3.7k • written 6.4 years ago by rowe0
4

With what do you want help? This task and many like it is quite simple using e.g. a Perl or shell script. Is that what you would like to learn? Right now, the tone of the question suggests that you just want someone to do it for you. That does not help you, in the long run or the people with the answer, in the short term.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Neilfws48k

duplicate of

Any Script to parse fasta headers?

ADD REPLYlink written 6.4 years ago by Pierre Lindenbaum122k
1
gravatar for Pierre Lindenbaum
6.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

duplicate of

Any Script to parse fasta headers?

ADD COMMENTlink written 6.4 years ago by Pierre Lindenbaum122k
0
gravatar for Daniel
6.4 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

Fire up perl: If starts with > , regex to extract between pipe and comma, print >[regex] else print.

Further info: http://learn.perl.org/

ADD COMMENTlink written 6.4 years ago by Daniel3.7k
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