search

fhcrc / seqmagick

An imagemagick-like frontend to Biopython SeqIO
http://seqmagick.readthedocs.org
GNU General Public License v3.0
113 stars 22 forks source link

Request: Make sequence IDs unique #40

Closed sjackman closed 10 years ago

sjackman commented 10 years ago

I have a feature request. I have a FASTA file with a number of duplicate sequence IDs. I'd like to add an incrementing suffix to duplicate sequence IDs. So, for example, two sequences both named cox1 become cox1_1 and cox1_2. Thoughts?

bunnyhutch commented 10 years ago

We'd gladly accept a pull request!

On Wed, May 7, 2014 at 3:20 PM, Shaun Jackman notifications@github.comwrote:

I have a feature request. I have a FASTA file with a number of duplicate sequence IDs. I'd like to add an incrementing suffix to duplicate sequence IDs. So, for example, two sequences both named cox1 become cox1_1 and cox1_2. Thoughts?

— Reply to this email directly or view it on GitHubhttps://github.com/fhcrc/seqmagick/issues/40 .

Frederick "Erick" Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://matsen.fhcrc.org/

sjackman commented 10 years ago

I may just do something hacky like use awk to replace each sequence with its line number. If I do fix it up proper in seqmagick, I'll submit a pull request. =)