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Old 05-25-2015, 10:29 PM   #1
Location: Denmark

Join Date: Nov 2013
Posts: 10
Default Getting genbank annotation file from JGI

Hi All,

I would like to extract the genbank or (embl) annotation file from genomes sequenced at JGI. At JGI you can download the annotation of the genomes in gff format, and you can get the genome or CDS in fasta format.

So my question is:

Is there any way of retrieving the genbank file from jgi or do I have to use a conversion tool to generate the genbank file myself from the gff and fasta files.

If so, which conversion tool would you recommend (I guess people must have had this problem before, so I hope I donít have to make a python converter myself)

EricSchon is offline   Reply With Quote
Old 05-26-2015, 02:12 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079

See if one of the following works
GenoMax is offline   Reply With Quote
Old 05-27-2015, 06:25 AM   #3
Location: Denmark

Join Date: Nov 2013
Posts: 10
Default No module named BCBio

Originally Posted by GenoMax View Post

I tried to run the file from your github repository:

However I get an import error:

Traceback (most recent call last):
File "", line 13, in <module>
from BCBio import GFF
ImportError: No module named BCBio

Iíve tried to pip install

(gff2genbank)[user@cluster scripts]$ pip install bcbio-gff
Requirement already satisfied (use --upgrade to upgrade): bcbio-gff in /c3se/users/user/Glenn/virtualenvs/gff2genbank/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): six in /c3se/users/user/Glenn/virtualenvs/gff2genbank/lib/python2.7/site-packages (from bcbio-gff)
Cleaning up...

But it doesnít help. Can you help me how to get the BCBio this module imported?

Specs: non-sudo user on a CentOS release 6.6 distro. Python 2.7.6 and biopython 1.62
EricSchon is offline   Reply With Quote
Old 05-27-2015, 12:25 PM   #4
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Location: Ohio

Join Date: Jan 2010
Posts: 144

There is a tool on the IMG that generates Genbank format directly - there is a button at the bottom of the genome main page ("Taxon Details") saying Export Genome Data and Generate Genbank File. It worked ok for what I wanted, which was to look at the annotation with Artemis.

The help says:


This tool was provided to you as an aid. We do not guarantee the output is a valid Genbank format.
You still need to spend extra effort to make the Genbank file accepted by NCBI. And we will no longer support this tool, why?

You may generate a custom Genbank File for one or more scaffolds.
Your MyIMG gene annotation may override the default product name.
(You must be logged into MyIMG to use your annotations.)
If an IMG term is associated with a gene, this can also override the product name.
IMG term, if present and the override option selected, also overrides MyIMG annotation.
cliffbeall is offline   Reply With Quote

conversion, genbank files, jgi

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