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Old 05-25-2015, 09:29 PM   #1
EricSchon
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Location: Denmark

Join Date: Nov 2013
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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)

Thanks!
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Old 05-26-2015, 01:12 AM   #2
GenoMax
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Default

See if one of the following works

https://github.com/chapmanb/bcbb/blo..._to_genbank.py
https://www.biostars.org/p/72220/
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Old 05-27-2015, 05:25 AM   #3
EricSchon
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Default No module named BCBio

Quote:
Originally Posted by GenoMax View Post
Thanks!

I tried to run the gff2genbank.py file from your github repository: https://github.com/chapmanb/bcbb/blo..._to_genbank.py

However I get an import error:

Traceback (most recent call last):
File "gff2genbank.py", 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
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Old 05-27-2015, 11:25 AM   #4
cliffbeall
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Default

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.
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