Comments on: Python GFF parser update — parallel parsing and GFF2

By: Brad Chapman

Brad Chapman — Sat, 08 May 2010 14:55:55 +0000

James;
Sounds like a cool idea. I’m a big fan of MongoDB. Celery and RabbitMQ look cool but haven’t had an opportunity to play with them. I’d be interested in hearing what you come up with.

By: James Casbon

James Casbon — Fri, 07 May 2010 14:41:22 +0000

Interesting … I have been looking at something similar, but my stack is mongodb and celery with ghettoq.

The point here is to parse the GFF into json and then store in mongodb. With ghettoq and celery you drop the need for erlang.

By: Brad Chapman

Brad Chapman — Fri, 14 Aug 2009 20:54:41 +0000

Vipin;
Thanks for the report. A detailed response is on the Biopython mailing list:

http://lists.open-bio.org/pipermail/biopython/2009-August/005437.html

Let me know if you have any other problems,
Brad

By: Vipin T S

Vipin T S — Fri, 14 Aug 2009 13:17:48 +0000

To whom it may concern,

Thanks for the development of a quick parser for GFF files. It is very useful.

I have a doubt,
I used the GFFParser.py program to extract the genome annotation from the file attached with this mail. Please find the attached file. (Because of the size of file here I included a few lines)
I wrote a python script like this

##################################################
import GFFParser

pgff = GFFParser.GFFMapReduceFeatureAdder(dict(), None)

cds_limit_info = dict(
gff_type = ["gene","mRNA","CDS","exon"],
gff_id = ["Chr1"]
)

pgff.add_features(‘../PythonGFF/TAIR9_GFF_genes.gff3′, cds_limit_info)

pgff.base["Chr1"]

final = pgff.base["Chr1"]

##################################################

By executing this script I am able to extract gene, mRNA and exon annotation from specified GFF file. But I am unable to extract the CDS related information from GFF file.
It will be great if you can suggest me an idea to include gene, mRNA, exon and CDS information in a single strech of parsing of GFF file.

Thanks in advance,

Vipin T S
vipin.ts@gmail.com

By: Paolo

Paolo — Mon, 27 Jul 2009 09:09:27 +0000

Thanks Brad!
I don’t know why but with update option I obtained the 1.49 version of Biopython, but I manually downloaded the v1.51 and now the converter perfectly works!

Paolo

By: Brad Chapman

Brad Chapman — Fri, 24 Jul 2009 21:32:51 +0000

Paolo;
Thanks for giving this a try. It looks like you have an older version of Biopython without the UnknownSeq class. You can check your version with:

>>> import Bio
>>> Bio.__version__
’1.51b+’

You’ll want 1.50 or later to work with the GFF parser. You can upgrade with:

easy_install -U biopython

as the root user. Let me know if you have any other problems,
Brad

By: Paolo

Paolo — Fri, 24 Jul 2009 15:53:39 +0000

I would like to use the parser to convert my gff2 in gff3, but the application gave me this error:

student@410083:~/Desktop/chap/gff/Scripts/gff$ python gff2_to_gff3.py install
Traceback (most recent call last):
File “gff2_to_gff3.py”, line 12, in
from BCBio.GFF import GFFParser, GFF3Writer
File “build/bdist.linux-x86_64/egg/BCBio/GFF/__init__.py”, line 3, in
# $Id: __init__.py 2134 2004-10-06 08:55:20Z fredrik $
File “build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py”, line 33, in
ImportError: cannot import name UnknownSeq

Do you have any suggestion to resolve it?

Thanx

By: Brad Chapman

Brad Chapman — Sun, 19 Apr 2009 18:54:38 +0000

Thanks for the message on the GFF parser. If you have an example file that is not working as expected, please do send along details about the file. You can do so here, or on the Biopython development list (http://biopython.org/wiki/Mailing_lists).

By: Anonymous

Anonymous — Sun, 19 Apr 2009 06:57:04 +0000

The GFF parser seems to be pretty good
Thanks
I have a doubt whether we can parse information for gene, mRNA, CDS, exon and UTR region in a single strech from a GFF file…