Comments on: Initial GFF parser for Biopython http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/ Wed, 22 May 2013 16:09:08 +0000 hourly 1 http://wordpress.com/ By: Brad Chapman http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-540 Sat, 10 Mar 2012 22:13:01 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-540 Hugo,
Thanks again. I checked in fixes so the GenBank to GFF conversion should be cleaner and be handled by genometools:

https://github.com/chapmanb/bcbb/commit/540b030c40e17a6a76b173aadefa8beb56a660f0

let me know if you run into other issues.

]]> By: macabro22 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-539 Sat, 10 Mar 2012 20:22:22 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-539 Sure Brad. Here is the reply from Gnometools’ author Sasha: http://genometools.lighthouseapp.com/projects/17855/tickets/61-error-parsing-gff3-file

The tp53 file on github: https://github.com/mercutio22/biopython/blob/master/Tests/sample_files/tp53.gff

]]> By: Brad Chapman http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-538 Sat, 10 Mar 2012 13:01:12 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-538 Hugo,
Thanks for the report. Would you be able to send along some of ‘tp53.gff’? From the error message it sounds like I’ll need at least the first 3 lines. If you could post this on GitHub I can take a look.

]]> By: macabro22 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-537 Sat, 10 Mar 2012 04:14:15 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-537 Hi Brad. Thanks for your work.

I trying your GFF parser software to write gff files from genbank files and subsequently use AnnotatationSketch from genometools.org to draw some schematics.

They have an online demo here: http://genometools.org/cgi-bin/annotationsketch_demo.cgi
Asuming that tool is parsing GFFs properly you could use that to test if your parser is working ok.

I tried here and it seems to fail with gt.core.error.GTError: GenomeTools error: could not parse number ‘.’ on line 3 in file ‘/home/merc/gitcode/mirna-django/src/scripts/tp53.gff’

The gff3 parsed from the biopearl tool bp_genbank2gff3 works so I am asuming your parser put a dot in the wrong place.

Let me know if I can help.

]]> By: Brad Chapman http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-218 Wed, 17 Nov 2010 12:10:12 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-218 Steve;
Yes it supports the ‘##FASTA’ directive so you can include FASTA in the GFF file. However, better practice is to keep the FASTA and GFF separate, since you’ll likely need FASTA files in programs where you don’t want to parse it out of a GFF file first.

]]> By: Steve Moss http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-217 Tue, 16 Nov 2010 15:00:10 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-217 Thanks for the reply Brad!

Does the module also support inline FASTA? I notice from some parsers, particularly for GFF2 that you have to load the FASTA and GFF files separately.

I’d like to be able to parse the GFF file and then have access to the sequence for the particular annotation objects.

Cheers,

Steve

]]> By: Brad Chapman http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-216 Tue, 16 Nov 2010 14:34:09 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-216 Steve;
Glad you are interested in using it. The latest documentation for use is on the Biopython website:

http://biopython.org/wiki/GFF_Parsing

The module works great for GFF data I’ve been using in my regular research. If you have any questions or find GFF that is giving it issues, definitely let me know.

Thanks,
Brad

]]> By: gawbul http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-215 Sat, 13 Nov 2010 08:59:41 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-215 Hi Brad,

Have the GFF parsers come on much since this post? I’m hoping to use BioPython and PyCogent for comparative genomics analyses and would like to write some wrappers to pull data in from multiple genome databases into GFF3, so I can work with the data locally in a common format!

Here’s a post I made on BioStar http://biostar.stackexchange.com/questions/3566/how-can-i-unify-genome-data-from-different-sources

Cheers,

Steve

]]> By: Brad Chapman http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-37 Wed, 11 Mar 2009 21:42:05 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-37 Giovanni;
No problem. Hopefully we will get the module in good enough shape that it’ll be ready the next time you need to parse GFF.

Thanks for the suggested patches for the tests on github. I’ve got a couple of questions for you about your style; it differs a bit from what I’ve done in the past on testing. Why do you prefer to have the defined stuff be class attributes instead of just sticking them in the setUp function? Is it because of performance concerns?

Also, I noticed your doctest note. I always felt the unittest approach is more natural for development; I write the tests as I write the code, formalizing areas where I imagine errors sneaking in during future development. Why do you prefer doctest?

I’d like to try and sync this with Biopython git when it is finalized; it will hopefully help me learn git more thoroughly. I’m still getting over my fears of branching and merging from many years of CVS/SVN work.

Thanks again for the feedback,
Brad

]]> By: dalloliogm http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-36 Wed, 11 Mar 2009 08:59:48 +0000 http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/#comment-36 hi,
thank you for doing this.. I have used gff a lot during my master’s project, but now I am using different formats.

I just wanted to say that if you want, you can use the unofficial biopython migration branch on github to keep this code synchronized with the biopython repository.

You’ll have to fork the biopython branch here:
- http://github.com/biopython/biopython/network
and push your changes to your forked branch.

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