-
Notifications
You must be signed in to change notification settings - Fork 244
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Genbank Parsing Problem? #52
Comments
Hugo; http://www.sequenceontology.org/gff3.shtml while codon_start from the GenBank file is 1, 2 or 3: http://www.ddbj.nig.ac.jp/FT/full_index.html#7.2 so I've made the adjustment from 1 to 0 in the GFF output when converting. Let me know if your interaction with the GenomeTools developers indicate I've missed something in the conversion. |
Thanks Brad. I will contact them and will let you know asap. .'' On Mon, Mar 12, 2012 at 3:04 PM, Brad Chapman
|
HI Brad, perhaps this might be useful for testing your program: I tried and the tool pointed for instance is that the produced gff3 Here, I paste you a sample report: GFF3 File Validation Reportontology_file(s):http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo generated: 12-Mar-12 15:27:10############################################################################### THIS FILE HAS NOT BEEN VALIDATED, IT CONTAINS ERRORS, PLEASE REVIEW REPORT!(NO WARNINGS HAVE BEEN ISSUED FOR THIS FILE)############################################################################### ############################################################################### THIS FILE HAS BEEN PROCESSED ENTIRELY AND ALL ERRORS/WARNINGS ARE REPORTED!############################################################################### First 10 lines of the analyzed GFF3 file follows:[line 1]> ##gff-version 3 ...Line Number Error/Warning 4 [ERROR] invalid type (type: source) .'' On Mon, Mar 12, 2012 at 3:50 PM, A M Torres, Hugo
|
Hugo; http://bcbio.wordpress.com/2008/12/14/standard-ontologies-in-biosql/ Practically, most tools will not enforce this requirement, so being unable to map the entire thing I took the approach of keeping the output GFF similar to the input GenBank. If you wanted to take on a mapping of GenBank to Sequence Ontology I'd be happy to incorporate in. Is GenomeTools requiring the ontology matches, or just that online validator? |
Hi Brad,
Hmm, It seems only the validator. GenomeTools seems only to be I have already posted your considerations on their issue tracker. I |
Thanks Hugo -- let me know if there ends up being anything I can change on my end to improve the phase information. Hopefully that'll do it and get things working smoothly with GenomeTools. Thanks for your patience with this. |
Hugo; |
Hi Brad, AnnotationSketch is complaining about the parsed file again:
GenomeTools error: CDS feature on line 27 in file "../../mirna-django/src/scripts/tp53.gff3" has the wrong phase 0 (should be 1)
I don't know if the problem is with their GFF3 parser though. Can you tell me what you think?
http://paste.debian.net/159462/
The text was updated successfully, but these errors were encountered: