[Biopython-dev] [Biopython (old issues only) - Bug #2762] (Closed) GFF capability in SeqIO

[redmine at redmine.open-bio.org]

Issue #2762 has been updated by Vincent Davis.

Description updated
Status changed from New to Closed
Assignee changed from Biopython Dev Mailing List to Vincent Davis
% Done changed from 0 to 100

This is a now issue, http://biopython.org/wiki/GFF_Parsing
The solution is to use https://github.com/chapmanb/bcbb/tree/master/gff
There is no solution in this issue and I don't see the need to add it to github unless someone currently wants to integrate bcbb
Closing issue

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Bug #2762: GFF capability in SeqIO
https://redmine.open-bio.org/issues/2762#change-15353

* Author: Leighton Pritchard
* Status: Closed
* Priority: Normal
* Assignee: Vincent Davis
* Category: Main Distribution
* Target version: 1.49b
* URL: 
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I'm increasingly coming across GFF format files, and SeqIO currently can't handle them.  It might be useful if at some point in the future, it could.  Also, the Bio.GFF module handles access to a database, and doesn't provide a mechanism for importing or writing GFF format files.  I'm not sure that there is currently any facility to handle this format in Biopython.

There are at least two variants of the GFF format that I've seen in use...

GFF2 is the one I'm working with at the moment, and its specification is here: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml

I've come across GFF3 in other contexts, and it is defined here: http://www.sequenceontology.org/gff3.shtml

Note that GFF3 is similar to GenBank files in that it may explicitly describe both sequence features, and the sequence itself (potentially for multiple sequences).  GFF2 has the potential for this in the specification for the Comments section, which includes a recommended syntax for defining sequences to which the features refer, although that spec makes the reasonable assumption that you would be able to obtain the sequence from elsewhere, knowing the sequence ID from the GFF file.



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