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tanghaibao / goatools

Python library to handle Gene Ontology (GO) terms
BSD 2-Clause "Simplified" License
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pygraphviz.Agraph().name returns AttributeError #22

Closed trgibbons closed 9 years ago

trgibbons commented 9 years ago

Thanks for writing this handy module! I ran into a bit of trouble when I tried to generate a GML file. Line 306 in obo_parser.py throws an AttributeError when the "gml" option in the draw_lineage() function is set to True. It appears that the name must be set when the graph is initialized. Deleting line 306 and changing line 269 to:

G = pgv.AGraph(name="GO tree")

seemed to fix the problem

tanghaibao commented 9 years ago

There must have been a change in the behavior of pygraphviz. I've updated the code as you suggested. Thanks for contributing.

trgibbons commented 9 years ago

huh? No, you reached the right guy. Glad I could help. Goatools has been quite useful for me recently.

On Dec 10, 2014, at 6:11 PM, annabelhao notifications@github.com wrote:

wrong email recipient?

On Wed, Dec 10, 2014 at 3:00 PM, Haibao Tang notifications@github.com wrote:

Closed #22 https://github.com/tanghaibao/goatools/issues/22.

— Reply to this email directly or view it on GitHub https://github.com/tanghaibao/goatools/issues/22#event-205849890.

Zhangying Hao

Ph.D Department of Plant Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road, Athens, GA 30602 706-248-1024 — Reply to this email directly or view it on GitHub.