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igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
MIT License
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Improved annotation field parsing #34

Closed FelixMoelder closed 5 years ago

FelixMoelder commented 5 years ago

This PR separates the ANN-field to create a more detailed and cleaner table. Additionally, google and ensemble lookups have been added.

jrobinso commented 5 years ago

@FelixMoelder thanks for the PR. Can you zip and attach an example file I can use to test this with?

@brianjohnhaas @johanneskoester any comments on this?

johanneskoester commented 5 years ago

LGTM, you have to see how this looks like in your default template though. We are using a custom one now, which moves parts of the table to a detail view.

jrobinso commented 5 years ago

The Genecards link is problematic because of their license, "Free for academic non-profit institutions. Other users need a Commercial license".

FelixMoelder commented 5 years ago

@jrobinso Good point. We have replaced the Gencards link by a Ensembl.org link. Additionally, there is now a command-line parameter to specify the species needed for the links.

For testing purpose, I've attached a vcf- and html-file. Latter has been created using the default template. example.zip

jrobinso commented 5 years ago

OK, very nice. I'm merging this, bug in the future we might consider adding a command line template of some kind for the search engine. Google is blocked in China.

FelixMoelder commented 5 years ago

@jrobinso Thanks! Would you mind to create another release for us?