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PitchInteractiveInc / Phinch

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.
http://phinch.org/
BSD 2-Clause "Simplified" License
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phinch won't load mothur-exported BIOM file #84

Open stritttt opened 5 years ago

stritttt commented 5 years ago

This is the output of the biom format using the mothur tool. stability.opti_mcc.0.03.subsample.0.03.biom.gz

However, this was not suitable for the phinch input format. So I fount a similar issue. (#48) And I used the following two codes. biom convert -i stability.opti_mcc.0.03.subsample.0. 03.biom -o file-for-phinch.biom --table-type="OTU table" --to-json sed -i 's#null#{}#g' file-for-phinch.biom

But still phinch did not work. So we changed null to [] as #82 But it still does not work.

hollybik commented 5 years ago

We've updated and revised the BIOM upload feature in the new Phinch desktop app. However, you also need to include taxonomy/ontology metadata and sample mapping information in the BIOM file that you upload into Phinch. Is that information in your current BIOM file?

I would recommend converting your mothur file outputs to tab-delimited format, and then using the BIOM conversion tools to combine this OTU table with your taxonomy data and sample mapping files.

Let me know if this works. If not, I can download your original file and look into this issue further.