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jameshadfield / phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny
http://phandango.net
MIT License
115 stars 27 forks source link

Metadata is not being displayed #147

Closed mirulee closed 11 months ago

mirulee commented 11 months ago

I used Roary to generate the core_gene_alignment.aln.treefile.newick and gene_presence_absence.csv files. I added metadata.csv to visualize the data, but some entries are missing in the metadata display. I have verified and corrected both the sample names and the metadata entries, but the issue persists. Can you please help me resolve this problem?

Phandango (2)

jameshadfield commented 11 months ago

but some entries are missing in the metadata display. I have verified and corrected both the sample names and the metadata entries, but the issue persists.

Are you able to produce a small tree (you can create it manually, the tree shape's not important) with some samples for which the metadata is not appearing (and for some samples for which it is ok), together with a metadata file for just those samples? If you can share that data here I can try to work out what's going on

jameshadfield commented 11 months ago

Thanks! The missing data is due to the taxa names having a trailing space in the metadata file, e.g. "X" in the tree has a trailing space in the metadata file "X ". Removing the trailing spaces of the example data fixes the issue for me.

jameshadfield commented 11 months ago

(Closing this as the underlying data files had strain names which didn't match. Please re-open if this doesn't fix the issue for you!)

mirulee commented 11 months ago

Thanks! The missing data is due to the taxa names having a trailing space in the metadata file, e.g. "INU030" in the tree has a trailing space in the metadata file "INU030 ". Removing the trailing spaces of the example data gives the following:

I hadn’t even thought about the spacebar. Thank you so much. Also, I would appreciate it if you could take down the post related to the sample names. Since it's our data, it could potentially be a sensitive matter.