Closed jairideout closed 5 years ago
Is this still a relevant issue? The error definitely isn't being raised, but it looks like all of the methods that even use metadata in gneiss are deprecated.
It might still be relevant:
Thanks @thermokarst - yes this is still an outstanding issue
It'll boil down to something as follows here: https://github.com/qiime2/q2-gneiss/blob/master/q2_gneiss/cluster/_cluster.py#L93
difference = set(table.index) - set(gradient.index)
if difference and not ignore_missing_samples:
raise KeyError("There are samples not included in the mapping "
"file. Override this error by using the "
"`ignore_missing_samples` argument. Offending "
"samples: %s"
% ', '.join(sorted([str(i) for i in difference])))
Concerning deprecation - the stats methods are being deprecated in favor of other differential abundance methods such as songbird and hopefully aldex2. CC @ggloor
And this should be a thing in all q2-gneiss methods taking a Metadata or MetadataColumn as input?
Yes - especially if it isn't deprecated
On Fri, Aug 2, 2019, 5:18 PM Oddant1 notifications@github.com wrote:
And this should be a thing in all q2-gneiss methods taking a Metadata or MetadataColumn as input?
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:laughing: those poor lonely deprecated methods
I'm not finding any relevant methods other than gradient_clustering
Also, do we want ignore_missing_samples
arguments to be included in any relevant methods?
Why not - that's the parameter used in emperor. There's definitely the use case that you do want to remove non overlapping samples.
On Fri, Aug 2, 2019, 5:39 PM Oddant1 notifications@github.com wrote:
Also, do we want ignore_missing_samples arguments to be included in any relevant methods?
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Not quite - that's testing to see if all of the samples are dropped. The code previously tests to see if there is a complete overlap in samples
On Fri, Aug 2, 2019, 6:22 PM Oddant1 notifications@github.com wrote:
is this exception already doing something similar to this?
[image: image] https://user-images.githubusercontent.com/10642616/62401675-0c8f6c00-b539-11e9-9062-80f11b187b31.png
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Yeah I realized that after looking at it a bit more closely
yes we are getting close to having ALDEx2 up and running inside QIIME2. https://github.com/dgiguer is just putting the finishing touches on this
An error should be raised if any sample IDs in the feature table aren't present in the sample metadata. This is to match the behavior in QIIME 1 and 2 where metadata IDs can be a superset of the table IDs, but every table ID must have corresponding metadata.
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