ctf won't work if metadata file has extra samples

[mestaki]

Hey @cameronmartino,

A little feature-request:

QIIME 2 Plugin 'gemelli' version 0.0.8 (from package 'gemelli' version 0.0.8)
q2cli version 2021.8.0

In the example below, my table ends up with 5 fewer samples than that in the sample-metadata file after filtering based on min-sample-count

!qiime gemelli ctf \
  --i-table table.qza \
  --m-sample-metadata-file ../clean_metadata.tsv \
  --p-state-column stage_char \
  --p-min-sample-count 5000 \
  --p-individual-id-column host_subject_id \
  --output-dir gemelli/ctf-results \
  --verbose 

And so I get the following error:

/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/gemelli/preprocessing.py:884: RuntimeWarning: Subject(s) (131-05,131-09,131-15,131-12,131-07,131-13,131-02,131-08,131-06,131-11) contains multiple samples. Multiple subject counts will be meaned across samples by subject.
  warnings.warn(''.join(["Subject(s) (", str(duplicated_ids),
Traceback (most recent call last):
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-564>", line 2, in ctf
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/gemelli/ctf.py", line 620, in ctf
    helper_results = ctf_helper(table,
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/gemelli/ctf.py", line 669, in ctf_helper
    tensal_results = tensals_helper(table,
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/gemelli/ctf.py", line 799, in tensals_helper
    tensor.construct(table, sample_metadata,
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/gemelli/preprocessing.py", line 855, in construct
    self._construct()
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/gemelli/preprocessing.py", line 891, in _construct
    table[dup[0]] = table.loc[:, dup].mean(axis=1).astype(int)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/pandas/core/indexing.py", line 889, in __getitem__
    return self._getitem_tuple(key)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/pandas/core/indexing.py", line 1069, in _getitem_tuple
    return self._getitem_tuple_same_dim(tup)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/pandas/core/indexing.py", line 775, in _getitem_tuple_same_dim
    retval = getattr(retval, self.name)._getitem_axis(key, axis=i)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/pandas/core/indexing.py", line 1113, in _getitem_axis
    return self._getitem_iterable(key, axis=axis)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/pandas/core/indexing.py", line 1053, in _getitem_iterable
    keyarr, indexer = self._get_listlike_indexer(key, axis, raise_missing=False)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/pandas/core/indexing.py", line 1266, in _get_listlike_indexer
    self._validate_read_indexer(keyarr, indexer, axis, raise_missing=raise_missing)
  File "/home/mestaki/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/pandas/core/indexing.py", line 1321, in _validate_read_indexer
    raise KeyError(
KeyError: "Passing list-likes to .loc or [] with any missing labels is no longer supported. The following labels were missing: Index(['14010.131.08.1SC.swab.28'], dtype='object'). See [https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike"](https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike%22)

Plugin error from gemelli:

  "Passing list-likes to .loc or [] with any missing labels is no longer supported. The following labels were missing: Index(['14010.131.08.1SC.swab.28'], dtype='object'). See [https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike"](https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike%22)

See above for debug info.

The issue is resolved if I manually remove those 5 samples from my metadata beforehand.

Would be nice if gemelli could do a check/filter on the sample-metadata after filtering the input table, or, include an ignore-missing-samples option like in empress.