frequencies: error with --region flag

[joverlee521]

This bug initially discovered in the private seasonal flu workflow.

Use of the --region flag results in the following error:

[batch] [2024-02-22T16:28:59-08:00] Traceback (most recent call last):
[batch] [2024-02-22T16:28:59-08:00]   File "/nextstrain/augur/augur/__init__.py", line 66, in run
[batch] [2024-02-22T16:28:59-08:00]     return args.__command__.run(args)
[batch] [2024-02-22T16:28:59-08:00]   File "/nextstrain/augur/augur/frequencies.py", line 148, in run
[batch] [2024-02-22T16:28:59-08:00]     tree_freqs = tree_frequencies(tree, pivots, method='SLSQP',
[batch] [2024-02-22T16:28:59-08:00]   File "/nextstrain/augur/augur/frequency_estimators.py", line 502, in __init__
[batch] [2024-02-22T16:28:59-08:00]     self.prepare()
[batch] [2024-02-22T16:28:59-08:00]   File "/nextstrain/augur/augur/frequency_estimators.py", line 516, in prepare
[batch] [2024-02-22T16:28:59-08:00]     if self.node_filter(node):
[batch] [2024-02-22T16:28:59-08:00]   File "/nextstrain/augur/augur/frequencies.py", line 145, in <lambda>
[batch] [2024-02-22T16:28:59-08:00]     node_filter_func = lambda node: (node.attr["region"] == region
[batch] [2024-02-22T16:28:59-08:00] KeyError: 'region'
[batch] [2024-02-22T16:28:59-08:00] An error occurred (see above) that has not been properly handled by Augur.
[batch] [2024-02-22T16:28:59-08:00] To report this, please open a new issue including the original command and the error above:
[batch] [2024-02-22T16:28:59-08:00]     <https://github.com/nextstrain/augur/issues/new/choose>

[joverlee521]

Hmm, most likely a result of the change to read a subset of metadata columns in #1294

[joverlee521]

Errors for any regions that are not global because it requires the region metadata field:

augur/augur/frequencies.py

Lines 139 to 146 in f81e6a3

	for region in args.regions:
	# Omit strains sampled prior to the first pivot from frequency calculations.
	# (these tend to be reference strains included for phylogenetic context)
	if region=='global':
	node_filter_func = lambda node: node.attr["num_date"] >= pivots[0]
	else:
	node_filter_func = lambda node: (node.attr["region"] == region
	and node.attr["num_date"] >= pivots[0])

[joverlee521]

Ah, also because we changed to only annotating tips with weight_attributes in dde857a