def test_typevars(self):
T, U, V, W, X = TypeMap({
(Foo, Bar, Str % Choices('A', 'B')): (C1[Foo], C1[Bar]),
(Foo | Bar, Foo, Str): (C1[Bar], C1[Foo])
})
scope = {}
T1 = ast_to_type(T.to_ast(), scope=scope)
U1 = ast_to_type(U.to_ast(), scope=scope)
V1 = ast_to_type(V.to_ast(), scope=scope)
W1 = ast_to_type(W.to_ast(), scope=scope)
X1 = ast_to_type(X.to_ast(), scope=scope)
self.assertEqual(len(scope), 1)
self.assertEqual(scope[id(T.mapping)], [T1, U1, V1, W1, X1])
self.assertEqual(T1.mapping.lifted, T.mapping.lifted)
self.assertIs(T1.mapping, U1.mapping)
self.assertIs(U1.mapping, V1.mapping)
self.assertIs(V1.mapping, W1.mapping)
self.assertIs(W1.mapping, X1.mapping)
from .plugin import dummy_plugin, C1, C2, C3, Foo, Bar, Baz, EchoFormat
from qiime2.plugin import (TypeMap, TypeMatch, Properties, Visualization, Bool,
Choices)
def constrained_input_visualization(output_dir: str, a: EchoFormat,
b: EchoFormat):
with open(os.path.join(output_dir, 'index.html'), 'w') as fh:
fh.write("<p>%s</p>" % a.path.read_text())
fh.write("<p>%s</p>" % b.path.read_text())
T, U, V = TypeMap({
(Foo, Foo): Visualization,
(Bar, Bar): Visualization,
(Baz, Baz): Visualization,
(C1[Foo], C1[Foo]): Visualization,
(C1[Bar], C1[Bar]): Visualization,
(C1[Baz], C1[Baz]): Visualization
})
dummy_plugin.visualizers.register_function(
function=constrained_input_visualization,
inputs={
'a': T,
'b': U
},
parameters={},
name="Constrained Input Visualization",
description="Ensure Foo/Bar/Baz match")
del T, U, V
output_descriptions={
'grouped_table':
'A table that has been grouped along the given '
'`axis`. IDs on that axis are replaced by values in '
'the `metadata` column.'
},
name="Group samples or features by a metadata column",
description="Group samples or features in a feature table using metadata "
"to define the mapping of IDs to a group.")
i_table, p_overlap_method, o_table = TypeMap({
(FeatureTable[Frequency], Str % Choices(
sorted(q2_feature_table.overlap_methods()))):
FeatureTable[Frequency],
(
FeatureTable[RelativeFrequency],
# We don't want to allow summing of RelativeFrequency tables, so remove
# that option from the overlap methods
Str % Choices(sorted(q2_feature_table.overlap_methods() - {'sum'}))):
FeatureTable[RelativeFrequency]
})
plugin.methods.register_function(
function=q2_feature_table.merge,
inputs={'tables': List[i_table]},
parameters={'overlap_method': p_overlap_method},
outputs=[('merged_table', o_table)],
input_descriptions={
'tables': 'The collection of feature tables to be merged.',
},
parameter_descriptions={
description=(
'Filter sequences by length with VSEARCH. For a combination of global '
'and conditional taxonomic filtering, see filter_seqs_length_by_taxon.'
),
citations=[citations['rognes2016vsearch']])
INCLUDE_SPECIES_LABELS_DESCRIPTION = (
'Include species rank labels in taxonomy output. Note: species-labels may '
'not be reliable in all cases.')
_SILVA_VERSIONS = ['128', '132', '138']
_SILVA_TARGETS = ['SSURef_NR99', 'SSURef', 'LSURef']
version_map, target_map, _ = TypeMap({
(Str % Choices('128', '132'), Str % Choices('SSURef_NR99', 'SSURef', 'LSURef')):
Visualization,
(Str % Choices('138'), Str % Choices('SSURef_NR99', 'SSURef')):
Visualization,
})
plugin.pipelines.register_function(
function=get_silva_data,
inputs={},
parameters={
'version': version_map,
'target': target_map,
'include_species_labels': Bool,
'download_sequences': Bool
},
outputs=[('silva_sequences', FeatureData[RNASequence]),
('silva_taxonomy', FeatureData[Taxonomy])],
input_descriptions={},
'sensitivity':
'Bowtie2 alignment sensitivity. See bowtie2 manual for '
'details.',
'ref_gap_open_penalty':
'Reference gap open penalty.',
'ref_gap_ext_penalty':
'Reference gap extend penalty.',
'exclude_seqs':
'Exclude sequences that align to reference. Set this '
'option to False to exclude sequences that do not align '
'to the reference database.'
}
P_method, P_left_justify, _ = TypeMap({
(Str % Choices("blast", "blastn-short"), Bool % Choices(False)):
Visualization,
(Str % Choices("vsearch"), Bool):
Visualization,
})
plugin.methods.register_function(
function=exclude_seqs,
inputs=seq_inputs,
parameters={
'method': P_method,
'perc_identity': Float % Range(0.0, 1.0, inclusive_end=True),
'evalue': Float,
'perc_query_aligned': Float,
'threads': Int % Range(1, None),
'left_justify': P_left_justify,
},
outputs=[('sequence_hits', FeatureData[Sequence]),
'example, if we are missing the genus label for '
'\'f__Pasteurellaceae; g__\'then the \'f__\' rank will be propagated to '
'become: \'f__Pasteurellaceae; g__Pasteurellaceae\'.')
RANK_DESCRIPTION = ('List of taxonomic ranks for building a taxonomy from the '
'SILVA Taxonomy database. Use \'include_species_labels\' '
'to append the organism name as the species label. '
"[default: '" + "', '".join(DEFAULT_RANKS) + "']")
_SILVA_VERSIONS = ['128', '132', '138', '138.1']
_SILVA_TARGETS = ['SSURef_NR99', 'SSURef', 'LSURef_NR99', 'LSURef']
version_map, target_map, _ = TypeMap({
(Str % Choices('128', '132'), Str % Choices('SSURef_NR99', 'SSURef', 'LSURef')):
Visualization,
(Str % Choices('138'), Str % Choices('SSURef_NR99', 'SSURef')):
Visualization,
(Str % Choices('138.1'), Str % Choices('SSURef_NR99', 'SSURef', 'LSURef_NR99', 'LSURef')):
Visualization,
})
plugin.pipelines.register_function(
function=get_silva_data,
inputs={},
parameters={
'version': version_map,
'target': target_map,
'include_species_labels': Bool,
'rank_propagation': Bool,
'ranks': List[Str % Choices(ALLOWED_RANKS)],
'download_sequences': Bool
},
case_transformer = {
'upper': str.upper,
'lower': str.lower,
'invert': str.swapcase,
}[capitalization]
for i, line in enumerate(contents, 0):
contents[i] = case_transformer(line)
return contents
sort_ascending, sort_descending, out_text = TypeMap({
(Bool % Choices([False]), Bool % Choices([False])):
IceCream,
(Bool % Choices([True]), Bool % Choices([False])):
IceCream,
(Bool % Choices([False]), Bool % Choices([True])):
IceCream,
})
plugin.methods.register_function(
function=sprinkle,
inputs={
'icecream': IceCream,
},
parameters={
'capitalization': Str % Choices(['upper', 'lower', 'invert']),
'sort_ascending': sort_ascending,
'sort_descending': sort_descending,
},
outputs={('modified', out_text)},