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REF: fix private imports for q2-types refactor #95

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merged 2 commits into from
Aug 27, 2024
Merged

REF: fix private imports for q2-types refactor #95

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d6cbf5a
REF: fix private imports for q2-types refactor
ebolyen Jul 25, 2024
de6a69d
Merge branch 'main' into Trial-type-refactor
ebolyen Jul 31, 2024
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15 changes: 8 additions & 7 deletions q2_assembly/iss/tests/test_iss.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@
import biom
import pandas as pd
from q2_types.feature_data import DNAIterator
from q2_types.feature_table._transformer import _table_to_dataframe
from qiime2.plugin.testing import TestPluginBase
from qiime2.plugin.util import transform

from q2_assembly.iss.iss import (
_abundances_to_biom,
Expand Down Expand Up @@ -153,13 +153,13 @@ def test_abundances_to_biom(self):
glob.glob(os.path.join(self.get_data_path("abundances"), "*.txt"))
)
obs_table = _abundances_to_biom(abunds_fp)
obs_df = transform(obs_table, to_type=pd.DataFrame)

with open(self.get_data_path("abundances/biom_table.tsv"), "r") as f:
exp_table = biom.Table.from_tsv(f, None, None, lambda x: x)
exp_df = transform(exp_table, to_type=pd.DataFrame)

pd.testing.assert_frame_equal(
_table_to_dataframe(obs_table), _table_to_dataframe(exp_table)
)
pd.testing.assert_frame_equal(obs_df, exp_df)

def test_generate_reads_wrong_genome_counts(self):
with self.assertRaisesRegex(Exception, r".*provided 2 kingdom\(s\) but 1.*"):
Expand Down Expand Up @@ -189,6 +189,8 @@ def test_generate_reads_action(self, p1, p2, p3):
["samp1", "samp2"], self.test_params_list, test_temp_dir.name
)

obs_abundances_df = transform(obs_abundances, to_type=pd.DataFrame)

exp_genomes = {
"genome1": "ATGCATGC",
"genome2": "GATCGCATGA",
Expand All @@ -201,9 +203,8 @@ def test_generate_reads_action(self, p1, p2, p3):

with open(self.get_data_path("abundances/biom_table.tsv"), "r") as f:
exp_biom_table = biom.Table.from_tsv(f, None, None, lambda x: x)
pd.testing.assert_frame_equal(
_table_to_dataframe(obs_abundances), _table_to_dataframe(exp_biom_table)
)
exp_df = transform(exp_biom_table, to_type=pd.DataFrame)
pd.testing.assert_frame_equal(obs_abundances_df, exp_df)


if __name__ == "__main__":
Expand Down
2 changes: 1 addition & 1 deletion q2_assembly/plugin_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
SequencesWithQuality,
SingleBowtie2Index,
)
from q2_types.per_sample_sequences._type import AlignmentMap
from q2_types.per_sample_sequences import AlignmentMap
from q2_types.sample_data import SampleData
from qiime2.core.type import Bool, Choices, Properties, Str, TypeMap, Visualization
from qiime2.plugin import Citations, Collection, Int, List, Plugin, Range
Expand Down
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