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MAINT: Updates for new pandas API #323

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May 2, 2024
Merged

MAINT: Updates for new pandas API #323

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2 changes: 1 addition & 1 deletion q2_types/feature_data/_transformer.py
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Expand Up @@ -255,7 +255,7 @@ def _fastaformats_to_metadata(ff, constructor=skbio.DNA, lowercase=False):

def _series_to_fasta_format(ff, data, sequence_type="DNA", lowercase=False):
with ff.open() as f:
for id_, seq in data.iteritems():
for id_, seq in data.items():
if sequence_type == "protein":
sequence = skbio.Protein(seq, metadata={'id': id_},
lowercase=lowercase)
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2 changes: 1 addition & 1 deletion q2_types/feature_data_mag/_transformer.py
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Expand Up @@ -37,7 +37,7 @@ def _get_filename(full_path):
def _series_to_fasta(series, ff, seq_type='DNA'):
fp = os.path.join(str(ff), f'{series.name}.fasta')
with open(fp, 'w') as fh:
for id_, seq in series.iteritems():
for id_, seq in series.items():
if seq:
sequence = CONSTRUCTORS[seq_type](seq, metadata={'id': id_})
skbio.io.write(sequence, format='fasta', into=fh)
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2 changes: 1 addition & 1 deletion q2_types/genome_data/_transformer.py
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Expand Up @@ -42,7 +42,7 @@ def _8(ortholog_file: OrthologFileFmt) -> pd.DataFrame:
def _series_to_fasta(series, ff, seq_type='DNA'):
fp = os.path.join(ff.path, f'{series.name}.fasta')
with open(fp, 'w') as fh:
for id_, seq in series.iteritems():
for id_, seq in series.items():
if seq:
sequence = CONSTRUCTORS[seq_type](seq, metadata={'id': id_})
skbio.io.write(sequence, format='fasta', into=fh)
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6 changes: 3 additions & 3 deletions q2_types/sample_data/tests/test_transformer.py
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Expand Up @@ -27,9 +27,9 @@ def test_pd_series_to_alpha_diversity_format(self):

obs = transformer(exp)

# Squeeze equals true to return series instead of dataframe
obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0,
squeeze=True)
obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0)
# Squeeze into series instead of dataframe
obs = obs.squeeze('columns')

assert_series_equal(exp, obs)

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