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SKIP: revert tabulate-seqs changes but still allow FeatureData[LinkedSequence] as input (#367)
<!-- PR guidance and examples: https://github.com/rachis-org/governance/blob/main/pr_template_guidelines.md --> <!-- rachis Generative AI Policy: https://github.com/rachis-org/governance/blob/main/ai_policy.md --> # Description <!-- REQUIRED: Briefly describe this PR, or link the issue it closes. --> Reverts changes from #366 # AI Disclosure <!-- REQUIRED: Check exactly one option. --> - [x] NO AI USED. - [ ] AI USED.
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3 files changed

Lines changed: 8 additions & 34 deletions

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‎q2_feature_table/_summarize/_visualizer.py‎

Lines changed: 6 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -42,20 +42,12 @@ def tabulate_seqs(output_dir: str, data: DNAIterator,
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for sequence in data:
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skbio.io.write(sequence, format='fasta', into=fh)
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str_seq = str(sequence)
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seqs = str_seq.split(' ')
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urls = [_blast_url_template % seq for seq in seqs]
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seq_id = sequence.metadata['id']
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display_sequences.add(seq_id)
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sequences[seq_id] = {
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'len': len(str_seq)
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}
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if len(seqs) == 2:
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sequences[seq_id]['url_and_seq'] = zip(
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urls, seqs, ['forward', 'reverse']
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)
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else:
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sequences[seq_id]['url_and_seq'] = zip(urls, seqs)
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seq_len = len(str_seq)
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display_sequences.add(sequence.metadata['id'])
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sequences[sequence.metadata['id']]\
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= {'len': seq_len,
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'url': _blast_url_template % str_seq,
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'seq': str_seq}
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if metadata is not None:
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metadata_df = metadata.to_dataframe()

‎q2_feature_table/_summarize/tabulate_seqs_assets/index.html‎

Lines changed: 1 addition & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -133,25 +133,7 @@ <h3>Sequence Table</h3>
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{% endif %}
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{% if sequence in data %}
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<td>{{ data[sequence].len }}</td>
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<td><samp>
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{% for item in data[sequence].url_and_seq %}
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{% if item|length == 3 %}
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{% set link, seq, direction = item %}
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{% if direction == 'reverse' %}
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<br>
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{% endif %}
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{{ direction }}:
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<a target="_blank" href="{{ link }}" rel="noopener noreferrer">
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{{ seq }}
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</a>
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{% else %}
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{% set link, seq = item %}
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<a target="_blank" href="{{ link }}" rel="noopener noreferrer">
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{{ seq }}
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</a>
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{% endif %}
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{% endfor %}
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</samp></td>
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<td><samp><a target="_blank" href="{{ data[sequence].url }}" rel="noopener noreferrer">{{ data[sequence].seq }}</a></samp></td>
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{% else %}
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<td>-</td>
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<td>-</td>

‎q2_feature_table/tests/test_summarize.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -50,7 +50,7 @@ def test_basic(self):
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self.assertTrue(os.path.exists(expected_fp))
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with open(expected_fp) as fh:
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file_text = fh.read()
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self.assertTrue('ACGT' in file_text)
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self.assertTrue('ACGT</a>' in file_text)
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self.assertTrue('<td>4</td>' in file_text)
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self.assertTrue('<td>seq2</td>' in file_text)
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