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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,141 @@ | ||
| from collections import defaultdict | ||
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| from conekt.models.expression.specificity import ExpressionSpecificity | ||
| from conekt.models.relationships.sequence_family import SequenceFamilyAssociation | ||
| from conekt.models.relationships.sequence_interpro import SequenceInterproAssociation | ||
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| from sqlalchemy.orm import joinedload | ||
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| class SpecificityComparison: | ||
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| @staticmethod | ||
| def get_specific_genes(method_id, cutoff, condition): | ||
| results = ExpressionSpecificity.query.filter(ExpressionSpecificity.method_id == method_id). \ | ||
| filter(ExpressionSpecificity.score >= cutoff). \ | ||
| filter(ExpressionSpecificity.condition == condition). \ | ||
| options( | ||
| joinedload(ExpressionSpecificity.profile).undefer("profile") | ||
| ). \ | ||
| all() | ||
| return results | ||
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| @staticmethod | ||
| def get_specificity_comparison(method_a_id, method_b_id, cutoff_a, cutoff_b, condition_a, condition_b, | ||
| use_interpro, family_method=0): | ||
| # Fetch results | ||
| results_a = SpecificityComparison.get_specific_genes(method_a_id, cutoff_a, condition_a) | ||
| results_b = SpecificityComparison.get_specific_genes(method_b_id, cutoff_b, condition_b) | ||
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| sequence_ids = [r.profile.sequence_id for r in results_a] + [r.profile.sequence_id for r in results_b] | ||
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| counts = { | ||
| 'left': 0, | ||
| 'right': 0, | ||
| 'intersection': 0 | ||
| } | ||
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| table_data = {} | ||
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| if use_interpro: | ||
| interpro_associations = SequenceInterproAssociation.query. \ | ||
| filter(SequenceInterproAssociation.sequence_id.in_(sequence_ids)).all() | ||
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| sequence_id_left = [r.profile.sequence_id for r in results_a if r.profile.sequence_id is not None] | ||
| sequence_id_right = [r.profile.sequence_id for r in results_b if r.profile.sequence_id is not None] | ||
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| abundance = defaultdict(lambda: False) | ||
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| for r in results_a + results_b: | ||
| if r.profile.sequence_id is not None: | ||
| abundance[r.profile.sequence_id] = r.profile.low_abundance | ||
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| interpro_id_to_name = { | ||
| i.interpro_id: "%s (%s)" % ( | ||
| i.domain.label, i.domain.description if i.domain.description else "no description") | ||
| for i in interpro_associations} | ||
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| for i in interpro_associations: | ||
| if i.interpro_id not in table_data.keys(): | ||
| table_data[i.interpro_id] = {'id': i.interpro_id, | ||
| 'name': interpro_id_to_name[i.interpro_id], | ||
| 'left_genes': [], | ||
| 'right_genes': []} | ||
| if i.sequence_id in sequence_id_left: | ||
| table_data[i.interpro_id]['left_genes'].append({'id': i.sequence_id, | ||
| 'name': i.sequence.name, | ||
| 'shortest_alias': i.sequence.shortest_alias, | ||
| 'low_abundance': abundance[i.sequence_id]}) | ||
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| if i.sequence_id in sequence_id_right: | ||
| table_data[i.interpro_id]['right_genes'].append({'id': i.sequence_id, | ||
| 'name': i.sequence.name, | ||
| 'shortest_alias': i.sequence.shortest_alias, | ||
| 'low_abundance': abundance[i.sequence_id]}) | ||
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| if len(table_data[i.interpro_id]['left_genes']) > 0 and len( | ||
| table_data[i.interpro_id]['right_genes']) == 0: | ||
| table_data[i.interpro_id]['type'] = 'left' | ||
| counts['left'] += 1 | ||
| elif len(table_data[i.interpro_id]['right_genes']) > 0 and len( | ||
| table_data[i.interpro_id]['left_genes']) == 0: | ||
| table_data[i.interpro_id]['type'] = 'right' | ||
| counts['right'] += 1 | ||
| else: | ||
| table_data[i.interpro_id]['type'] = 'intersection' | ||
| counts['intersection'] += 1 | ||
|
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| else: | ||
| family_associations = SequenceFamilyAssociation.query. \ | ||
| filter(SequenceFamilyAssociation.family.has(method_id=family_method)). \ | ||
| filter(SequenceFamilyAssociation.sequence_id.in_(sequence_ids)).all() | ||
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| seq_to_fam = {f.sequence_id: f.gene_family_id for f in family_associations} | ||
| fam_to_data = defaultdict(list) | ||
| famID_to_name = {} | ||
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| for f in family_associations: | ||
| fam_to_data[f.gene_family_id].append({'id': f.sequence_id, 'name': f.sequence.name}) | ||
| famID_to_name[f.gene_family_id] = f.family.name | ||
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| for r in results_a: | ||
| f = seq_to_fam[r.profile.sequence_id] if r.profile.sequence_id in seq_to_fam.keys() else None | ||
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| if f is None: | ||
| continue | ||
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| if f not in table_data.keys(): | ||
| table_data[f] = {'id': f, 'name': famID_to_name[f], 'left_genes': [], 'right_genes': []} | ||
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| table_data[f]['left_genes'].append({'id': r.profile.sequence_id, | ||
| 'name': r.profile.sequence.name, | ||
| 'shortest_alias': r.profile.sequence.shortest_alias, | ||
| 'low_abundance': r.profile.low_abundance}) | ||
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| for r in results_b: | ||
| f = seq_to_fam[r.profile.sequence_id] if r.profile.sequence_id in seq_to_fam.keys() else None | ||
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| if f is None: | ||
| continue | ||
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| if f not in table_data.keys(): | ||
| table_data[f] = {'id': f, 'name': famID_to_name[f], 'left_genes': [], 'right_genes': []} | ||
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| table_data[f]['right_genes'].append({'id': r.profile.sequence_id, | ||
| 'name': r.profile.sequence.name, | ||
| 'shortest_alias': r.profile.sequence.shortest_alias, | ||
| 'low_abundance': r.profile.low_abundance | ||
| }) | ||
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| for f in table_data.keys(): | ||
| if len(table_data[f]['left_genes']) > 0 and len(table_data[f]['right_genes']) == 0: | ||
| table_data[f]['type'] = 'left' | ||
| counts['left'] += 1 | ||
| elif len(table_data[f]['right_genes']) > 0 and len(table_data[f]['left_genes']) == 0: | ||
| table_data[f]['type'] = 'right' | ||
| counts['right'] += 1 | ||
| else: | ||
| table_data[f]['type'] = 'intersection' | ||
| counts['intersection'] += 1 | ||
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| return counts, table_data |