def add_convenience_annotations(annotation):
"""
Add a bunch of convenience lookups to an annotation.
This is kind of a historical relic - should try to remove as many as we can
TODO: yeah let's aim to get rid of this completely
"""
vep_annotation = annotation['vep_annotation']
annotation['gene_ids'] = vep_annotations.get_gene_ids(vep_annotation)
annotation["coding_gene_ids"] = vep_annotations.get_coding_gene_ids(vep_annotation)
annotation['worst_vep_annotation_index'] = vep_annotations.get_worst_vep_annotation_index(vep_annotation)
annotation['worst_vep_index_per_gene'] = {}
annotation['annotation_tags'] = list({a['consequence'] for a in vep_annotation})
for gene_id in annotation['gene_ids']:
annotation['worst_vep_index_per_gene'][gene_id] = vep_annotations.get_worst_vep_annotation_index(
vep_annotation,
gene_id=gene_id
)
per_gene = {}
for gene_id in annotation['coding_gene_ids']:
per_gene[gene_id] = vep_annotations.get_worst_vep_annotation_index(vep_annotation, gene_id=gene_id)
annotation['worst_vep_index_per_gene'] = per_gene
worst_vep_annotation = vep_annotation[annotation['worst_vep_annotation_index']]
annotation['vep_consequence'] = None
if worst_vep_annotation:
annotation['vep_consequence'] = worst_vep_annotation['consequence']
annotation['vep_group'] = None
if worst_vep_annotation:
annotation['vep_group'] = constants.ANNOTATION_GROUP_REVERSE_MAP[annotation['vep_consequence']]
def add_convenience_annotations(annotation):
"""
Add a bunch of convenience lookups to an annotation.
This is kind of a historical relic - should try to remove as many as we can
TODO: yeah let's aim to get rid of this completely
"""
vep_annotation = annotation['vep_annotation']
annotation['gene_ids'] = vep_annotations.get_gene_ids(vep_annotation)
annotation["coding_gene_ids"] = vep_annotations.get_coding_gene_ids(vep_annotation)
annotation['worst_vep_annotation_index'] = vep_annotations.get_worst_vep_annotation_index(vep_annotation)
annotation['worst_vep_index_per_gene'] = {}
annotation['annotation_tags'] = list({a['consequence'] for a in vep_annotation})
for gene_id in annotation['gene_ids']:
annotation['worst_vep_index_per_gene'][gene_id] = vep_annotations.get_worst_vep_annotation_index(
vep_annotation,
gene_id=gene_id
)
per_gene = {}
for gene_id in annotation['coding_gene_ids']:
per_gene[gene_id] = vep_annotations.get_worst_vep_annotation_index(vep_annotation, gene_id=gene_id)
annotation['worst_vep_index_per_gene'] = per_gene
worst_vep_annotation = vep_annotation[annotation['worst_vep_annotation_index']]
annotation['vep_consequence'] = None
if worst_vep_annotation:
annotation['vep_consequence'] = worst_vep_annotation['consequence']
annotation['vep_group'] = None
if worst_vep_annotation:
annotation['vep_group'] = constants.ANNOTATION_GROUP_REVERSE_MAP[annotation['vep_consequence']]