def __init__(self, **kwargs):
filters = [
Filter(
Mutation, 'sources', comparators=['in'],
choices=list(source_manager.visible_fields.keys()),
default=None, nullable=True,
as_sqlalchemy=sqlalchemy_filter_from_source_name
),
Filter(
Site, 'types', comparators=['in'],
choices={
site_type.name: site_type
for site_type in SiteType.available_types()
},
as_sqlalchemy=SiteType.fuzzy_filter,
as_sqlalchemy_joins=[SiteType]
),
Filter(
Gene, 'has_ptm_muts',
comparators=['eq'],
as_sqlalchemy=lambda value: text('ptm_muts_cnt > 0') if value else text('true')
),
Filter(
Gene, 'is_known_kinase',
comparators=['eq'],
as_sqlalchemy=lambda value: Protein.kinase.any()
)
] + [
filter
for filter in source_dependent_filters()
if filter.has_sqlalchemy # filters without sqlalchemy interface are not supported for table views
]
super().__init__(filters)
self.update_from_request(request)
def common_filters(protein,
default_source='MC3',
source_nullable=False,
custom_datasets_ids=[]):
return [
Filter(Mutation,
'sources',
comparators=['in'],
choices=list(source_manager.visible_fields.keys()),
default=default_source,
nullable=source_nullable,
as_sqlalchemy=sqlalchemy_filter_from_source_name),
Filter(UserMutations,
'sources',
comparators=['in'],
choices=list(custom_datasets_ids),
default=None,
nullable=True),
Filter(Mutation, 'is_ptm', comparators=['eq']),
Filter(Drug,
'groups.name',
comparators=['in'],
nullable=False,
choices=cached_queries.drug_groups,
default=['approved'],
multiple='all',
as_sqlalchemy=True),
Filter(Site,
'types',
comparators=['in'],
choices={
site_type.name: site_type
for site_type in SiteType.available_types()
},
custom_comparators={'in': SiteType.fuzzy_comparator},
as_sqlalchemy=SiteType.fuzzy_filter,
as_sqlalchemy_joins=[Site.types])
] + source_dependent_filters(protein)
def show(self, refseq):
"""Show a protein by:
+ needleplot
+ tracks (sequence + data tracks)
"""
protein, filter_manager = self.get_protein_and_manager(refseq)
user_datasets = current_user.datasets_names_by_uri()
return template(
'protein/show.html',
protein=protein,
filters=filter_manager,
widgets=create_widgets(
protein,
filter_manager.filters,
custom_datasets_names=user_datasets.values()),
site_types=['multi_ptm'] + SiteType.available_types(),
mutation_types=Mutation.types,
)
from models import SiteType, AnySiteType
site_types_with_any = SiteType.available_types(include_any=True)
site_types = SiteType.available_types()
site_types_names = [site_type.name for site_type in site_types]
any_site_type = AnySiteType()
class Motif:
def __init__(self, name, pattern):
self.name = name
self.pattern = pattern
motifs = [
Motif(pattern='.{7}N[^P][STCV].{5}', name='n_linked'),
Motif(pattern='.{7}(TAPP|TSAPP|TV.P|[ST].P).{4}', name='o_linked'),
Motif(pattern='(.{7}W..W.{4}|.{4}W..W.{7}|.{7}W[ST].C.{4})', name='c_linked')
]