Index

A

active_strand (shmir.data.models.Backbone attribute) adjusted_frames() (in module shmir.designer.utils)

as_json() (shmir.data.models.Result method)

B

Backbone (class in shmir.data.models) backbone (shmir.data.models.Result attribute) BAD_MNRA (shmir.tests.test_ncbi_api.TestGetDataFromNcbi attribute)

BaseException blast_path() (in module shmir.contextmanagers)

C

catch_errors() (in module shmir.decorators) check_is_in_sequence() (shmir.data.models.Immuno class method)

create_backbone() (in module shmir.testing)

D

DATA_BASE (shmir.tests.test_ncbi_api.TestGetDataFromNcbi attribute)

F

flanks3_a (shmir.data.models.Backbone attribute) flanks3_s (shmir.data.models.Backbone attribute)

flanks5_a (shmir.data.models.Backbone attribute) flanks5_s (shmir.data.models.Backbone attribute)

G

generate_regexp() (shmir.data.models.Backbone method) generate_regexp_all() (shmir.data.models.Backbone class method) generic_path() (in module shmir.contextmanagers) get_all() (shmir.testing.TestModelBase method) get_async_result() (in module shmir.async) get_bool() (in module shmir.settings) get_config() (in module shmir.settings)

get_data() (in module shmir.data.ncbi_api) get_db_config() (in module shmir.settings) get_int() (in module shmir.settings) get_mRNA() (in module shmir.data.ncbi_api) get_task_id() (shmir.data.models.Result method) GOOD_MRNA (shmir.tests.test_ncbi_api.TestGetDataFromNcbi attribute)

H

homogeneity (shmir.data.models.Backbone attribute)

I

id (shmir.data.models.Backbone attribute) (shmir.data.models.Immuno attribute) (shmir.data.models.InputData attribute) (shmir.data.models.Result attribute) (shmir.tests.test_db.TestModelBaseCase.TestModel attribute) Immuno (class in shmir.data.models) immunostimulatory (shmir.data.models.InputData attribute) IncorrectDataError

input_data (shmir.data.models.Result attribute) input_id (shmir.data.models.Result attribute) InputData (class in shmir.data.models)

L

link (shmir.data.models.Immuno attribute) loop_a (shmir.data.models.Backbone attribute)

loop_s (shmir.data.models.Backbone attribute)

M

maximum_CG (shmir.data.models.InputData attribute) maximum_offtarget (shmir.data.models.InputData attribute) mfold_path() (in module shmir.contextmanagers) mfold_task_creator() (in module shmir.views) mfold_task_result() (in module shmir.views) mfold_task_status() (in module shmir.views) minimum_CG (shmir.data.models.InputData attribute) miRBase_link (shmir.data.models.Backbone attribute)

miRNA_a (shmir.data.models.Backbone attribute) miRNA_end_3 (shmir.data.models.Backbone attribute) miRNA_end_5 (shmir.data.models.Backbone attribute) miRNA_length (shmir.data.models.Backbone attribute) miRNA_max (shmir.data.models.Backbone attribute) miRNA_min (shmir.data.models.Backbone attribute) miRNA_s (shmir.data.models.Backbone attribute)

N

name (shmir.data.models.Backbone attribute)

NoResultError

P

pdf (shmir.data.models.Result attribute)

put_to_db() (shmir.testing.TestModelBase method)

R

receptor (shmir.data.models.Immuno attribute) regexp (shmir.data.models.Backbone attribute) Result (class in shmir.data.models)

results (shmir.data.models.InputData attribute) reverse_complement() (in module shmir.designer.utils)

S

scaffold (shmir.data.models.InputData attribute) scaffolds() (in module shmir.views) score (shmir.data.models.Result attribute) send_email() (in module shmir.decorators) sequence (shmir.data.models.Immuno attribute) (shmir.data.models.Result attribute) setUp() (shmir.testing.TestModelBase method) shmir (module), [1] (shmir.data.models.Result attribute) shmir.async (module), [1] shmir.context_managers (module) shmir.contextmanagers (module) shmir.data (module), [1] shmir.data.models (module) shmir.data.ncbi_api (module), [1] shmir.decorators (module), [1] shmir.designer (module), [1] shmir.designer.error (module) shmir.designer.errors (module)

shmir.designer.models (module) shmir.designer.utils (module), [1] shmir.result_handlers (module), [1] shmir.settings (module), [1] shmir.testing (module), [1] shmir.tests (module) shmir.tests.test_db (module) shmir.tests.test_ncbi_api (module) shmir.tests.test_validators (module) shmir.views (module), [1] siRNA1 (shmir.data.models.Backbone attribute) siRNA2 (shmir.data.models.Backbone attribute) sirna_task_creator() (in module shmir.views) sirna_task_result() (in module shmir.views) sirna_task_status() (in module shmir.views) structure (shmir.data.models.Backbone attribute)

T

tearDown() (shmir.testing.TestModelBase method) template() (shmir.data.models.Backbone method) test_adjusted_frames() (shmir.tests.test_db.TestBackboneModel method) test_calculate_gc_content() (shmir.tests.test_validators.TestTranscriptValidators method) test_get_and_put_to_db() (shmir.tests.test_db.TestModelBaseCase method) test_get_data() (shmir.tests.test_ncbi_api.TestGetDataFromNcbi method) test_get_mRNA() (shmir.tests.test_ncbi_api.TestGetDataFromNcbi method) test_incorrect_get_mRNA() (shmir.tests.test_ncbi_api.TestGetDataFromNcbi method) test_no_results_get_mRNA() (shmir.tests.test_ncbi_api.TestGetDataFromNcbi method) test_reverse_complement() (shmir.tests.test_db.TestBackboneModel method) test_template() (shmir.tests.test_db.TestBackboneModel method) test_validate_gc_content() (shmir.tests.test_validators.TestTranscriptValidators method)

test_validate_gc_content_not_in_range() (shmir.tests.test_validators.TestTranscriptValidators method) TestBackboneModel (class in shmir.tests.test_db) TestGetDataFromNcbi (class in shmir.tests.test_ncbi_api) TestModelBase (class in shmir.testing) TestModelBaseCase (class in shmir.tests.test_db) TestModelBaseCase.TestModel (class in shmir.tests.test_db) TestTranscriptValidators (class in shmir.tests.test_validators) transcript_name (shmir.data.models.InputData attribute) transcript_task_creator() (in module shmir.views) transcript_task_result() (in module shmir.views) transcript_task_status() (in module shmir.views)

V

ValidationError

Z

zip_file_mfold() (in module shmir.result_handlers) zip_files_from_sirna() (in module shmir.result_handlers)

zip_files_from_transcript() (in module shmir.result_handlers)