Application Mutation

The MUTATION application contains the actions to generate index mutation from Nextclade.

Key files of the « MUTATION » application

management.commands

run_index_mutation.py

class apps.mutation.management.commands.run_index_mutation.Command(stdout=None, stderr=None, no_color=False, force_color=False)
handle(*args, **kwargs)

SUMMARY LINE

Run task for non index file

HOW TO USE

docker-compose exec web python manage.py run_index_mutation

Add -f docker-compose.prod.yml in Prod

models.py

class apps.mutation.models.GenomicFeature(*args, **kwargs)

Genomic Feature table

exception DoesNotExist
exception MultipleObjectsReturned
class apps.mutation.models.IntermediateMutationGenomic(id, mutation, result)
exception DoesNotExist
exception MultipleObjectsReturned
class apps.mutation.models.IntermediateMutationProteomic(id, mutation, result)
exception DoesNotExist
exception MultipleObjectsReturned
class apps.mutation.models.MutationGenomic(*args, **kwargs)

Mutation nucleotide table

exception DoesNotExist
exception MultipleObjectsReturned
class apps.mutation.models.MutationProteomic(*args, **kwargs)

Mutation proteomic table

exception DoesNotExist
exception MultipleObjectsReturned
class apps.mutation.models.Protein(*args, **kwargs)

Protein table

exception DoesNotExist
exception MultipleObjectsReturned
class apps.mutation.models.ProteomicFeature(*args, **kwargs)

Proteomic Feature table

exception DoesNotExist
exception MultipleObjectsReturned
class apps.mutation.models.SeqName(*args, **kwargs)

Sequence name table

exception DoesNotExist
exception MultipleObjectsReturned

test.py

class apps.mutation.tests.mutationTaskTestCase(methodName='runTest')

Test for mutation task functions

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_index_mutation()

Test index mutation

test_index_mutation_auto()

Test index mutation auto

class apps.mutation.tests.mutationTestCase(methodName='runTest')

Test for mutation app

setUp()

Hook method for setting up the test fixture before exercising it.

test_str_Protein()

Test model : get str from Protein

test_str_SeqName()

Test model : get str from Seqnam

test_upload_gene_bad_extension()

Test admin upload gene bad extension

test_upload_gene_bad_file()

Test admin upload gene bad file

test_upload_gene_error()

Test admin upload gene error

test_upload_genomic()

Test admin upload genomic feature

test_upload_proteomic()

Test admin upload proteomic feature

test_upload_proteomic_bad_extension()

Test admin upload proteomi bad extension

test_upload_proteomic_bad_file()

Test admin upload proteomic bad file

test_upload_proteomic_error()

Test admin upload proteomic error

view.py