SweFreq
docs/rtd-helper
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
access (Dataset attribute)
access_current (Dataset attribute)
(User attribute)
access_logs (Dataset attribute)
(User attribute)
access_pending (Dataset attribute)
(User attribute)
access_requested (DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
account_expires (SFTPUser attribute)
action (UserAccessLog attribute)
add_consequence_to_variant() (in module backend.modules.browser.utils)
add_consequence_to_variants() (in module backend.modules.browser.utils)
AdminHandler (class in backend.handlers)
affiliation (User attribute)
allele_count (Variant attribute)
(VariantMate attribute)
allele_freq (Variant attribute)
(VariantMate attribute)
allele_num (Variant attribute)
(VariantMate attribute)
alt (Variant attribute)
(VariantMate attribute)
AngularTemplate (class in backend.handlers)
annotation_severity() (in module backend.modules.browser.utils)
Application (class in backend.route)
ApproveUser (class in backend.application)
assertHTTPCode() (RequestTests method)
AuthorizedHandler (class in backend.handlers)
AuthorizedStaticNginxFileHandler (class in backend.handlers)
Autocomplete (class in backend.modules.browser.browser_handlers)
autocomplete() (in module backend.modules.browser.lookups)
available_from (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
avg_seq_depth (Dataset attribute)
B
backend.application (module)
backend.auth (module)
backend.db (module)
backend.handlers (module)
backend.modules.browser.browser_handlers (module)
backend.modules.browser.lookups (module)
backend.modules.browser.route (module)
backend.modules.browser.utils (module)
backend.route (module)
backend.settings (module)
backend.test (module)
BaseHandler (class in backend.handlers)
BaseModel (class in backend.db)
BaseStaticNginxFileHandler (class in backend.handlers)
beacon_access (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
beacon_uri (Dataset attribute)
BeaconCounts (class in backend.db)
browser (module)
browser_uri (Dataset attribute)
build_dataset_structure() (in module backend.application)
build_dict_from_row() (in module backend.db)
C
callcount (BeaconCounts attribute)
canonical_transcript (Gene attribute)
chrom (Coverage attribute)
(Feature attribute)
(Gene attribute)
(Transcript attribute)
(Variant attribute)
(VariantMate attribute)
chrom_id (VariantMate attribute)
Collection (class in backend.application)
(class in backend.db)
collection (SampleSet attribute)
collection_id (SampleSet attribute)
consent_logs (DatasetVersion attribute)
(User attribute)
contact_email (Study attribute)
contact_name (Study attribute)
cookies (RequestTests attribute)
country (User attribute)
country_list (CountryList attribute)
CountryList (class in backend.application)
Coverage (class in backend.db)
coverage (Coverage attribute)
coverage_levels (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
coverage_set (DatasetVersion attribute)
current_version (Dataset attribute)
(ReferenceSet attribute)
D
data (DatasetLogo attribute)
data_contact_link (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
data_contact_name (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
Dataset (class in backend.db)
dataset (DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
(DatasetLogo attribute)
(DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(SampleSet attribute)
(UserAccessLog attribute)
dataset_access (User attribute)
dataset_file (UserDownloadLog attribute)
dataset_file_id (UserDownloadLog attribute)
dataset_id (DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
(DatasetLogo attribute)
(DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(SampleSet attribute)
(UserAccessLog attribute)
dataset_size (Dataset attribute)
dataset_version (Coverage attribute)
(DatasetFile attribute)
(Linkhash attribute)
(Metrics attribute)
(UserConsentLog attribute)
(Variant attribute)
(VariantMate attribute)
dataset_version_id (Coverage attribute)
(DatasetFile attribute)
(Linkhash attribute)
(Metrics attribute)
(UserConsentLog attribute)
(Variant attribute)
(VariantMate attribute)
dataset_versions (ReferenceSet attribute)
DatasetAccess (class in backend.db)
DatasetAccessCurrent (class in backend.db)
DatasetAccessPending (class in backend.db)
DatasetFile (class in backend.db)
DatasetFiles (class in backend.application)
datasetid (BeaconCounts attribute)
DatasetLogo (class in backend.db)
datasets (Study attribute)
DatasetUsersCurrent (class in backend.application)
DatasetUsersPending (class in backend.application)
DatasetVersion (class in backend.db)
DatasetVersionCurrent (class in backend.db)
db_field (EnumField attribute)
db_value() (EnumField method)
dbnsfp_version (ReferenceSet attribute)
description (Dataset attribute)
(DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(Study attribute)
destroySession() (RequestTests method)
DeveloperLoginHandler (class in backend.auth)
DeveloperLogoutHandler (class in backend.auth)
DoesNotExist (BaseModel attribute)
(BeaconCounts attribute)
(Collection attribute)
(Coverage attribute)
(Dataset attribute)
(DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
(DatasetFile attribute)
(DatasetLogo attribute)
(DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(Feature attribute)
(Gene attribute)
(GeneOtherNames attribute)
(Linkhash attribute)
(Metrics attribute)
(ReferenceSet attribute)
(SFTPUser attribute)
(SampleSet attribute)
(Study attribute)
(Transcript attribute)
(User attribute)
(UserAccessLog attribute)
(UserConsentLog attribute)
(UserDownloadLog attribute)
(Variant attribute)
(VariantGenes attribute)
(VariantMate attribute)
(VariantTranscripts attribute)
Download (class in backend.modules.browser.browser_handlers)
download_logs (DatasetFile attribute)
(User attribute)
E
ElixirLoginHandler (class in backend.auth)
ElixirLogoutHandler (class in backend.auth)
email (User attribute)
ensembl_version (ReferenceSet attribute)
EnumField (class in backend.db)
ethnicity (Collection attribute)
exons (Gene attribute)
expires_on (Linkhash attribute)
F
Feature (class in backend.db)
feature_type (Feature attribute)
file_access (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
file_size (DatasetFile attribute)
files (DatasetVersion attribute)
filter_string (Variant attribute)
format_bytes() (in module backend.application)
full_name (Dataset attribute)
(Gene attribute)
G
gencode_version (ReferenceSet attribute)
Gene (class in backend.db)
gene (Feature attribute)
(GeneOtherNames attribute)
(Transcript attribute)
(VariantGenes attribute)
gene_id (Feature attribute)
(Gene attribute)
(GeneOtherNames attribute)
(Transcript attribute)
(VariantGenes attribute)
GeneOtherNames (class in backend.db)
generate_password() (SFTPAccess method)
GenerateTemporaryLink (class in backend.application)
genes (ReferenceSet attribute)
(Variant attribute)
get() (AngularTemplate method)
(Autocomplete method)
(BaseStaticNginxFileHandler method)
(Collection method)
(CountryList method)
(DatasetFiles method)
(DatasetUsersCurrent method)
(DatasetUsersPending method)
(DeveloperLoginHandler method)
(DeveloperLogoutHandler method)
(Download method)
(ElixirLoginHandler method)
(ElixirLogoutHandler method)
(GetCoverage method)
(GetCoveragePos method)
(GetDataset method)
(GetGene method)
(GetRegion method)
(GetSchema method)
(GetTranscript method)
(GetUser method)
(GetVariant method)
(GetVariants method)
(ListDatasetVersions method)
(ListDatasets method)
(QuitHandler method)
(RequestTests method)
(SFTPAccess method)
(Search method)
(ServeLogo method)
(TemporaryStaticNginxFileHandler method)
(UserDatasetAccess method)
get_admin_datasets() (in module backend.db)
get_awesomebar_result() (in module backend.modules.browser.lookups)
get_coverage() (in module backend.modules.browser.utils)
get_coverage_for_bases() (in module backend.modules.browser.lookups)
get_coverage_for_transcript() (in module backend.modules.browser.lookups)
get_coverage_pos() (in module backend.modules.browser.utils)
get_current_user() (BaseHandler method)
get_dataset() (in module backend.db)
get_dataset_version() (in module backend.db)
get_exons_in_transcript() (in module backend.modules.browser.lookups)
get_flags_from_variant() (in module backend.modules.browser.utils)
get_gene() (in module backend.modules.browser.lookups)
get_gene_by_dbid() (in module backend.modules.browser.lookups)
get_gene_by_name() (in module backend.modules.browser.lookups)
get_genes_in_region() (in module backend.modules.browser.lookups)
get_next_free_uid() (in module backend.db)
get_proper_hgvs() (in module backend.modules.browser.utils)
get_protein_hgvs() (in module backend.modules.browser.utils)
get_raw_variant() (in module backend.modules.browser.lookups)
get_transcript() (in module backend.modules.browser.lookups)
get_transcript_hgvs() (in module backend.modules.browser.utils)
get_transcripts_in_gene() (in module backend.modules.browser.lookups)
get_transcripts_in_gene_by_dbid() (in module backend.modules.browser.lookups)
get_user() (ElixirLoginHandler method)
get_user_token() (ElixirLoginHandler method)
get_variant() (in module backend.modules.browser.lookups)
get_variant_list() (in module backend.modules.browser.utils)
get_variants_by_rsid() (in module backend.modules.browser.lookups)
get_variants_in_gene() (in module backend.modules.browser.lookups)
get_variants_in_region() (in module backend.modules.browser.lookups)
get_variants_in_transcript() (in module backend.modules.browser.lookups)
GetCoverage (class in backend.modules.browser.browser_handlers)
GetCoveragePos (class in backend.modules.browser.browser_handlers)
GetDataset (class in backend.application)
GetGene (class in backend.modules.browser.browser_handlers)
GetRegion (class in backend.modules.browser.browser_handlers)
GetSchema (class in backend.application)
GetTranscript (class in backend.modules.browser.browser_handlers)
getUrl() (RequestTests method)
GetUser (class in backend.application)
GetVariant (class in backend.modules.browser.browser_handlers)
GetVariants (class in backend.modules.browser.browser_handlers)
H
has_access (DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
has_access() (User method)
has_image() (Dataset method)
has_requested_access() (User method)
hash (Linkhash attribute)
hist (Metrics attribute)
hom_count (Variant attribute)
HOST (RequestTests attribute)
I
id (BaseModel attribute)
(Collection attribute)
(Coverage attribute)
(Dataset attribute)
(DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
(DatasetFile attribute)
(DatasetLogo attribute)
(DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(Feature attribute)
(Gene attribute)
(GeneOtherNames attribute)
(Linkhash attribute)
(Metrics attribute)
(ReferenceSet attribute)
(SFTPUser attribute)
(SampleSet attribute)
(Study attribute)
(Transcript attribute)
(User attribute)
(UserAccessLog attribute)
(UserConsentLog attribute)
(UserDownloadLog attribute)
(Variant attribute)
(VariantGenes attribute)
(VariantMate attribute)
(VariantTranscripts attribute)
identity (User attribute)
identity_type (User attribute)
initialize() (AngularTemplate method)
(BaseStaticNginxFileHandler method)
is_admin (DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
is_admin() (User method)
is_region_too_large() (in module backend.modules.browser.utils)
L
link_hashes (DatasetVersion attribute)
(User attribute)
Linkhash (class in backend.db)
ListDatasets (class in backend.application)
ListDatasetVersions (class in backend.application)
LogEvent (class in backend.application)
login_user() (RequestTests method)
logo (Dataset attribute)
M
mate (DatasetVersion attribute)
mate_chrom (VariantMate attribute)
mate_id (VariantMate attribute)
mate_start (VariantMate attribute)
mean (Coverage attribute)
median (Coverage attribute)
metric (Metrics attribute)
Metrics (class in backend.db)
metrics_set (DatasetVersion attribute)
mids (Metrics attribute)
mim_annotation (Transcript attribute)
mim_gene_accession (Transcript attribute)
mimetype (DatasetLogo attribute)
N
name (Collection attribute)
(DatasetFile attribute)
(Gene attribute)
(GeneOtherNames attribute)
(ReferenceSet attribute)
(User attribute)
newSession() (RequestTests method)
num_variants (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
O
on_finish() (BaseHandler method)
order_vep_by_csq() (in module backend.modules.browser.utils)
orig_alt_alleles (Variant attribute)
other_names (Gene attribute)
P
parse_dataset() (in module backend.modules.browser.utils)
parse_region() (in module backend.modules.browser.utils)
password_hash (SFTPUser attribute)
phenotype (SampleSet attribute)
pi_email (Study attribute)
pi_name (Study attribute)
portal_avail (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
pos (Coverage attribute)
(Variant attribute)
(VariantMate attribute)
post() (ApproveUser method)
(GenerateTemporaryLink method)
(LogEvent method)
(RequestAccess method)
(RequestTests method)
(RevokeUser method)
(SFTPAccess method)
prepare() (AdminHandler method)
(AuthorizedHandler method)
(BaseHandler method)
(SafeHandler method)
publication_date (Study attribute)
python_value() (EnumField method)
Q
quality_metrics (Variant attribute)
QuitHandler (class in backend.application)
R
ref (Variant attribute)
(VariantMate attribute)
ref_doi (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(Study attribute)
reference_build (ReferenceSet attribute)
reference_set (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(Gene attribute)
reference_set_id (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
(Gene attribute)
ReferenceSet (class in backend.db)
remove_extraneous_information() (in module backend.modules.browser.utils)
remove_extraneous_vep_annotations() (in module backend.modules.browser.utils)
RequestAccess (class in backend.application)
RequestTests (class in backend.test)
RevokeUser (class in backend.application)
rsid (Variant attribute)
S
SafeHandler (class in backend.handlers)
SafeStaticFileHandler (class in backend.handlers)
sample_sets (Collection attribute)
(Dataset attribute)
sample_size (SampleSet attribute)
SampleSet (class in backend.db)
Search (class in backend.modules.browser.browser_handlers)
seq_center (Dataset attribute)
seq_tech (Dataset attribute)
seq_type (Dataset attribute)
ServeLogo (class in backend.application)
session (RequestTests attribute)
set_user_msg() (BaseHandler method)
setUp() (TestAdminAccess method)
(TestLoggedInUser method)
(TestRequestAccess method)
(TestUserManagement method)
sftp_user (User attribute)
SFTPAccess (class in backend.application)
SFTPUser (class in backend.db)
short_name (Dataset attribute)
site_quality (Variant attribute)
start (Feature attribute)
(Gene attribute)
(Transcript attribute)
stop (Feature attribute)
(Gene attribute)
(Transcript attribute)
strand (Feature attribute)
(Gene attribute)
(Transcript attribute)
Study (class in backend.db)
study (Dataset attribute)
study_id (Dataset attribute)
T
tearDown() (TestAdminAccess method)
(TestLoggedInUser method)
(TestRequestAccess method)
(TestUserManagement method)
TemporaryStaticNginxFileHandler (class in backend.handlers)
terms (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
test_admin_approve_user() (TestUserManagement method)
test_admin_is_admin() (TestAdminAccess method)
test_admin_list_users() (TestAdminAccess method)
test_admin_list_users_get_data() (TestAdminAccess method)
test_admin_list_users_only_own_project_1() (TestAdminAccess method)
test_admin_list_users_only_own_project_2() (TestAdminAccess method)
test_create_temporary_link() (TestEndpoints method)
test_dataset_collection() (TestEndpoints method)
test_dataset_logo() (TestEndpoints method)
test_datasets() (TestEndpoints method)
test_full_user_roundabout() (TestUserManagement method)
test_get_one_version() (TestEndpoints method)
test_get_users_current() (TestEndpoints method)
test_get_users_pending() (TestEndpoints method)
test_get_versions() (TestEndpoints method)
test_get_xsrf_token() (TestRequestAccess method)
test_list_files() (TestEndpoints method)
test_login() (TestRequestAccess method)
test_login_admin() (TestAdminAccess method)
test_one_dataset() (TestEndpoints method)
test_recently_approved_user_can_list_files() (TestUserManagement method)
test_recently_revoked_user_cant_list_files() (TestUserManagement method)
test_request_access() (TestEndpoints method)
test_request_access_correctly() (TestRequestAccess method)
test_request_access_with_get() (TestRequestAccess method)
test_request_access_with_wrong_xsrf_1() (TestRequestAccess method)
test_request_access_with_wrong_xsrf_2() (TestRequestAccess method)
test_request_access_without_xsrf() (TestRequestAccess method)
test_user_datasets() (TestEndpoints method)
test_user_me() (TestEndpoints method)
TestAdminAccess (class in backend.test)
TestEndpoints (class in backend.test)
testLoggedInFiles() (TestLoggedInUser method)
testLoggedInTempLinkGet() (TestLoggedInUser method)
testLoggedInTempLinkPost() (TestLoggedInUser method)
testLoggedInTempLinkPostXSRF1() (TestLoggedInUser method)
testLoggedInTempLinkPostXSRF2() (TestLoggedInUser method)
TestLoggedInUser (class in backend.test)
TestRequestAccess (class in backend.test)
TestUserManagement (class in backend.test)
title (Study attribute)
Transcript (class in backend.db)
transcript (Feature attribute)
(VariantTranscripts attribute)
transcript_id (Feature attribute)
(Transcript attribute)
(VariantTranscripts attribute)
transcripts (Gene attribute)
(Transcript attribute)
(Variant attribute)
ts (UserAccessLog attribute)
(UserConsentLog attribute)
(UserDownloadLog attribute)
U
UnsafeHandler (class in backend.handlers)
uri (DatasetFile attribute)
User (class in backend.db)
user (DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
(Linkhash attribute)
(SFTPUser attribute)
USER (TestRequestAccess attribute)
user (UserAccessLog attribute)
(UserConsentLog attribute)
(UserDownloadLog attribute)
user_id (DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
(Linkhash attribute)
(SFTPUser attribute)
(UserAccessLog attribute)
(UserConsentLog attribute)
(UserDownloadLog attribute)
user_name (SFTPUser attribute)
user_uid (SFTPUser attribute)
UserAccessLog (class in backend.db)
UserConsentLog (class in backend.db)
UserDatasetAccess (class in backend.application)
UserDownloadLog (class in backend.db)
V
Variant (class in backend.db)
variant (VariantGenes attribute)
(VariantTranscripts attribute)
variant_id (Variant attribute)
(VariantGenes attribute)
(VariantMate attribute)
(VariantTranscripts attribute)
variantcount (BeaconCounts attribute)
VariantGenes (class in backend.db)
VariantMate (class in backend.db)
variants (DatasetVersion attribute)
(Gene attribute)
(Transcript attribute)
VariantTranscripts (class in backend.db)
vep_annotations (Variant attribute)
version (DatasetVersion attribute)
(DatasetVersionCurrent attribute)
versions (Dataset attribute)
W
wants_newsletter (DatasetAccess attribute)
(DatasetAccessCurrent attribute)
(DatasetAccessPending attribute)
worst_csq_from_csq() (in module backend.modules.browser.utils)
worst_csq_from_list() (in module backend.modules.browser.utils)
worst_csq_index() (in module backend.modules.browser.utils)
worst_csq_with_vep() (in module backend.modules.browser.utils)
write() (BaseHandler method)
write_error() (BaseHandler method)
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