Assay Information
genie_registry.assay
¶
Assay information class
Classes¶
Assayinfo
¶
Bases: FileTypeFormat
Assay information file type
Functions¶
process_steps(assay_info_df, newPath, databaseSynId)
¶
Process bed input and update bed database
| PARAMETER | DESCRIPTION |
|---|---|
assay_info_df
|
Assay information dataframe
|
newPath
|
Path to processed assay information
|
databaseSynId
|
assay information database synapse id
|
| RETURNS | DESCRIPTION |
|---|---|
|
path to assay information dataframe |
validate_all_seq_assay_ids_exist_in_clinical_database(all_seq_assays, skip_database_checks)
¶
Validates that all SEQ_ASSAY_IDs in the clinical sample database for that center exists in the assay information file for that center.
Conditions
| Condition | Result |
|---|---|
| Assay information file has more SEQ_ASSAY_IDs than in clinical database | ✅ PASS |
| Assay information file has the same SEQ_ASSAY_IDs as in clinical database | ✅ PASS |
| Assay information file has less SEQ_ASSAY_IDs than in clinical database | ❌ FAIL |
| PARAMETER | DESCRIPTION |
|---|---|
all_seq_assays
|
list of all the SEQ_ASSAY_IDs in the assay information file
TYPE:
|
skip_database_checks
|
Whether to skip this validation check since it requires access to the internal clinical sample database
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
str
|
error message
TYPE:
|