Allow for incremental addition of data to alt_allele [VS-52] #7993
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #7993 +/- ##
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Coverage ? 77.030%
Complexity ? 21708
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Files ? 1375
Lines ? 82251
Branches ? 13121
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Hits ? 63358
Misses ? 13764
Partials ? 5129 |
mcovarr
reviewed
Aug 18, 2022
mcovarr
approved these changes
Aug 19, 2022
gbggrant
approved these changes
Aug 22, 2022
| @@ -39,6 +39,7 @@ def populate_alt_allele_table(call_set_identifier, query_project, vet_table_name | |||
| parser.add_argument('--query_project',type=str, help='Google project where query should be executed', required=True) | |||
| parser.add_argument('--vet_table_name',type=str, help='vet table name to ingest', required=True) | |||
| parser.add_argument('--fq_dataset',type=str, help='project and dataset for data', required=True) | |||
| parser.add_argument('--max_sample_id',type=str, help='Maximum value of sample_id already loaded', required=True) | |||
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Annoying nit:
Suggested change
| parser.add_argument('--max_sample_id',type=str, help='Maximum value of sample_id already loaded', required=True) | |
| parser.add_argument('--max_sample_id', type=str, help='Maximum value of sample_id already loaded', required=True) |
kcibul
reviewed
Aug 22, 2022
| @@ -103,7 +157,7 @@ task CreateAltAlleleTable { | |||
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| echo "project_id = ~{project_id}" > ~/.bigqueryrc | |||
| bq query --location=US --project_id=~{project_id} --format=csv --use_legacy_sql=false ~{bq_labels} \ | |||
| 'CREATE OR REPLACE TABLE `~{project_id}.~{dataset_name}.alt_allele` ( | |||
| 'CREATE TABLE IF NOT EXISTS `~{project_id}.~{dataset_name}.alt_allele` ( | |||
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ooh, I wasn't aware of this command… nice!
kcibul
reviewed
Aug 22, 2022
| position1 as (select * from `{fq_vet_table}` WHERE call_GT IN ('0/1', '1/0', '1/1', '0|1', '1|0', '1|1', '0/2', '0|2','2/0', '2|0')), | ||
| position2 as (select * from `{fq_vet_table}` WHERE call_GT IN ('1/2', '1|2', '2/1', '2|1'))""" | ||
| WITH | ||
| position1 as (select * from `{fq_vet_table}` WHERE call_GT IN ('0/1', '1/0', '1/1', '0|1', '1|0', '1|1', '0/2', '0|2','2/0', '2|0') AND sample_id > {max_sample_id}), |
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smart, I like the use of > rather than some IN kind of clause
This was referenced Mar 17, 2023
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alt_allelealt_alleleto figure out whichvet_table to start with and what sample IDs data to grabgvs-internal.rsa_gvs_quickstart_dev.alt_allele(done with existing version) vs.gvs-internal.rsa_gvs_quickstart_dev.alt_allele_incremental(done in two batches with code from this branch)Closed https://broadworkbench.atlassian.net/browse/VS-52