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Updated resource paths to requester pays #233

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Merged
mike-w-wilson merged 5 commits into from
Jul 9, 2020
Merged

Updated resource paths to requester pays #233

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e9b7db4
Updated ld paths to requester pays
mike-w-wilson Jun 5, 2020
676ed3b
resources hail tables to requester pays
mike-w-wilson Jun 11, 2020
6c82441
Updated change log to include PR
mike-w-wilson Jun 11, 2020
94a6ddc
Added vep context ht
mike-w-wilson Jun 12, 2020
7e8571e
Merge branch 'master' into mw/update_ld_resource_rp
mike-w-wilson Jun 12, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@
* Created `training.py` in variant QC and added `sample_training_examples` [(224)](https://github.com/broadinstitute/gnomad_methods/pull/224)
* Added variant QC pipeline function `train_rf_model` [(224)](https://github.com/broadinstitute/gnomad_methods/pull/224)
* Use local copy of VEP config instead of reading from bucket [(#231)](https://github.com/broadinstitute/gnomad_methods/pull/231)
* Updated gnomAD resources paths for hail tables to requester pays buckets [(#233)](https://github.com/broadinstitute/gnomad_methods/pull/233)

## Version 0.3.0 - April 28th, 2020

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7 changes: 3 additions & 4 deletions gnomad/resources/grch37/gnomad.py
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@@ -1,6 +1,5 @@
from gnomad.resources.resource_utils import (
DataException,
PedigreeResource,
TableResource,
VersionedTableResource,
)
Expand Down Expand Up @@ -67,7 +66,7 @@ def _public_release_ht_path(data_type: str, version: str) -> str:
:param version: One of the release versions of gnomAD on GRCh37
:return: Path to release Table
"""
return f"gs://gnomad-public/release/{version}/ht/{data_type}/gnomad.{data_type}.r{version}.sites.ht"
return f"gs://gnomad-public-requester-pays/release/{version}/ht/{data_type}/gnomad.{data_type}.r{version}.sites.ht"


def _public_coverage_ht_path(data_type: str, version: str) -> str:
Expand All @@ -78,7 +77,7 @@ def _public_coverage_ht_path(data_type: str, version: str) -> str:
:param version: One of the release versions of gnomAD on GRCh37
:return: path to coverage Table
"""
return f"gs://gnomad-public/release/{version}/coverage/{data_type}/gnomad.{data_type}.r{version}.coverage.ht"
return f"gs://gnomad-public-requester-pays/release/{version}/coverage/{data_type}/gnomad.{data_type}.r{version}.coverage.ht"


def _public_pca_ht_path(subpop: str) -> str:
Expand All @@ -100,7 +99,7 @@ def _liftover_data_path(data_type: str, version: str) -> str:
:param version: One of the release versions of gnomAD on GRCh37
:return: Path to chosen Table
"""
return f"gs://gnomad-public/release/{version}/liftover_grch38/ht/{data_type}/gnomad.{data_type}.r{version}.sites.liftover_grch38.ht"
return f"gs://gnomad-public-requester-pays/release/{version}/liftover_grch38/ht/{data_type}/gnomad.{data_type}.r{version}.sites.liftover_grch38.ht"


def public_release(data_type: str) -> VersionedTableResource:
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12 changes: 6 additions & 6 deletions gnomad/resources/grch37/gnomad_ld.py
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Expand Up @@ -15,7 +15,7 @@ def _ld_matrix_path(
CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
)
subdir = "sv/" if data_type == "genomes_snv_sv" else ""
return f'gs://gnomad-public/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.bm'
return f'gs://gnomad-public-requester-pays/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.bm'


def _ld_index_path(
Expand All @@ -30,15 +30,15 @@ def _ld_index_path(
CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
)
subdir = "sv/" if data_type == "genomes_snv_sv" else ""
return f'gs://gnomad-public/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.variant_indices.ht'
return f'gs://gnomad-public-requester-pays/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.variant_indices.ht'


def _ld_snv_sv_path(pop):
return f"gs://gnomad-public/release/2.1.1/ld/sv/gnomad.genomes_snv_sv.r2.1.1.{pop}.snv_sv.ld.ht"
return f"gs://gnomad-public-requester-pays/release/2.1.1/ld/sv/gnomad.genomes_snv_sv.r2.1.1.{pop}.snv_sv.ld.ht"


def _ld_snv_sv_index_path(pop, type):
return f"gs://gnomad-public/release/2.1.1/ld/sv/gnomad.genomes_snv_sv.r2.1.1.{pop}.snv_sv.ld.{type}.txt.bgz"
return f"gs://gnomad-public-requester-pays/release/2.1.1/ld/sv/gnomad.genomes_snv_sv.r2.1.1.{pop}.snv_sv.ld.{type}.txt.bgz"


def _cross_pop_ld_scores_path(
Expand All @@ -52,7 +52,7 @@ def _cross_pop_ld_scores_path(
version = (
CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
)
return f'gs://gnomad-public/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop1}.{pop2}.{"adj." if adj else ""}ld_scores.ht'
return f'gs://gnomad-public-requester-pays/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop1}.{pop2}.{"adj." if adj else ""}ld_scores.ht'


def _ld_scores_path(
Expand All @@ -62,7 +62,7 @@ def _ld_scores_path(
version = (
CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
)
return f'gs://gnomad-public/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop}.{"adj." if adj else ""}ld_scores.ht'
return f'gs://gnomad-public-requester-pays/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop}.{"adj." if adj else ""}ld_scores.ht'


def ld_matrix(pop: str) -> BlockMatrixResource:
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4 changes: 2 additions & 2 deletions gnomad/resources/grch38/gnomad.py
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Expand Up @@ -42,7 +42,7 @@ def _public_release_ht_path(data_type: str, version: str) -> str:
:param version: One of the release versions of gnomAD on GRCh38
:return: Path to release Table
"""
return f"gs://gnomad-public/release/{version}/ht/{data_type}/gnomad.{data_type}.r{version}.sites.ht"
return f"gs://gnomad-public-requester-pays/release/{version}/ht/{data_type}/gnomad.{data_type}.r{version}.sites.ht"


def _public_coverage_ht_path(data_type: str, version: str) -> str:
Expand All @@ -53,7 +53,7 @@ def _public_coverage_ht_path(data_type: str, version: str) -> str:
:param version: One of the release versions of gnomAD on GRCh38
:return: path to coverage Table
"""
return f"gs://gnomad-public/release/{version}/coverage/{data_type}/gnomad.{data_type}.r{version}.coverage.ht"
return f"gs://gnomad-public-requester-pays/release/{version}/coverage/{data_type}/gnomad.{data_type}.r{version}.coverage.ht"


def public_release(data_type: str) -> VersionedTableResource:
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4 changes: 2 additions & 2 deletions gnomad/utils/vep.py
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Expand Up @@ -65,11 +65,11 @@
VEP_REFERENCE_DATA = {
"GRCh37": {
"vep_config": "file:///vep_data/vep-gcloud.json",
"all_possible": "gs://gnomad-public/papers/2019-flagship-lof/v1.0/context/Homo_sapiens_assembly19.fasta.snps_only.vep_20181129.ht",
"all_possible": "gs://gnomad-public-requester-pays/resources/context/grch37_context_vep_annotated.ht",
},
"GRCh38": {
"vep_config": "file:///vep_data/vep-gcloud.json",
"all_possible": "gs://gnomad-public/resources/context/grch38_context_vep_annotated.ht",
"all_possible": "gs://gnomad-public-requester-pays/resources/context/grch38_context_vep_annotated.ht",
},
}

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