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bpblanken d30d2f8
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bpblanken 524de9d
do it correctly :/
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ruff
bpblanken 116bb9b
correct feature flag
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strvctvre
bpblanken 2b6ab30
updates for directory structure
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| # Run locally with: | ||
| # | ||
| # gcloud builds submit --quiet --config .cloudbuild/strvctvre-docker.cloudbuild.yaml v03_pipeline/deploy | ||
| steps: | ||
| - name: 'gcr.io/kaniko-project/executor:v1.3.0' | ||
| args: | ||
| - --destination=gcr.io/seqr-project/strvctvre-docker-image | ||
| - --dockerfile=Dockerfile.strvctvre | ||
| - --cache=true | ||
| - --cache-ttl=168h | ||
|
|
||
| timeout: 1800s |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| #!/usr/bin/env bash | ||
|
|
||
| set -eux | ||
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|
||
| REFERENCE_GENOME=$1 | ||
| STRVCTVRE_REFERENCE_DATASETS_DIR=${STRVCTVRE_REFERENCE_DATASETS_DIR:-/var/seqr/strvctvre-reference-data} | ||
|
|
||
| case $REFERENCE_GENOME in | ||
| GRCh38) | ||
| STRVCTVRE_REFERENCE_DATA_FILES=( | ||
| 'gs://seqr-reference-data/strvctvre_data/hg38.phyloP100way.bw' | ||
| ) | ||
| ;; | ||
| *) | ||
| echo "Invalid reference genome $REFERENCE_GENOME, should be GRCh38" | ||
| exit 1 | ||
| esac | ||
|
|
||
| if [ -f "$STRVCTVRE_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then | ||
| echo "Skipping download because already successful" | ||
| exit 0; | ||
| fi | ||
|
|
||
| mkdir -p "$STRVCTVRE_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"; | ||
| rm -rf "${STRVCTVRE_REFERENCE_DATASETS_DIR:?}"/"${REFERENCE_GENOME:?}"/*; | ||
|
|
||
| for reference_data_file in "${STRVCTVRE_REFERENCE_DATA_FILES[@]}"; do | ||
| echo "Downloading" "$reference_data_file"; | ||
| gsutil cp "$reference_data_file" "$STRVCTVRE_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/ & | ||
| done; | ||
| wait | ||
| touch "$STRVCTVRE_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -eux | ||
|
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| STRVCTVRE_REFERENCE_DATASETS_DIR=${STRVCTVRE_REFERENCE_DATASETS_DIR:-/var/seqr/strvctvre-reference-data} | ||
| STRVCTVRE_DOCKER_IMAGE="gcr.io/seqr-project/strvctvre-docker-image" | ||
| docker run --platform linux/amd64 -i -v $STRVCTVRE_DOCKER_IMAGE:$STRVCTVRE_DOCKER_IMAGE:ro $STRVCTVRE_DOCKER_IMAGE -p $WORKDIR "$@" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| FROM python:3.11-bullseye as build | ||
| LABEL maintainer="Broad TGG" | ||
|
|
||
| # Sourced from https://stackoverflow.com/a/58269633 | ||
| ENV PATH="/root/miniconda3/bin:${PATH}" | ||
| RUN apt-get update && \ | ||
| apt-get install -y wget && \ | ||
| apt-get clean && \ | ||
| rm -rf /var/lib/apt/lists/* | ||
| RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \ | ||
| mkdir -p /root/.conda && \ | ||
| bash miniconda.sh -b -p /root/miniconda3 && \ | ||
| rm -f miniconda.sh | ||
|
|
||
| RUN git clone --depth 1 https://github.com/andrewSharo/StrVCTVRE | ||
| WORKDIR /StrVCTVRE | ||
| RUN conda env create -f environment_py3.yml | ||
| ENTRYPOINT ["conda", "run", "-n", "StrVCTVRE_py_3", "python3", "StrVCTVRE.py"] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| import hail as hl | ||
|
|
||
| from v03_pipeline.lib.annotations import sv | ||
| from v03_pipeline.lib.misc.pedigree import Family | ||
| from v03_pipeline.lib.model import ReferenceGenome, Sex | ||
|
|
||
|
|
||
| def overwrite_male_non_par_calls( | ||
| mt: hl.MatrixTable, | ||
| families: set[Family], | ||
| ) -> hl.MatrixTable: | ||
| male_sample_ids = { | ||
| s.sample_id for f in families for s in f.samples.values() if s.sex == Sex.MALE | ||
| } | ||
| male_sample_ids = ( | ||
| hl.set(male_sample_ids) if male_sample_ids else hl.empty_set(hl.str) | ||
| ) | ||
| par_intervals = hl.array( | ||
| [ | ||
| i | ||
| for i in hl.get_reference(ReferenceGenome.GRCh38).par | ||
| if i.start.contig == ReferenceGenome.GRCh38.x_contig | ||
| ], | ||
| ) | ||
| non_par_interval = hl.interval( | ||
| par_intervals[0].end, | ||
| par_intervals[1].start, | ||
| ) | ||
| # NB: making use of existing formatting_annotation_fns. | ||
| # We choose to annotate & drop here as the sample level | ||
| # fields are dropped by the time we format variants. | ||
| mt = mt.annotate_rows( | ||
| start_locus=sv.start_locus(mt), | ||
| end_locus=sv.end_locus(mt), | ||
| ) | ||
| mt = mt.annotate_entries( | ||
| GT=hl.if_else( | ||
| ( | ||
| male_sample_ids.contains(mt.s) | ||
| & non_par_interval.overlaps( | ||
| hl.interval( | ||
| mt.start_locus, | ||
| mt.end_locus, | ||
| ), | ||
| ) | ||
| ), | ||
| hl.Call([1, 1], phased=False), | ||
| mt.GT, | ||
| ), | ||
| ) | ||
| return mt.drop('start_locus', 'end_locus') |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| import unittest | ||
|
|
||
| import hail as hl | ||
|
|
||
| from v03_pipeline.lib.misc.io import import_callset, select_relevant_fields | ||
| from v03_pipeline.lib.misc.pedigree import Family, Sample | ||
| from v03_pipeline.lib.misc.sample_ids import subset_samples | ||
| from v03_pipeline.lib.misc.sv import overwrite_male_non_par_calls | ||
| from v03_pipeline.lib.model import DatasetType, ReferenceGenome, Sex | ||
|
|
||
| TEST_SV_VCF = 'v03_pipeline/var/test/callsets/sv_1.vcf' | ||
|
|
||
|
|
||
| class SVTest(unittest.TestCase): | ||
| def test_overwrite_male_non_par_calls(self) -> None: | ||
| mt = import_callset(TEST_SV_VCF, ReferenceGenome.GRCh38, DatasetType.SV) | ||
| mt = select_relevant_fields( | ||
| mt, | ||
| DatasetType.SV, | ||
| ) | ||
| mt = subset_samples( | ||
| mt, | ||
| hl.Table.parallelize( | ||
| [{'s': sample_id} for sample_id in ['RGP_164_1', 'RGP_164_2']], | ||
| hl.tstruct(s=hl.dtype('str')), | ||
| key='s', | ||
| ), | ||
| ) | ||
| mt = overwrite_male_non_par_calls( | ||
| mt, | ||
| { | ||
| Family( | ||
| family_guid='family_1', | ||
| samples={ | ||
| 'RGP_164_1': Sample(sample_id='RGP_164_1', sex=Sex.FEMALE), | ||
| 'RGP_164_2': Sample(sample_id='RGP_164_2', sex=Sex.MALE), | ||
| }, | ||
| ), | ||
| }, | ||
| ) | ||
| mt = mt.filter_rows(mt.locus.contig == 'chrX') | ||
| self.assertEqual( | ||
| [ | ||
| hl.Locus(contig='chrX', position=3, reference_genome='GRCh38'), | ||
| hl.Locus(contig='chrX', position=2781700, reference_genome='GRCh38'), | ||
| ], | ||
| mt.locus.collect(), | ||
| ) | ||
| self.assertEqual( | ||
| [ | ||
| hl.Call(alleles=[0, 0], phased=False), | ||
| # END of this variant < start of the non-par region. | ||
| hl.Call(alleles=[0, 1], phased=False), | ||
| hl.Call(alleles=[0, 0], phased=False), | ||
| hl.Call(alleles=[1, 1], phased=False), | ||
| ], | ||
| mt.GT.collect(), | ||
| ) | ||
| self.assertFalse( | ||
| hasattr(mt, 'start_locus'), | ||
| ) |
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this worked! Verified the
StrVCTVREannotation is present in the VCF in the right format.