diff --git a/.github/workflows/test-runner.yml b/.github/workflows/test-runner.yml index a443b567..8886ca39 100644 --- a/.github/workflows/test-runner.yml +++ b/.github/workflows/test-runner.yml @@ -42,24 +42,3 @@ jobs: - name: Run pytest preprocessing run: pytest -v ${{ github.workspace }}/tests/preprocessing shell: micromamba-shell {0} - - DeepRVAT-Tests-Runner-Annotations: - runs-on: ubuntu-latest - steps: - - - name: Check out repository code - uses: actions/checkout@v4 - - uses: mamba-org/setup-micromamba@v1.8.0 - with: - environment-name: deeprvat-annotation-gh-action - environment-file: ${{ github.workspace }}/deeprvat_annotations.yml - cache-environment: true - cache-downloads: true - - - name: Install DeepRVAT - run: pip install -e ${{ github.workspace }} - shell: micromamba-shell {0} - - - name: Run pytest annotations - run: pytest -v ${{ github.workspace }}/tests/annotations - shell: micromamba-shell {0} diff --git a/deeprvat/annotations/annotations.py b/deeprvat/annotations/annotations.py index ba08e5a2..ee534712 100644 --- a/deeprvat/annotations/annotations.py +++ b/deeprvat/annotations/annotations.py @@ -1,7 +1,5 @@ import logging import os - -os.environ["TF_CPP_MIN_LOG_LEVEL"] = "1" import pickle import random import sys @@ -1362,6 +1360,45 @@ def merge_deepsea_pcas( merged.to_parquet(out_file) +@cli.command() +@click.argument("in_variants", type=click.Path(exists=True)) +@click.argument("out_variants", type=click.Path()) +def process_annotations(in_variants: str, out_variants: str): + """ + Process variant annotations, filter for canonical variants, and aggregate consequences. + + Parameters: + - in_variants (str): Path to the input variant annotation file in parquet format. + - out_variants (str): Path to save the processed variant annotation file in parquet format. + + Returns: + None + + Notes: + - The function reads the input variant annotation file. + - It filters for canonical variants where the 'CANONICAL' column is equal to 'YES'. + - The 'Gene' column is renamed to 'gene_id'. + - Consequences for different alleles are aggregated by combining the variant ID with the gene ID. + - The processed variant annotations are saved to the specified output file. + + Example: + $ python annotations.py process_annotations input_variants.parquet output_variants.parquet + """ + variant_path = Path(in_variants) + variants = pd.read_parquet(variant_path) + + logger.info("filtering for canonical variants") + + variants = variants.loc[variants.CANONICAL == "YES"] + variants.rename(columns={"Gene": "gene_id"}, inplace=True) + + logger.info("aggregating consequences for different alleles") + + # combining variant id with gene id + variants["censequence_id"] = variants["id"].astype(str) + variants["gene_id"] + variants.to_parquet(out_variants, compression="zstd") + + def process_chunk_addids(chunk: pd.DataFrame, variants: pd.DataFrame) -> pd.DataFrame: """ Process a chunk of data by adding identifiers from a variants dataframe. @@ -1470,14 +1507,16 @@ def add_ids(annotation_file: str, variant_file: str, njobs: int, out_file: str): @cli.command() @click.argument("annotation_file", type=click.Path(exists=True)) @click.argument("variant_file", type=click.Path(exists=True)) +@click.argument("njobs", type=int) @click.argument("out_file", type=click.Path()) -def add_ids_dask(annotation_file: str, variant_file: str, out_file: str): +def add_ids_dask(annotation_file: str, variant_file: str, njobs: int, out_file: str): """ Add identifiers from a variant file to an annotation file using Dask and save the result. Parameters: - annotation_file (str): Path to the input annotation file in Parquet format. - variant_file (str): Path to the input variant file in Parquet format. + - njobs (int): Number of parallel jobs to process the data. - out_file (str): Path to save the processed data in Parquet format. Returns: @@ -1493,7 +1532,7 @@ def add_ids_dask(annotation_file: str, variant_file: str, out_file: str): $ python annotations.py add_ids_dask annotation_data.parquet variant_data.parquet 4 processed_data.parquet """ data = dd.read_parquet(annotation_file, blocksize=25e9) - all_variants = pd.read_parquet(variant_file) + all_variants = pd.read_table(variant_file) data = data.rename( columns={ "#CHROM": "chrom", @@ -1666,7 +1705,7 @@ def merge_annotations( logger.info("load variant_file") logger.info(f"reading in {variant_file}") - variants = pd.read_parquet(variant_file) + variants = pd.read_csv(variant_file, sep="\t") logger.info("merge vep to variants M:1") ca = vep_df.merge( @@ -1738,19 +1777,7 @@ def process_vep( vcf_file, names=["chrom", "pos", "#Uploaded_variation", "ref", "alt"] ) if "#Uploaded_variation" in vep_file.columns: - vep_file = vep_file.merge(vcf_df, on="#Uploaded_variation", how="left") - if vep_file.chrom.isna().sum() > 0: - vep_file.loc[vep_file.chrom.isna(), ["chrom", "pos", "ref", "alt"]] = ( - vep_file[vep_file["chrom"].isna()]["#Uploaded_variation"] - .str.replace("_", ":") - .str.replace("/", ":") - .str.split(":", expand=True) - .values - ) - assert vep_file.chrom.isna().sum() == 0 - assert vep_file.pos.isna().sum() == 0 - assert vep_file.ref.isna().sum() == 0 - assert vep_file.alt.isna().sum() == 0 + vep_file = vep_file.merge(vcf_df, on="#Uploaded_variation") if "pos" in vep_file.columns: vep_file["pos"] = vep_file["pos"].astype(int) @@ -1952,7 +1979,7 @@ def get_af_from_gt(genotype_file: str, variants_filepath: str, out_file: str): """ import h5py - variants = pd.read_parquet(variants_filepath) + variants = pd.read_table(variants_filepath) max_variant_id = variants["id"].max() logger.info("Computing allele frequencies") @@ -2015,19 +2042,19 @@ def calculate_maf(annotations_path: str, out_file: str): @cli.command() -@click.argument("gene_id_file", type=click.Path(exists=True)) +@click.argument("protein_id_file", type=click.Path(exists=True)) @click.argument("annotations_path", type=click.Path(exists=True)) @click.argument("out_file", type=click.Path()) -def add_gene_ids(gene_id_file: str, annotations_path: str, out_file: str): +def add_protein_ids(protein_id_file: str, annotations_path: str, out_file: str): """ - Add gene IDs to the annotations based on gene ID mapping file. + Add protein IDs to the annotations based on protein ID mapping file. Parameters: - - gene_id_file (str): Path to the gene ID mapping file. + - protein_id_file (str): Path to the protein ID mapping file. - annotations_path (str): Path to the annotations file. - out_file (str): Path to the output file to save the annotations with protein IDs. """ - genes = pd.read_parquet(gene_id_file) + genes = pd.read_parquet(protein_id_file) genes[["gene_base", "feature"]] = genes["gene"].str.split(".", expand=True) genes.drop(columns=["feature", "gene", "gene_name", "gene_type"], inplace=True) genes.rename(columns={"id": "gene_id"}, inplace=True) @@ -2042,7 +2069,7 @@ def add_gene_ids(gene_id_file: str, annotations_path: str, out_file: str): @cli.command() @click.argument("gtf_filepath", type=click.Path(exists=True)) @click.argument("out_file", type=click.Path()) -def create_gene_id_file(gtf_filepath: str, out_file: str): +def create_protein_id_file(gtf_filepath: str, out_file: str): """ Create a protein ID mapping file from the GTF file. diff --git a/deeprvat_annotations.yml b/deeprvat_annotations.yml index dd6feb6e..0c4b6896 100644 --- a/deeprvat_annotations.yml +++ b/deeprvat_annotations.yml @@ -16,7 +16,6 @@ dependencies: - tensorflow=2.11.0 - pyarrow=11.0.0 - fastparquet=2023.4.0 - - bioconda::pyranges=0.0.129 #comment out lines below if you want to use preinstalled bcftools or samtools - bcftools=1.17 - samtools=1.17 diff --git a/docs/annotations.md b/docs/annotations.md index 29e079fa..94bd9ff7 100644 --- a/docs/annotations.md +++ b/docs/annotations.md @@ -88,12 +88,6 @@ Data for VEP plugins and the CADD cache are stored in `annotation data`. ## Running the annotation pipeline ### Preconfiguration -- Install the annotation environment - ```shell - mamba env create -f path/to/deeprvat/deeprvat_annotations.yml - mamba activate deeprvat_annotations - pip install -e path/to/deeprvat - ``` - Clone the repositories mentioned in [requirements](#requirements) into `repo_dir` and install the needed conda environments with ```shell mamba env create -f repo_dir/absplice/environment.yaml diff --git a/example/annotations/preprocessing_workdir/norm/variants/variants.parquet b/example/annotations/preprocessing_workdir/norm/variants/variants.tsv.gz similarity index 100% rename from example/annotations/preprocessing_workdir/norm/variants/variants.parquet rename to example/annotations/preprocessing_workdir/norm/variants/variants.tsv.gz diff --git a/pipelines/annotations.snakefile b/pipelines/annotations.snakefile index db3c6d4d..f3b617c5 100644 --- a/pipelines/annotations.snakefile +++ b/pipelines/annotations.snakefile @@ -52,7 +52,7 @@ included_chromosomes = config.get( ) preprocess_dir = Path(config.get("preprocessing_workdir", "")) -variant_pq = config.get("variant_parquetfile_path") or preprocess_dir / 'norm' / 'variants' / 'variants.parquet' +variant_file = config.get("variant_file_path") or preprocess_dir / 'norm' / 'variants' / 'variants.tsv.gz' genotype_file = config.get("genotype_file_path") or preprocess_dir / 'preprocessed' / 'genotypes.h5' saved_deepripe_models_path = ( Path(config["faatpipe_repo_dir"]) / "data" / "deepripe_models" @@ -84,10 +84,7 @@ vep_input_format = config.get("vep_input_format") or "vcf" vep_nfork = int(config.get("vep_nfork") or 5) af_mode = config.get("af_mode") or "af" condel_config_path = vep_plugin_dir / "config" / "Condel" / "config" -if config.get('additional_vep_plugin_cmds'): - VEP_plugin_cmds = config['additional_vep_plugin_cmds'].values() -else: - VEP_plugin_cmds = [] + #init deepSEA deepSEA_tmp_dir = config.get('deepSEA_tmp_dir')or anno_tmp_dir / 'deepSEA_PCA' @@ -118,8 +115,7 @@ file_paths = [ file_paths = list(chain.from_iterable(file_paths)) human_sort(file_paths) -file_stems = [re.compile(source_variant_file_pattern.format(chr = "(\d+|X|Y)",block='\d+')).search(i).group() for i in file_paths] - +file_stems = [Path(p).stem.split('.')[0] for p in file_paths] absplice_download_dir = config.get('absplice_download_dir') or absplice_repo_dir /'example'/'data'/'resources'/'downloaded_files' absplice_output_dir = config.get('absplice_output_dir', anno_tmp_dir /'absplice') @@ -169,7 +165,7 @@ rule select_rename_fill_columns: resources: mem_mb = lambda wildcards, attempt: 15_000 * (attempt + 1), shell: " ".join([ - f"deeprvat_annotations", + f"python {annotation_python_file}", "select-rename-fill-annotations", "{input.yaml_file}", "{input.annotations_path}", @@ -186,8 +182,8 @@ if not gene_id_file: resources: mem_mb = lambda wildcards, attempt: 15_000 * (attempt + 1), shell: " ".join([ - f"deeprvat_annotations", - "create-gene-id-file", + f"python {annotation_python_file}", + "create-protein-id-file", "{input}", "{output}" ]) @@ -202,7 +198,7 @@ rule filter_by_exon_distance: resources: mem_mb = lambda wildcards, attempt: 25_000 * (attempt + 1), shell: " ".join([ - f"deeprvat_annotations", + f"python {annotation_python_file}", "filter-annotations-by-exon-distance", "{input.annotations_path}", "{input.gtf_file}", @@ -218,8 +214,8 @@ rule add_gene_ids: resources: mem_mb = lambda wildcards, attempt: 19_000 * (attempt + 1), shell: " ".join([ - f"deeprvat_annotations", - "add-gene-ids", + f"python {annotation_python_file}", + "add-protein-ids", "{input.gene_id_file}", "{input.annotations_path}", "{output}" @@ -234,7 +230,7 @@ rule calculate_MAF: resources: mem_mb = lambda wildcards, attempt: 15_000 * (attempt + 1), shell: " ".join([ - f"deeprvat_annotations", + f"python {annotation_python_file}", "calculate-maf", "{input}", "{output}" @@ -253,7 +249,7 @@ rule merge_allele_frequency: resources: mem_mb = lambda wildcards, attempt: 15_000 * (attempt + 1), shell: " ".join([ - f"deeprvat_annotations", + f"python {annotation_python_file}", "merge-af", "{input.annotation_file}", "{input.allele_frequencies}", @@ -268,13 +264,13 @@ rule merge_allele_frequency: rule calculate_allele_frequency: input: genotype_file = genotype_file, - variants = variant_pq + variants = variant_file output: allele_frequencies = anno_tmp_dir / "af_df.parquet" resources: mem_mb = lambda wildcards, attempt: 15_000 * (attempt + 1), shell: " ".join([ - f"deeprvat_annotations", + f"python {annotation_python_file}", "get-af-from-gt", "{input.genotype_file}", "{input.variants}", @@ -297,7 +293,8 @@ rule merge_absplice_scores: shell: " ".join( [ - "deeprvat_annotations", + "python", + f"{annotation_python_file}", "merge-abscores", "{input.current_annotation_file}", "{input.absplice_scores}", @@ -315,7 +312,8 @@ rule aggregate_absplice_scores: shell: " ".join( [ - "deeprvat_annotations", + "python", + f"{annotation_python_file}", "aggregate-abscores {input.current_annotation_file}", str(absplice_output_dir / absplice_main_conf['genome'] / 'dna' ), "{output.score_file} {threads}" @@ -333,7 +331,8 @@ rule merge_deepsea_pcas: shell: " ".join( [ - "deeprvat_annotations", + "python", + f"{annotation_python_file}", "merge-deepsea-pcas", "{input.annotations}", "{input.deepsea_pcas}", @@ -356,7 +355,8 @@ rule concat_annotations: shell: " ".join( [ - "deeprvat_annotations", + "python", + str(annotation_python_file), "concat-annotations", '{params.joined}', "{output}" @@ -373,7 +373,7 @@ rule merge_annotations: / (source_variant_file_pattern + "_variants.eclip_k5_deepripe.csv.gz"), deepripe_hg2=anno_dir / (source_variant_file_pattern + "_variants.eclip_hg2_deepripe.csv.gz"), - variant_file=variant_pq, + variant_file=variant_file, vcf_file= anno_tmp_dir / (source_variant_file_pattern + "_variants.vcf"), output: anno_dir / f"{source_variant_file_pattern}_merged.parquet", @@ -382,7 +382,8 @@ rule merge_annotations: ( "HEADER=$(grep -n '#Uploaded_variation' " + "{input.vep}" - + "| head | cut -f 1 -d ':') && deeprvat_annotations " + + "| head | cut -f 1 -d ':') && python " + + f"{annotation_python_file} " + "merge-annotations $(($HEADER-1)) {input.vep} {input.deepripe_parclip} {input.deepripe_hg2} {input.deepripe_k5} {input.variant_file} {input.vcf_file} {output}" ) @@ -397,7 +398,8 @@ rule deepSea_PCA: ["mkdir -p", str(deepSEA_tmp_dir), "&&", - "deeprvat_annotations", + "python", + f"{annotation_python_file}", "deepsea-pca", "{input.deepsea_anno}", f"{str(deepSEA_pca_obj)}", @@ -410,7 +412,7 @@ rule deepSea_PCA: rule add_ids_deepSea: input: - variant_file=variant_pq, + variant_file=variant_file, annotation_file=deepSEA_tmp_dir / "deepsea_pca.parquet", output: directory(anno_dir / "all_variants.wID.deepSea.parquet"), @@ -419,10 +421,12 @@ rule add_ids_deepSea: shell: " ".join( [ - "deeprvat_annotations", + "python", + f"{annotation_python_file}", "add-ids-dask", "{input.annotation_file}", "{input.variant_file}", + "{threads}", "{output}", ] ) @@ -445,7 +449,8 @@ rule concat_deepSea: shell: " ".join( [ - "deeprvat_annotations", + "python", + f"{annotation_python_file}", "concatenate-deepsea", "{params.joined}", "{output}", @@ -479,7 +484,7 @@ rule deepRiPe_parclip: threads: n_jobs_deepripe resources: mem_mb = lambda wildcards, attempt: 5_000 * (attempt + 1), shell: - f"mkdir -p {pybedtools_tmp_path / 'parclip'} && deeprvat_annotations scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path / 'parclip'} {saved_deepripe_models_path} {{threads}} 'parclip'" + f"mkdir -p {pybedtools_tmp_path / 'parclip'} && python {annotation_python_file} scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path / 'parclip'} {saved_deepripe_models_path} {{threads}} 'parclip'" rule deepRiPe_eclip_hg2: @@ -491,7 +496,7 @@ rule deepRiPe_eclip_hg2: threads: lambda wildcards, attempt: n_jobs_deepripe * attempt resources: mem_mb = lambda wildcards, attempt: 5_000 * (attempt + 1), shell: - f"mkdir -p {pybedtools_tmp_path / 'hg2'} && deeprvat_annotations scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path / 'hg2'} {saved_deepripe_models_path} {{threads}} 'eclip_hg2'" + f"mkdir -p {pybedtools_tmp_path / 'hg2'} && python {annotation_python_file} scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path / 'hg2'} {saved_deepripe_models_path} {{threads}} 'eclip_hg2'" rule deepRiPe_eclip_k5: @@ -503,7 +508,7 @@ rule deepRiPe_eclip_k5: threads: lambda wildcards, attempt: n_jobs_deepripe * attempt resources: mem_mb = lambda wildcards, attempt: 5_000 * (attempt + 1), shell: - f"mkdir -p {pybedtools_tmp_path / 'k5'} && deeprvat_annotations scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path / 'k5'} {saved_deepripe_models_path} {{threads}} 'eclip_k5'" + f"mkdir -p {pybedtools_tmp_path / 'k5'} && python {annotation_python_file} scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path / 'k5'} {saved_deepripe_models_path} {{threads}} 'eclip_k5'" rule vep: @@ -557,7 +562,7 @@ rule vep: "--no_stats", "--per_gene", "--pick_order biotype,mane_select,mane_plus_clinical,canonical,appris,tsl,ccds,rank,length,ensembl,refseq" - ]+['--plugin '+i for i in VEP_plugin_cmds] + ]+['--plugin '+i for i in config['additional_vep_plugin_cmds'].values()] ) diff --git a/pipelines/resources/absplice.yaml b/pipelines/resources/absplice.yaml index e837f1d8..08494895 100755 --- a/pipelines/resources/absplice.yaml +++ b/pipelines/resources/absplice.yaml @@ -29,4 +29,3 @@ dependencies: - interpret == 0.2.7 - interpret-core == 0.2.7 - git+https://github.com/gagneurlab/splicemap.git@9e9831f32c221e850e26757a5f1c132dcd565640 - - git+https://github.com/gagneurlab/absplice.git@e4060e63cca074ac938ea28850a38290c7e8b198 diff --git a/pipelines/resources/absplice_splicing_pred_DNA.snakefile b/pipelines/resources/absplice_splicing_pred_DNA.snakefile index 47106018..913780d3 100644 --- a/pipelines/resources/absplice_splicing_pred_DNA.snakefile +++ b/pipelines/resources/absplice_splicing_pred_DNA.snakefile @@ -119,7 +119,7 @@ rule absplice_dna: params: extra_info = absplice_main_conf['extra_info_dna'] conda: - "absplice" + "absplice" output: absplice_dna = absplice_output_dir / '{genome}' / 'dna' / '{vcf_id}_AbSplice_DNA.csv' script: @@ -127,6 +127,7 @@ rule absplice_dna: rule all_predict_dna: input: + #expand([absplice_output_dir / absplice_main_conf['genome'] / 'dna' / source_variant_file_pattern],zip, chr=chromosomes, block=block) expand([absplice_output_dir / absplice_main_conf['genome'] / 'dna' / '{file_stem}_AbSplice_DNA.csv'],file_stem=file_stems) del splicemap5 diff --git a/setup.py b/setup.py index 5aa4fa41..15f5830b 100644 --- a/setup.py +++ b/setup.py @@ -29,7 +29,6 @@ "deeprvat_train=deeprvat.deeprvat.train:cli", "deeprvat_associate=deeprvat.deeprvat.associate:cli", "deeprvat_preprocess=deeprvat.preprocessing.preprocess:cli", - "deeprvat_annotations=deeprvat.annotations.annotations:cli", "deeprvat_evaluate=deeprvat.deeprvat.evaluate:evaluate", "seed_gene_pipeline=deeprvat.seed_gene_discovery.seed_gene_discovery:cli", "seed_gene_evaluate=deeprvat.seed_gene_discovery.evaluate:cli", diff --git a/tests/annotations/test_annotations.py b/tests/annotations/test_annotations.py deleted file mode 100644 index 4056eed4..00000000 --- a/tests/annotations/test_annotations.py +++ /dev/null @@ -1,652 +0,0 @@ -from pathlib import Path - -import pandas as pd -import pytest -from click.testing import CliRunner -from pandas.testing import assert_frame_equal -from deeprvat.annotations.annotations import cli as annotations_cli - -script_dir = Path(__file__).resolve().parent -tests_data_dir = script_dir / "test_data" - - -@pytest.mark.parametrize( - "test_data_name_dir, deepsea_scores_1, deepsea_scores_2, out_scores, expected_out_scores", - [ - ( - "concatenate_deepseascores_small", - "deepsea_scores_1.tsv", - "deepsea_scores_2.tsv", - "out_scores.parquet", - "expected.parquet", - ), - ( - "concatenate_deepseascores_medium", - "deepsea_scores_1.tsv", - "deepsea_scores_2.tsv", - "out_scores.parquet", - "expected.parquet", - ), - ], -) -def test_concatenate_deepsea( - test_data_name_dir, - deepsea_scores_1, - deepsea_scores_2, - out_scores, - expected_out_scores, - tmp_path, -): - cli_runner = CliRunner() - - current_test_data_dir = tests_data_dir / "concatenate_deepsea" / test_data_name_dir - - deepsea_score_file_1 = current_test_data_dir / "input" / deepsea_scores_1 - deepsea_score_file_2 = current_test_data_dir / "input" / deepsea_scores_2 - out_scores_file = tmp_path / out_scores - expected_out_scores_file = current_test_data_dir / "expected" / expected_out_scores - - cli_parameters = [ - "concatenate-deepsea", - ",".join([deepsea_score_file_1.as_posix(), deepsea_score_file_2.as_posix()]), - out_scores_file.as_posix(), - "8", - ] - - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - - written_results = pd.read_parquet(out_scores_file) - - expected_scores = pd.read_parquet(expected_out_scores_file) - assert_frame_equal(written_results, expected_scores, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, deapseascores_file, variant_file, out_df, expected_out_df", - [ - ( - "add_ids_small", - "deepseascores.parquet", - "variants.parquet", - "out_df.parquet", - "expected.parquet", - ), - ( - "add_ids_medium", - "deepseascores.parquet", - "variants.parquet", - "out_df.parquet", - "expected.parquet", - ), - ], -) -def test_add_ids_dask( - test_data_name_dir, - deapseascores_file, - variant_file, - out_df, - expected_out_df, - tmp_path, -): - cli_runner = CliRunner() - - current_test_data_dir = tests_data_dir / "add_ids_dask" / test_data_name_dir - - deepsea_score_file = current_test_data_dir / "input" / deapseascores_file - variant_path = current_test_data_dir / "input" / variant_file - out_scores_file = tmp_path / out_df - expected_out_scores_file = current_test_data_dir / "expected" / expected_out_df - - cli_parameters = [ - "add-ids-dask", - deepsea_score_file.as_posix(), - variant_path.as_posix(), - out_scores_file.as_posix(), - ] - - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - - written_results = pd.read_parquet(out_scores_file) - - expected_scores = pd.read_parquet(expected_out_scores_file) - assert_frame_equal(written_results, expected_scores, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, deapseascores_file, pca_file, mean_sds_file, expected_out_df", - [ - ( - "deepsea_pca_small", - "deepseascores.parquet", - "deepsea_pca/pca.npy", - "deepsea_pca/mean_sds.parquet", - "deepsea_pca.parquet", - ), - ( - "deepsea_pca_small", - "deepseascores.parquet", - "deepsea_pca/pca.npy", - "{tmp_path}/mean_sds.parquet", - "deepsea_pca.parquet", - ), - ( - "deepsea_pca_small", - "deepseascores.parquet", - "{tmp_path}/pca.npy", - "deepsea_pca/mean_sds.parquet", - "deepsea_pca.parquet", - ), - ( - "deepsea_pca_small", - "deepseascores.parquet", - "{tmp_path}/pca.npy", - "{tmp_path}/mean_sds.parquet", - "deepsea_pca.parquet", - ), - ], -) -def test_deepsea_pca( - test_data_name_dir, - deapseascores_file, - pca_file, - mean_sds_file, - expected_out_df, - tmp_path, -): - cli_runner = CliRunner() - - current_test_data_dir = tests_data_dir / "deepsea_pca" / test_data_name_dir - - deepsea_score_file = current_test_data_dir / "input" / deapseascores_file - pca_file = current_test_data_dir / pca_file.format(tmp_path=tmp_path) - mean_sds_file = current_test_data_dir / mean_sds_file.format(tmp_path=tmp_path) - expected_out_scores_file = current_test_data_dir / "expected" / expected_out_df - - cli_parameters = [ - "deepsea-pca", - deepsea_score_file.as_posix(), - pca_file.as_posix(), - mean_sds_file.as_posix(), - tmp_path.as_posix(), - ] - - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - - written_results = pd.read_parquet(tmp_path / expected_out_df) - - expected_scores = pd.read_parquet(expected_out_scores_file) - assert_frame_equal(written_results, expected_scores, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, expected, hg2_output, k5_output, parclip_output, variants, vcf, vep_output, vep_header_line", - [ - ( - "merge_annotations_small", - "merged_annotations_expected.parquet", - "test_hg2_deepripe.csv.gz", - "test_k5_deepripe.csv.gz", - "test_parclip.csv.gz", - "variants.parquet", - "test.vcf", - "test_vep.tsv", - "49", - ), - ( - "merge_annotations_mixedIDs", - "merged_annotations_expected.parquet", - "test_hg2_deepripe.csv.gz", - "test_k5_deepripe.csv.gz", - "test_parclip.csv.gz", - "variants.parquet", - "test.vcf", - "test_vep.tsv", - "49", - ), - ], -) -def test_merge_annotations( - test_data_name_dir, - expected, - hg2_output, - k5_output, - parclip_output, - variants, - vcf, - vep_output, - vep_header_line, - tmp_path, -): - current_test_data_dir = tests_data_dir / "merge_annotations" / test_data_name_dir - expected_path = current_test_data_dir / "expected" / expected - hg2_deepripe_path = current_test_data_dir / "input" / hg2_output - k5_deepripe_path = current_test_data_dir / "input" / k5_output - parclip_deepripe_path = current_test_data_dir / "input" / parclip_output - vcf_path = current_test_data_dir / "input" / vcf - vep_output_path = current_test_data_dir / "input" / vep_output - variants_path = current_test_data_dir / "input" / variants - output_path = tmp_path / "out_merged.parquet" - cli_runner = CliRunner() - - cli_parameters = [ - "merge-annotations", - vep_header_line, - vep_output_path.as_posix(), - parclip_deepripe_path.as_posix(), - hg2_deepripe_path.as_posix(), - k5_deepripe_path.as_posix(), - variants_path.as_posix(), - vcf_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal( - written_results[expected_results.columns], expected_results, check_exact=False - ) - - -@pytest.mark.parametrize( - "test_data_name_dir, expected, merged_files", - [ - ( - "concatenate_annotations_small", - "expected.parquet", - "chr3test_merged.parquet,chr4test_merged.parquet", - ), - ], -) -def test_concatenate_annotations(test_data_name_dir, expected, merged_files, tmp_path): - current_test_data_dir = ( - tests_data_dir / "concatenate_annotations" / test_data_name_dir - ) - expected_path = current_test_data_dir / "expected" / expected - merged_files = [ - (current_test_data_dir / "input" / file).as_posix() - for file in merged_files.split(",") - ] - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - - cli_parameters = [ - "concat-annotations", - ",".join(merged_files), - output_path.as_posix(), - ] - - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal( - written_results[expected_results.columns], expected_results, check_exact=False - ) - - -@pytest.mark.parametrize( - "test_data_name_dir, annotations, deepSEA_scores, annotation_columns_yaml_file, expected", - [ - ( - "merge_deepsea_pcas_small", - "vep_deepripe.parquet", - "all_variants.wID.deepSea.parquet", - "annotation_colnames_filling_values.yaml", - "expected.parquet", - ), - ], -) -def test_merge_deepsea_pcas( - test_data_name_dir, - annotations, - deepSEA_scores, - annotation_columns_yaml_file, - expected, - tmp_path, -): - current_test_data_dir = tests_data_dir / "merge_deepsea_pcas" / test_data_name_dir - expected_path = current_test_data_dir / "expected" / expected - annotations_path = current_test_data_dir / "input" / annotations - deepSEA_scores_path = current_test_data_dir / "input" / deepSEA_scores - annotation_columns_yaml_path = ( - current_test_data_dir / "input" / annotation_columns_yaml_file - ) - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "merge-deepsea-pcas", - annotations_path.as_posix(), - deepSEA_scores_path.as_posix(), - annotation_columns_yaml_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal( - written_results, expected_results[written_results.columns], check_exact=False - ) - - -@pytest.mark.parametrize( - "test_data_name_dir, annotations, abSplice_score_dir, njobs, expected", - [ - ( - "aggregate_absplice_scores_small", - "vep_deepripe_deepsea.parquet", - "absplice_res_dir", - "8", - "abSplice_score_file.parquet", - ), - ], -) -def test_aggregate_abscores( - test_data_name_dir, annotations, abSplice_score_dir, njobs, expected, tmp_path -): - current_test_data_dir = ( - tests_data_dir / "aggregate_absplice_scores" / test_data_name_dir - ) - annotations_path = current_test_data_dir / "input" / annotations - abscore_path = current_test_data_dir / "input" / abSplice_score_dir - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "aggregate-abscores", - annotations_path.as_posix(), - abscore_path.as_posix(), - output_path.as_posix(), - njobs, - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal( - written_results, expected_results[written_results.columns], check_exact=False - ) - - -@pytest.mark.parametrize( - "test_name_dir, absplice_scores, annotations, expected", - [ - ( - "merge_absplice_scores_small", - "abSplice_score_file.parquet", - "vep_deepripe_deepsea.parquet", - "vep_deepripe_deepsea_absplice.parquet", - ), - ], -) -def test_merge_absplice_scores( - test_name_dir, absplice_scores, annotations, expected, tmp_path -): - current_test_data_dir = tests_data_dir / "merge_absplice_scores" / test_name_dir - absplice_score_path = current_test_data_dir / "input" / absplice_scores - annotation_path = current_test_data_dir / "input" / annotations - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "merge-abscores", - annotation_path.as_posix(), - absplice_score_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal(written_results, expected_results, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, genotype_file, variant_file, expected", - [ - ( - "calculate_allele_frequency_small", - "genotypes.h5", - "variants.parquet", - "af_df.parquet", - ), - ], -) -def test_calculate_allele_frequencies( - test_data_name_dir, genotype_file, variant_file, expected, tmp_path -): - current_test_data_dir = ( - tests_data_dir / "calculate_allele_frequency" / test_data_name_dir - ) - genotype_filepath = current_test_data_dir / "input" / genotype_file - variant_filepath = current_test_data_dir / "input" / variant_file - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "get-af-from-gt", - genotype_filepath.as_posix(), - variant_filepath.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal(written_results, expected_results, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, af_df, annotaton_df, expected", - [ - ( - "merge_af_small", - "af_df.parquet", - "vep_deepripe_deepsea_absplice.parquet", - "vep_deepripe_deepsea_absplice_af.parquet", - ), - ], -) -def test_merge_af(test_data_name_dir, af_df, annotaton_df, expected, tmp_path): - current_test_data_dir = tests_data_dir / "merge_af" / test_data_name_dir - af_path = current_test_data_dir / "input" / af_df - annotaions_path = current_test_data_dir / "input" / annotaton_df - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "merge-af", - af_path.as_posix(), - annotaions_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal( - written_results, expected_results[written_results.columns], check_exact=False - ) - - -@pytest.mark.parametrize( - "test_data_name_dir, annotations, expected", - [ - ( - "calculate_MAF_small", - "annotations.parquet", - "expected.parquet", - ), - ], -) -def test_calculate_maf(test_data_name_dir, annotations, expected, tmp_path): - current_test_data_dir = tests_data_dir / "calculate_MAF" / test_data_name_dir - annotations_path = current_test_data_dir / "input" / annotations - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "calculate-maf", - annotations_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal(written_results, expected_results, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, gtf_file, expected", - [ - ( - "create_gene_id_file_small", - "gencode.v44.annotation.gtf.gz", - "protein_coding_genes.parquet", - ), - ], -) -def test_create_gene_id_file(test_data_name_dir, gtf_file, expected, tmp_path): - current_test_data_dir = tests_data_dir / "create_gene_id_file" / test_data_name_dir - input_path1 = current_test_data_dir / "input" / gtf_file - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "create-gene-id-file", - input_path1.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal( - written_results, expected_results[written_results.columns], check_exact=False - ) - - -@pytest.mark.parametrize( - "test_data_name_dir, annotations, gene_id_file , expected", - [ - ( - "add_gene_ids_small", - "annotations.parquet", - "protein_coding_genes.parquet", - "expected.parquet", - ), - ], -) -def test_add_gene_ids( - test_data_name_dir, annotations, gene_id_file, expected, tmp_path -): - current_test_data_dir = tests_data_dir / "add_gene_ids" / test_data_name_dir - annotations_path = current_test_data_dir / "input" / annotations - gene_id_path = current_test_data_dir / "input" / gene_id_file - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "add-gene-ids", - gene_id_path.as_posix(), - annotations_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal(written_results, expected_results, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, gtf_file, annotations, gene_id_file, expected", - [ - ( - "filter_by_exon_distance_small", - "gencode.v44.annotation.gtf.gz", - "annotations.parquet", - "protein_coding_genes.parquet", - "expected.parquet", - ), - ], -) -def test_filter_by_exon_distance( - test_data_name_dir, gtf_file, annotations, gene_id_file, expected, tmp_path -): - current_test_data_dir = ( - tests_data_dir / "filter_by_exon_distance" / test_data_name_dir - ) - gtf_file_path = current_test_data_dir / "input" / gtf_file - annotations_path = current_test_data_dir / "input" / annotations - gene_id_path = current_test_data_dir / "input" / gene_id_file - - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "filter-annotations-by-exon-distance", - annotations_path.as_posix(), - gtf_file_path.as_posix(), - gene_id_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal(written_results, expected_results, check_exact=False) - - -@pytest.mark.parametrize( - "test_data_name_dir, yaml_file, annotations, expected", - [ - ( - "select_rename_fill_columns_small", - "annotation_colnames_filling_values.yaml", - "annotations.parquet", - "expected.parquet", - ), - ], -) -def test_select_rename_fill_annotations( - test_data_name_dir, yaml_file, annotations, expected, tmp_path -): - current_test_data_dir = ( - tests_data_dir / "select_rename_fill_columns" / test_data_name_dir - ) - yaml_file_path = current_test_data_dir / "input" / yaml_file - annotations_path = current_test_data_dir / "input" / annotations - expected_path = current_test_data_dir / "expected" / expected - output_path = tmp_path / "out.parquet" - cli_runner = CliRunner() - cli_parameters = [ - "select-rename-fill-annotations", - yaml_file_path.as_posix(), - annotations_path.as_posix(), - output_path.as_posix(), - ] - result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False) - assert result.exit_code == 0 - written_results = pd.read_parquet(output_path) - expected_results = pd.read_parquet(expected_path) - assert written_results.shape == expected_results.shape - assert_frame_equal( - written_results, expected_results[written_results.columns], check_exact=False - ) diff --git a/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/expected/expected.parquet b/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/expected/expected.parquet deleted file mode 100644 index cf3bad1a..00000000 Binary files a/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/expected/expected.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/input/annotations.parquet b/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/input/annotations.parquet deleted file mode 100644 index 33835b07..00000000 Binary files a/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/input/annotations.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/input/protein_coding_genes.parquet b/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/input/protein_coding_genes.parquet deleted file mode 100644 index b693bbc4..00000000 Binary files a/tests/annotations/test_data/add_gene_ids/add_gene_ids_small/input/protein_coding_genes.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_ids_dask/add_ids_medium/expected/expected.parquet b/tests/annotations/test_data/add_ids_dask/add_ids_medium/expected/expected.parquet deleted file mode 100644 index ba7ffd78..00000000 Binary files a/tests/annotations/test_data/add_ids_dask/add_ids_medium/expected/expected.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_ids_dask/add_ids_medium/input/deepseascores.parquet b/tests/annotations/test_data/add_ids_dask/add_ids_medium/input/deepseascores.parquet deleted file mode 100644 index b022b25e..00000000 Binary files a/tests/annotations/test_data/add_ids_dask/add_ids_medium/input/deepseascores.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_ids_dask/add_ids_medium/input/variants.parquet b/tests/annotations/test_data/add_ids_dask/add_ids_medium/input/variants.parquet deleted file mode 100644 index 35d9aaf3..00000000 Binary files a/tests/annotations/test_data/add_ids_dask/add_ids_medium/input/variants.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_ids_dask/add_ids_small/expected/expected.parquet b/tests/annotations/test_data/add_ids_dask/add_ids_small/expected/expected.parquet deleted file mode 100644 index f998ee5c..00000000 Binary files a/tests/annotations/test_data/add_ids_dask/add_ids_small/expected/expected.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_ids_dask/add_ids_small/input/deepseascores.parquet b/tests/annotations/test_data/add_ids_dask/add_ids_small/input/deepseascores.parquet deleted file mode 100644 index 2d1f0146..00000000 Binary files a/tests/annotations/test_data/add_ids_dask/add_ids_small/input/deepseascores.parquet and /dev/null differ diff --git a/tests/annotations/test_data/add_ids_dask/add_ids_small/input/variants.parquet b/tests/annotations/test_data/add_ids_dask/add_ids_small/input/variants.parquet deleted file mode 100644 index 35d9aaf3..00000000 Binary files a/tests/annotations/test_data/add_ids_dask/add_ids_small/input/variants.parquet and /dev/null differ diff --git a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/expected/abSplice_score_file.parquet b/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/expected/abSplice_score_file.parquet deleted file mode 100644 index 2cef8024..00000000 Binary files a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/expected/abSplice_score_file.parquet and /dev/null differ diff --git a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/absplice_res_dir/chr3test_variants_header.vcf.gz_AbSplice_DNA.csv b/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/absplice_res_dir/chr3test_variants_header.vcf.gz_AbSplice_DNA.csv deleted file mode 100644 index 60f5e03a..00000000 --- a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/absplice_res_dir/chr3test_variants_header.vcf.gz_AbSplice_DNA.csv +++ /dev/null @@ -1,193 +0,0 @@ -variant,gene_id,tissue,delta_logit_psi,delta_psi,delta_score,splice_site_is_expressed,AbSplice_DNA -chr3:13336897:T>A,ENSG00000132182,Adrenal_Gland,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Pituitary,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Esophagus_Mucosa,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Kidney_Cortex,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Liver,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Lung,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Minor_Salivary_Gland,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Pancreas,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Prostate,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Cells_EBV_transformed_lymphocytes,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Small_Intestine_Terminal_Ileum,0.1271947632745491,0.0013409990441992,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Spleen,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Stomach,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Testis,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Thyroid,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Colon_Transverse,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Whole_Blood,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Brain_Cortex,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Brain_Nucleus_accumbens_basal_ganglia,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Brain_Hypothalamus,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Brain_Caudate_basal_ganglia,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Brain_Cerebellar_Hemisphere,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Brain_Cerebellum,-0.0987188615790356,-0.0010261192228098,0.0,1,0.002860864576028723 -chr3:13336897:T>A,ENSG00000132182,Breast_Mammary_Tissue,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Vagina,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Uterus,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Artery_Aorta,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Artery_Coronary,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Artery_Tibial,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Brain_Amygdala,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Brain_Anterior_cingulate_cortex_BA24,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Skin_Sun_Exposed_Lower_leg,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Skin_Not_Sun_Exposed_Suprapubic,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Ovary,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Brain_Substantia_nigra,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Nerve_Tibial,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Muscle_Skeletal,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Brain_Frontal_Cortex_BA9,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Brain_Hippocampus,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Heart_Left_Ventricle,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Heart_Atrial_Appendage,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Adipose_Visceral_Omentum,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Brain_Putamen_basal_ganglia,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Esophagus_Gastroesophageal_Junction,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Brain_Spinal_cord_cervical_c_1,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Colon_Sigmoid,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Esophagus_Muscularis,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Adipose_Subcutaneous,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Adipose_Visceral_Omentum,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Pituitary,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Heart_Left_Ventricle,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Kidney_Cortex,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Liver,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Lung,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Minor_Salivary_Gland,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Muscle_Skeletal,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Nerve_Tibial,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Ovary,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Pancreas,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Prostate,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Esophagus_Muscularis,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Skin_Not_Sun_Exposed_Suprapubic,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Skin_Sun_Exposed_Lower_leg,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Small_Intestine_Terminal_Ileum,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Spleen,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Stomach,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Testis,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Thyroid,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Uterus,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Vagina,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Heart_Atrial_Appendage,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Esophagus_Mucosa,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Adrenal_Gland,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Frontal_Cortex_BA9,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Artery_Aorta,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Artery_Coronary,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Artery_Tibial,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Amygdala,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Anterior_cingulate_cortex_BA24,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Caudate_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Cerebellar_Hemisphere,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Cerebellum,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Cortex,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Hippocampus,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Esophagus_Gastroesophageal_Junction,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Hypothalamus,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Nucleus_accumbens_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Putamen_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Spinal_cord_cervical_c_1,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Brain_Substantia_nigra,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Breast_Mammary_Tissue,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Cells_EBV_transformed_lymphocytes,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Colon_Sigmoid,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Colon_Transverse,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Adipose_Subcutaneous,,,0.0,0,0.0005700424787606313 -chr3:13336897:T>A,ENSG00000132182,Adipose_Subcutaneous,-0.0987188615790356,-0.0010261192228098,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Adipose_Visceral_Omentum,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Whole_Blood,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Heart_Atrial_Appendage,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Heart_Left_Ventricle,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Kidney_Cortex,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Liver,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Lung,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Minor_Salivary_Gland,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Muscle_Skeletal,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Nerve_Tibial,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Ovary,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Pancreas,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Pituitary,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Prostate,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Skin_Not_Sun_Exposed_Suprapubic,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Skin_Sun_Exposed_Lower_leg,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Small_Intestine_Terminal_Ileum,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Spleen,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Stomach,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Testis,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Thyroid,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Uterus,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Vagina,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Esophagus_Muscularis,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Esophagus_Mucosa,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Esophagus_Gastroesophageal_Junction,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Cortex,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Adrenal_Gland,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Artery_Aorta,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Artery_Coronary,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Artery_Tibial,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Amygdala,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Anterior_cingulate_cortex_BA24,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Caudate_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Cerebellar_Hemisphere,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Cerebellum,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Frontal_Cortex_BA9,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Colon_Transverse,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Hippocampus,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Hypothalamus,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Nucleus_accumbens_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Putamen_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Spinal_cord_cervical_c_1,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Brain_Substantia_nigra,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Breast_Mammary_Tissue,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Cells_EBV_transformed_lymphocytes,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Colon_Sigmoid,,,0.0,0,0.0005700424787606313 -chr3:10151779:G>T,ENSG00000134086,Whole_Blood,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Adipose_Subcutaneous,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Adipose_Visceral_Omentum,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Pituitary,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Heart_Left_Ventricle,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Kidney_Cortex,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Liver,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Lung,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Minor_Salivary_Gland,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Muscle_Skeletal,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Nerve_Tibial,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Ovary,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Pancreas,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Prostate,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Esophagus_Muscularis,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Skin_Not_Sun_Exposed_Suprapubic,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Skin_Sun_Exposed_Lower_leg,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Small_Intestine_Terminal_Ileum,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Spleen,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Stomach,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Testis,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Thyroid,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Uterus,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Vagina,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Heart_Atrial_Appendage,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Esophagus_Mucosa,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Adrenal_Gland,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Frontal_Cortex_BA9,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Artery_Aorta,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Artery_Coronary,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Artery_Tibial,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Amygdala,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Anterior_cingulate_cortex_BA24,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Caudate_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Cerebellar_Hemisphere,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Cerebellum,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Cortex,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Hippocampus,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Esophagus_Gastroesophageal_Junction,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Hypothalamus,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Nucleus_accumbens_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Putamen_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Spinal_cord_cervical_c_1,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Brain_Substantia_nigra,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Breast_Mammary_Tissue,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Cells_EBV_transformed_lymphocytes,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Colon_Sigmoid,,,0.0,0,0.0005700424787606313 -chr3:125013245:A>G,ENSG00000173706,Colon_Transverse,,,0.0,0,0.0005700424787606313 -chr3:139349025:T>C,ENSG00000175110,Whole_Blood,,,0.0,0,0.0005700424787606313 diff --git a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/absplice_res_dir/chr4test_variants_header.vcf.gz_AbSplice_DNA.csv b/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/absplice_res_dir/chr4test_variants_header.vcf.gz_AbSplice_DNA.csv deleted file mode 100644 index db7d0c74..00000000 --- a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/absplice_res_dir/chr4test_variants_header.vcf.gz_AbSplice_DNA.csv +++ /dev/null @@ -1,246 +0,0 @@ -variant,gene_id,tissue,delta_logit_psi,delta_psi,delta_score,splice_site_is_expressed,AbSplice_DNA -chr4:169007628:T>C,ENSG00000145439,Brain_Cerebellar_Hemisphere,-0.2924805955494345,-0.0588679816775568,0.05,1,0.006833637741834292 -chr4:169007628:T>C,ENSG00000145439,Brain_Cerebellum,-0.2924805955494345,-0.0573214450667628,0.05,1,0.006833637741834292 -chr4:169007628:T>C,ENSG00000145439,Brain_Substantia_nigra,-0.2924805955494345,-0.0566263142416471,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Nucleus_accumbens_basal_ganglia,-0.2924805955494345,-0.0542171459327623,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Hypothalamus,-0.2924805955494345,-0.0537109292025781,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Hippocampus,-0.2924805955494345,-0.0513790826672216,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Frontal_Cortex_BA9,-0.2924805955494345,-0.0539980667521867,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Cortex,-0.2924805955494345,-0.0520890438905559,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Putamen_basal_ganglia,-0.2924805955494345,-0.0551813984735419,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Caudate_basal_ganglia,-0.2924805955494345,-0.052206396676825,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Anterior_cingulate_cortex_BA24,-0.2924805955494345,-0.0537744175754923,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Amygdala,-0.2924805955494345,-0.0538417662920955,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Ovary,-0.2924805955494345,-0.0453503859773065,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Brain_Spinal_cord_cervical_c_1,-0.2924805955494345,-0.0510839631880544,0.05,1,0.006522249142751264 -chr4:169007628:T>C,ENSG00000145439,Pituitary,-0.2924805955494345,-0.0341719319284121,0.05,1,0.005140125524902324 -chr4:169007628:T>C,ENSG00000145439,Nerve_Tibial,-0.2924805955494345,-0.0339228709569385,0.05,1,0.004484302690380517 -chr4:169007628:T>C,ENSG00000145439,Thyroid,-0.2924805955494345,-0.0328589953455117,0.05,1,0.004480573733525163 -chr4:169007628:T>C,ENSG00000145439,Uterus,-0.2924805955494345,-0.0310821996594723,0.05,1,0.004480573733525163 -chr4:169007628:T>C,ENSG00000145439,Artery_Tibial,-0.2924805955494345,-0.0287037168558088,0.05,1,0.004480573733525163 -chr4:169007628:T>C,ENSG00000145439,Artery_Aorta,-0.2924805955494345,-0.0303005879830458,0.05,1,0.004480573733525163 -chr4:169007628:T>C,ENSG00000145439,Esophagus_Gastroesophageal_Junction,-0.2924805955494345,-0.0280732952512678,0.05,1,0.0043930876001134845 -chr4:169007628:T>C,ENSG00000145439,Kidney_Cortex,-0.2924805955494345,-0.0267086965806592,0.05,1,0.0043930876001134845 -chr4:169007628:T>C,ENSG00000145439,Artery_Coronary,-0.2924805955494345,-0.0273913899791004,0.05,1,0.0043930876001134845 -chr4:169007628:T>C,ENSG00000145439,Vagina,-0.2924805955494345,-0.0260689205351327,0.05,1,0.004273871261352944 -chr4:169007628:T>C,ENSG00000145439,Esophagus_Muscularis,-0.2924805955494345,-0.0255090745923955,0.05,1,0.0040471476529160035 -chr4:169007628:T>C,ENSG00000145439,Adipose_Subcutaneous,-0.2924805955494345,-0.0249133133651749,0.05,1,0.0040471476529160035 -chr4:169007628:T>C,ENSG00000145439,Breast_Mammary_Tissue,-0.2924805955494345,-0.0240961278969513,0.05,1,0.003882386621127518 -chr4:169007628:T>C,ENSG00000145439,Colon_Sigmoid,-0.2924805955494345,-0.024098663506736,0.05,1,0.003882386621127518 -chr4:169007628:T>C,ENSG00000145439,Prostate,-0.2924805955494345,-0.0236635694806509,0.05,1,0.003882386621127518 -chr4:169007628:T>C,ENSG00000145439,Lung,-0.2924805955494345,-0.0231295590665679,0.05,1,0.0035359001894868835 -chr4:169007628:T>C,ENSG00000145439,Adipose_Visceral_Omentum,-0.2924805955494345,-0.0229348909817636,0.05,1,0.0035359001894868835 -chr4:169007628:T>C,ENSG00000145439,Cells_EBV_transformed_lymphocytes,-0.2924805955494345,-0.0151715165568312,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Testis,-0.2924805955494345,-0.0181086649405058,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Heart_Atrial_Appendage,-0.2924805955494345,-0.0166600789232371,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Minor_Salivary_Gland,-0.2924805955494345,-0.0219233810154098,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Muscle_Skeletal,-0.2924805955494345,-0.0219827204341519,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Esophagus_Mucosa,-0.2924805955494345,-0.0160150577921673,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Pancreas,-0.2924805955494345,-0.0193831257243948,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Colon_Transverse,-0.2924805955494345,-0.0153900794275066,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Skin_Not_Sun_Exposed_Suprapubic,-0.2924805955494345,-0.019492169216431,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Skin_Sun_Exposed_Lower_leg,-0.2924805955494345,-0.0200246209787826,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Small_Intestine_Terminal_Ileum,-0.2924805955494345,-0.0164571845860465,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Spleen,-0.2924805955494345,-0.0185292383145769,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Stomach,-0.2924805955494345,-0.019371217400388,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Liver,-0.2924805955494345,-0.0151578033921386,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Adrenal_Gland,-0.2924805955494345,-0.0178600541748558,0.05,1,0.003530657395908191 -chr4:169007628:T>C,ENSG00000145439,Heart_Left_Ventricle,-0.2924805955494345,-0.0148995068950208,0.05,1,0.0030678102944556164 -chr4:169007628:T>C,ENSG00000145439,Cells_Cultured_fibroblasts,-0.2924805955494345,-0.0132909983842892,0.05,1,0.0030678102944556164 -chr4:86734352:C>T,ENSG00000163629,Skin_Sun_Exposed_Lower_leg,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Vagina,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Uterus,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Artery_Tibial,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Thyroid,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Testis,0.2628502134288226,0.0030646066609705,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Breast_Mammary_Tissue,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Esophagus_Mucosa,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Prostate,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Pituitary,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Ovary,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Nerve_Tibial,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Kidney_Cortex,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Cells_Cultured_fibroblasts,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Artery_Coronary,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Skin_Not_Sun_Exposed_Suprapubic,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Adipose_Visceral_Omentum,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:86734352:C>T,ENSG00000163629,Adipose_Subcutaneous,0.2628502134288226,0.0022936167070785,0.0,1,0.0028656508177969994 -chr4:122258831:A>T,ENSG00000138688,Adipose_Visceral_Omentum,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Artery_Tibial,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Frontal_Cortex_BA9,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Cortex,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Cerebellum,-0.0024281248594303,-3.241125210099068e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Cerebellar_Hemisphere,-0.0024281248594303,-2.7290232610815285e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Caudate_basal_ganglia,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Anterior_cingulate_cortex_BA24,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Amygdala,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Artery_Coronary,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Hippocampus,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Artery_Aorta,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Adipose_Visceral_Omentum,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Adipose_Subcutaneous,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Putamen_basal_ganglia,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Breast_Mammary_Tissue,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Cells_Cultured_fibroblasts,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Esophagus_Muscularis,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Lung,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Prostate,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:77035112:G>A,ENSG00000138758,Brain_Nucleus_accumbens_basal_ganglia,-0.0024281248594303,-2.400985783492307e-05,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Adipose_Subcutaneous,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Esophagus_Muscularis,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Brain_Cerebellum,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Cells_EBV_transformed_lymphocytes,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Vagina,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Uterus,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Colon_Sigmoid,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Thyroid,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Testis,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Breast_Mammary_Tissue,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Cells_Cultured_fibroblasts,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Small_Intestine_Terminal_Ileum,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Skin_Sun_Exposed_Lower_leg,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Brain_Cortex,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Skin_Not_Sun_Exposed_Suprapubic,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Esophagus_Gastroesophageal_Junction,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Pituitary,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Ovary,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Nerve_Tibial,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Minor_Salivary_Gland,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Lung,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Artery_Tibial,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Artery_Coronary,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Artery_Aorta,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:122258831:A>T,ENSG00000138688,Adrenal_Gland,-0.0812138713384427,-0.0008368600811415,0.0,1,0.002860864576028723 -chr4:86734352:C>T,ENSG00000163629,Brain_Cerebellum,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Nucleus_accumbens_basal_ganglia,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Hypothalamus,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Hippocampus,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Cortex,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Artery_Aorta,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Cerebellar_Hemisphere,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Caudate_basal_ganglia,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Anterior_cingulate_cortex_BA24,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Amygdala,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Spinal_cord_cervical_c_1,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Adrenal_Gland,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Putamen_basal_ganglia,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Frontal_Cortex_BA9,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Brain_Substantia_nigra,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Esophagus_Muscularis,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Small_Intestine_Terminal_Ileum,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Stomach,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Pancreas,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Lung,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Heart_Left_Ventricle,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Heart_Atrial_Appendage,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Minor_Salivary_Gland,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Spleen,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Colon_Sigmoid,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Colon_Transverse,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:86734352:C>T,ENSG00000163629,Esophagus_Gastroesophageal_Junction,0.2628502134288226,0.0022936167070785,0.0,0,0.0005709983575454501 -chr4:77035112:G>A,ENSG00000138758,Minor_Salivary_Gland,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Thyroid,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Amygdala,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Testis,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Stomach,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Spleen,-0.0024281248594303,-2.644437717536606e-05,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Nerve_Tibial,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Muscle_Skeletal,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Skin_Sun_Exposed_Lower_leg,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Skin_Not_Sun_Exposed_Suprapubic,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Esophagus_Mucosa,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Pituitary,-0.0024281248594303,-6.753186395330388e-05,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Uterus,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Pancreas,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Ovary,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Small_Intestine_Terminal_Ileum,-0.0024281248594303,-2.400985783492307e-05,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Caudate_basal_ganglia,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Vagina,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Nucleus_accumbens_basal_ganglia,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Liver,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Substantia_nigra,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Spinal_cord_cervical_c_1,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Putamen_basal_ganglia,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:86734352:C>T,ENSG00000163629,Liver,,,0.0,0,0.0005700424787606313 -chr4:86734352:C>T,ENSG00000163629,Muscle_Skeletal,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Hypothalamus,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Whole_Blood,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Hippocampus,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Colon_Transverse,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Frontal_Cortex_BA9,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Cerebellar_Hemisphere,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:86734352:C>T,ENSG00000163629,Cells_EBV_transformed_lymphocytes,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Brain_Anterior_cingulate_cortex_BA24,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Thyroid,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Esophagus_Gastroesophageal_Junction,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Kidney_Cortex,-0.0024281248594303,-4.652301549626717e-05,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Heart_Left_Ventricle,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Heart_Left_Ventricle,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Heart_Atrial_Appendage,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Esophagus_Muscularis,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Esophagus_Mucosa,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Esophagus_Gastroesophageal_Junction,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Colon_Transverse,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Colon_Sigmoid,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Cells_EBV_transformed_lymphocytes,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Cells_Cultured_fibroblasts,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Breast_Mammary_Tissue,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Substantia_nigra,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Spinal_cord_cervical_c_1,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Putamen_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Nucleus_accumbens_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Hypothalamus,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Kidney_Cortex,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Liver,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Lung,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Skin_Sun_Exposed_Lower_leg,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Vagina,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Whole_Blood,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Testis,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Stomach,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Spleen,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Small_Intestine_Terminal_Ileum,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Skin_Not_Sun_Exposed_Suprapubic,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Minor_Salivary_Gland,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Prostate,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Pituitary,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Pancreas,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Ovary,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Nerve_Tibial,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Muscle_Skeletal,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Hippocampus,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Frontal_Cortex_BA9,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Cortex,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Heart_Left_Ventricle,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Muscle_Skeletal,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Brain_Hypothalamus,-0.0024281248594303,-2.400985783492307e-05,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Liver,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Brain_Spinal_cord_cervical_c_1,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Brain_Substantia_nigra,-0.0024281248594303,-3.182189889891322e-05,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Kidney_Cortex,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Cells_EBV_transformed_lymphocytes,-0.0024281248594303,-0.0002068757826844,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Colon_Sigmoid,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Colon_Transverse,-0.0024281248594303,-2.400985783492307e-05,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Uterus,,,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Esophagus_Mucosa,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Heart_Atrial_Appendage,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Heart_Atrial_Appendage,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Pancreas,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Prostate,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Cerebellum,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Artery_Aorta,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Cerebellar_Hemisphere,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Caudate_basal_ganglia,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Anterior_cingulate_cortex_BA24,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Brain_Amygdala,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Artery_Tibial,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Artery_Coronary,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Adrenal_Gland,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Spleen,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Adipose_Visceral_Omentum,,,0.0,0,0.0005700424787606313 -chr4:154609484:A>C,ENSG00000171557,Adipose_Subcutaneous,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Whole_Blood,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:77035112:G>A,ENSG00000138758,Adrenal_Gland,,,0.0,0,0.0005700424787606313 -chr4:122258831:A>T,ENSG00000138688,Stomach,-0.0812138713384427,-0.0008368600811415,0.0,0,0.0005700424787606313 -chr4:86734352:C>T,ENSG00000163629,Whole_Blood,,,0.0,0,0.0005700424787606313 -chr4:169007628:T>C,ENSG00000145439,Whole_Blood,-0.2924805955494345,-0.0136947033424804,0.05,0,0.0005001247511210176 diff --git a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/vep_deepripe_deepsea.parquet b/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/vep_deepripe_deepsea.parquet deleted file mode 100644 index 675c2332..00000000 Binary files a/tests/annotations/test_data/aggregate_absplice_scores/aggregate_absplice_scores_small/input/vep_deepripe_deepsea.parquet and /dev/null differ diff --git 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b/tests/annotations/test_data/concatenate_deepsea/concatenate_deepseascores_medium/input/deepsea_scores_1.tsv deleted file mode 100644 index 2ada8291..00000000 --- a/tests/annotations/test_data/concatenate_deepsea/concatenate_deepseascores_medium/input/deepsea_scores_1.tsv +++ /dev/null @@ -1,61 +0,0 @@ -#CHROM POS ID REF ALT DeepSEA/predict/8988T_DNase_None/diff DeepSEA/predict/AoSMC_DNase_None/diff DeepSEA/predict/Chorion_DNase_None/diff DeepSEA/predict/CLL_DNase_None/diff DeepSEA/predict/Fibrobl_DNase_None/diff DeepSEA/predict/FibroP_DNase_None/diff DeepSEA/predict/Gliobla_DNase_None/diff DeepSEA/predict/GM12891_DNase_None/diff DeepSEA/predict/GM12892_DNase_None/diff DeepSEA/predict/GM18507_DNase_None/diff DeepSEA/predict/GM19238_DNase_None/diff DeepSEA/predict/GM19239_DNase_None/diff DeepSEA/predict/GM19240_DNase_None/diff DeepSEA/predict/H9ES_DNase_None/diff DeepSEA/predict/HeLa-S3_DNase_IFNa4h/diff DeepSEA/predict/Hepatocytes_DNase_None/diff DeepSEA/predict/HPDE6-E6E7_DNase_None/diff DeepSEA/predict/HSMM_emb_DNase_None/diff DeepSEA/predict/HTR8svn_DNase_None/diff DeepSEA/predict/Huh-7.5_DNase_None/diff DeepSEA/predict/Huh-7_DNase_None/diff DeepSEA/predict/iPS_DNase_None/diff DeepSEA/predict/Ishikawa_DNase_Estradiol_100nM_1hr/diff DeepSEA/predict/Ishikawa_DNase_4OHTAM_20nM_72hr/diff DeepSEA/predict/LNCaP_DNase_androgen/diff DeepSEA/predict/MCF-7_DNase_Hypoxia_LacAcid/diff DeepSEA/predict/Medullo_DNase_None/diff DeepSEA/predict/Melano_DNase_None/diff DeepSEA/predict/Myometr_DNase_None/diff DeepSEA/predict/Osteobl_DNase_None/diff DeepSEA/predict/PanIsletD_DNase_None/diff DeepSEA/predict/PanIslets_DNase_None/diff DeepSEA/predict/pHTE_DNase_None/diff DeepSEA/predict/ProgFib_DNase_None/diff DeepSEA/predict/RWPE1_DNase_None/diff DeepSEA/predict/Stellate_DNase_None/diff DeepSEA/predict/T-47D_DNase_None/diff DeepSEA/predict/Adult_CD4_Th0_DNase_None/diff DeepSEA/predict/Urothelia_DNase_None/diff DeepSEA/predict/Urothelia_DNase_UT189/diff DeepSEA/predict/AG04449_DNase_None/diff DeepSEA/predict/AG04450_DNase_None/diff DeepSEA/predict/AG09309_DNase_None/diff DeepSEA/predict/AG09319_DNase_None/diff DeepSEA/predict/AG10803_DNase_None/diff DeepSEA/predict/AoAF_DNase_None/diff DeepSEA/predict/BE2_C_DNase_None/diff DeepSEA/predict/BJ_DNase_None/diff DeepSEA/predict/Caco-2_DNase_None/diff DeepSEA/predict/CD20+_DNase_None/diff DeepSEA/predict/CD34+_Mobilized_DNase_None/diff DeepSEA/predict/CMK_DNase_None/diff DeepSEA/predict/A549_DNase_None/diff DeepSEA/predict/GM12878_DNase_None/diff DeepSEA/predict/H1-hESC_DNase_None/diff DeepSEA/predict/HeLa-S3_DNase_None/diff DeepSEA/predict/HepG2_DNase_None/diff DeepSEA/predict/HMEC_DNase_None/diff DeepSEA/predict/HSMMtube_DNase_None/diff DeepSEA/predict/HSMM_DNase_None/diff DeepSEA/predict/HUVEC_DNase_None/diff DeepSEA/predict/K562_DNase_None/diff DeepSEA/predict/LNCaP_DNase_None/diff DeepSEA/predict/MCF-7_DNase_None/diff DeepSEA/predict/NHEK_DNase_None/diff DeepSEA/predict/Th1_DNase_None/diff DeepSEA/predict/GM06990_DNase_None/diff DeepSEA/predict/GM12864_DNase_None/diff DeepSEA/predict/GM12865_DNase_None/diff DeepSEA/predict/H7-hESC_DNase_None/diff DeepSEA/predict/HAc_DNase_None/diff DeepSEA/predict/HAEpiC_DNase_None/diff DeepSEA/predict/HA-h_DNase_None/diff DeepSEA/predict/HA-sp_DNase_None/diff DeepSEA/predict/HBMEC_DNase_None/diff DeepSEA/predict/HCFaa_DNase_None/diff DeepSEA/predict/HCF_DNase_None/diff DeepSEA/predict/HCM_DNase_None/diff DeepSEA/predict/HConF_DNase_None/diff DeepSEA/predict/HCPEpiC_DNase_None/diff DeepSEA/predict/HCT-116_DNase_None/diff DeepSEA/predict/HEEpiC_DNase_None/diff DeepSEA/predict/HFF-Myc_DNase_None/diff DeepSEA/predict/HFF_DNase_None/diff DeepSEA/predict/HGF_DNase_None/diff DeepSEA/predict/HIPEpiC_DNase_None/diff DeepSEA/predict/HL-60_DNase_None/diff DeepSEA/predict/HMF_DNase_None/diff DeepSEA/predict/HMVEC-dAd_DNase_None/diff DeepSEA/predict/HMVEC-dBl-Ad_DNase_None/diff DeepSEA/predict/HMVEC-dBl-Neo_DNase_None/diff DeepSEA/predict/HMVEC-dLy-Ad_DNase_None/diff DeepSEA/predict/HMVEC-dLy-Neo_DNase_None/diff DeepSEA/predict/HMVEC-dNeo_DNase_None/diff DeepSEA/predict/HMVEC-LBl_DNase_None/diff DeepSEA/predict/HMVEC-LLy_DNase_None/diff DeepSEA/predict/HNPCEpiC_DNase_None/diff DeepSEA/predict/HPAEC_DNase_None/diff DeepSEA/predict/HPAF_DNase_None/diff DeepSEA/predict/HPdLF_DNase_None/diff DeepSEA/predict/HPF_DNase_None/diff DeepSEA/predict/HRCEpiC_DNase_None/diff DeepSEA/predict/HRE_DNase_None/diff DeepSEA/predict/HRGEC_DNase_None/diff DeepSEA/predict/HRPEpiC_DNase_None/diff DeepSEA/predict/HVMF_DNase_None/diff DeepSEA/predict/Jurkat_DNase_None/diff DeepSEA/predict/Monocytes-CD14+_RO01746_DNase_None/diff DeepSEA/predict/NB4_DNase_None/diff DeepSEA/predict/NH-A_DNase_None/diff DeepSEA/predict/NHDF-Ad_DNase_None/diff DeepSEA/predict/NHDF-neo_DNase_None/diff DeepSEA/predict/NHLF_DNase_None/diff DeepSEA/predict/NT2-D1_DNase_None/diff 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C T -chr3 6134790 rs881 A G -chr3 6492413 . A G -chr3 7479092 . T A -chr3 10151779 . G T -chr3 10963200 . C A -chr3 13336897 rs178 T A -chr3 25565017 rs37 C G -chr3 28027872 rs721 T C -chr3 30429305 rs135 T C -chr3 39059372 rs23 A C -chr3 47378509 rs727 T A -chr3 47839379 rs268 C T -chr3 55062103 rs873 A G -chr3 56288165 rs664 G C -chr3 64813843 rs815 A G -chr3 70306576 rs107 C G -chr3 72140079 rs492 A T -chr3 72906610 rs930 T G -chr3 74562325 rs523 G T -chr3 78839934 rs583 G A -chr3 81414874 rs170 A T -chr3 97458263 rs548 A T -chr3 97649369 rs546 C G -chr3 97949211 rs543 G A -chr3 99075824 rs838 T C -chr3 101580812 rs311 A C -chr3 103151123 rs382 C A -chr3 103329532 rs179 T C -chr3 103928516 rs19 A T -chr3 105180981 rs341 A G -chr3 111113126 rs470 A G -chr3 111866541 rs467 T A -chr3 117455785 rs718 C A -chr3 120258434 rs506 A C -chr3 120364684 rs367 T G -chr3 122803142 rs488 A C -chr3 125013245 rs146 A G -chr3 127342540 rs318 G T -chr3 133734681 rs104 G A -chr3 139349025 rs665 T C -chr3 140275153 rs791 G C -chr3 145304395 rs102 C G -chr3 147901161 rs274 C T -chr3 150051584 rs123 C A -chr3 150399452 rs648 T A -chr3 158349305 rs748 T A -chr3 158851780 rs408 A T -chr3 160382108 rs963 A C -chr3 168465216 rs751 G C -chr3 171089322 rs197 A T -chr3 177499702 rs376 G C -chr3 185836100 rs581 G T -chr3 191856146 rs596 G C -chr3 192824921 rs701 C G -chr3 193390684 rs434 A C -chr3 194577309 rs70 T G -chr3 194762766 rs598 G A -chr3 197345633 rs356 T A -chr3 197732094 rs693 G T diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_hg2_deepripe.csv.gz b/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_hg2_deepripe.csv.gz deleted file mode 100644 index 69a44862..00000000 Binary files a/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_hg2_deepripe.csv.gz and /dev/null differ diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_k5_deepripe.csv.gz 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a/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_vep.tsv +++ /dev/null @@ -1,122 +0,0 @@ -## ENSEMBL VARIANT EFFECT PREDICTOR v110.1 -## Output produced at 2024-04-24 15:05:38 -## Using cache in repo_dir/ensembl-vep/cache/homo_sapiens/110_GRCh38 -## Using API version 110, DB version ? -## ensembl-variation version 110.d34d25e -## ensembl-io version 110.b1a0d57 -## ensembl version 110.584a8f3 -## ensembl-funcgen version 110.24e6da6 -## dbSNP version 154 -## 1000genomes version phase3 -## gencode version GENCODE 44 -## polyphen version 2.2.3 -## sift version 6.2.1 -## gnomADe version r2.1.1 -## ClinVar version 202301 -## HGMD-PUBLIC version 20204 -## assembly version GRCh38.p14 -## COSMIC version 97 -## regbuild version 1.0 -## gnomADg version v3.1.2 -## genebuild version 2014-07 -## Column descriptions: -## Uploaded_variation : Identifier of uploaded variant -## Location : Location of variant in standard coordinate format (chr:start or chr:start-end) -## Allele : The variant allele used to calculate the consequence -## Gene : Stable ID of affected gene -## Feature : Stable ID of feature -## Feature_type : Type of feature - Transcript, RegulatoryFeature or MotifFeature -## Consequence : Consequence type -## cDNA_position : Relative position of base pair in cDNA sequence -## CDS_position : Relative position of base pair in coding sequence -## Protein_position : Relative position of amino acid in protein -## Amino_acids : Reference and variant amino acids -## Codons : Reference and variant codon sequence -## Existing_variation : Identifier(s) of co-located known variants -## IMPACT : Subjective impact classification of consequence type -## DISTANCE : Shortest distance from variant to transcript -## STRAND : Strand of the feature (1/-1) -## FLAGS : Transcript quality flags -## BIOTYPE : Biotype of transcript or regulatory feature -## CANONICAL : Indicates if transcript is canonical for this gene -## ENSP : Protein identifer -## SIFT : SIFT prediction and/or score -## PolyPhen : PolyPhen prediction and/or score -## AF : Frequency of existing variant in 1000 Genomes combined population -## CLIN_SIG : ClinVar clinical significance of the dbSNP variant -## SOMATIC : Somatic status of existing variant -## PHENO : Indicates if existing variant(s) is associated with a phenotype, disease or trait; multiple values correspond to multiple variants -## VEP command-line: vep --af --assembly GRCh38 --biotype --cache --canonical --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/Plugins --fasta [PATH]/GRCh38.primary_assembly.genome.fa --force_overwrite --fork 5 --format vcf --input_file [PATH]/chr3test_stripped.vcf.gz --no_escape --no_stats --offline --output_file [PATH]/chr3test_vep_anno.tsv --per_gene --pick_order biotype,mane_select,mane_plus_clinical,canonical,appris,tsl,ccds,rank,length,ensembl,refseq --polyphen s --protein --sift s --tab --total_length -#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS BIOTYPE CANONICAL ENSP SIFT PolyPhen AF CLIN_SIG SOMATIC PHENO -3_3474106_C/T 3:3474106 T ENSG00000223727 ENST00000420000 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs881 3:6134790 G - - - intergenic_variant - - - - - rs1007430246 MODIFIER - - - - - - - - - - - - -3_6492413_A/G 3:6492413 G ENSG00000189229 ENST00000655754 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -3_7479092_T/A 3:7479092 A ENSG00000196277 ENST00000357716 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000350348 - - - - - - -3_10151779_G/T 3:10151779 T ENSG00000287086 ENST00000660063 Transcript intron_variant,non_coding_transcript_variant - - - - - COSV56556349 MODIFIER - -1 - lncRNA YES - - - - - 1 1 -3_10151779_G/T 3:10151779 T ENSG00000134086 ENST00000256474 Transcript 3_prime_UTR_variant 2526/4414 - - - - COSV56556349 MODIFIER - 1 - protein_coding YES ENSP00000256474 - - - - 1 1 -3_10963200_C/A 3:10963200 A ENSG00000286962 ENST00000656787 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs178 3:13336897 A ENSG00000132182 ENST00000254508 Transcript missense_variant 3670/7206 3574/5664 1192/1887 I/F Atc/Ttc - MODERATE - -1 - protein_coding YES ENSP00000254508 0.01 0.712 - - - - -rs37 3:25565017 G ENSG00000077092 ENST00000330688 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000332296 - - - - - - -rs721 3:28027872 C ENSG00000235493 ENST00000356047 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA - - - - - - - - -rs135 3:30429305 C ENSG00000289450 ENST00000691186 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs23 3:39059372 C ENSG00000114742 ENST00000302313 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000307491 - - - - - - -rs727 3:47378509 A ENSG00000260236 ENST00000568593 Transcript downstream_gene_variant - - - - - - MODIFIER 580 -1 - lncRNA YES - - - - - - - -rs727 3:47378509 A ENSG00000076201 ENST00000265562 Transcript upstream_gene_variant - - - - - - MODIFIER 2512 1 - protein_coding YES ENSP00000265562 - - - - - - -rs268 3:47839379 T ENSG00000132153 ENST00000445061 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000405620 - - - - - - -rs873 3:55062103 G ENSG00000157445 ENST00000474759 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000419101 - - - - - - -rs664 3:56288165 C ENSG00000187672 ENST00000288221 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000288221 - - - - - - -rs815 3:64813843 G ENSG00000241684 ENST00000650103 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs107 3:70306576 G ENSG00000240405 ENST00000642114 Transcript intron_variant,non_coding_transcript_variant - - - - - rs536908099 MODIFIER - 1 - lncRNA YES - - - 0.0002 - - - -rs107 3:70306576 G ENSG00000242120 ENST00000567252 Transcript intron_variant - - - - - rs536908099 MODIFIER - -1 - protein_coding YES ENSP00000490638 - - 0.0002 - - - -rs492 3:72140079 T ENSG00000241163 ENST00000626474 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs930 3:72906610 G ENSG00000172986 ENST00000389617 Transcript intron_variant - - - - - COSV67474846 MODIFIER - 1 - protein_coding YES ENSP00000374268 - - - - 1 1 -rs523 3:74562325 T ENSG00000113805 ENST00000263665 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000263665 - - - - - - -rs583 3:78839934 A ENSG00000169855 ENST00000464233 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000420321 - - - - - - -rs170 3:81414874 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs548 3:97458263 T ENSG00000080224 ENST00000389672 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000374323 - - - - - - -rs546 3:97649369 G ENSG00000080224 ENST00000389672 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000374323 - - - - - - -rs543 3:97949211 A ENSG00000080200 ENST00000389622 Transcript downstream_gene_variant - - - - - - MODIFIER 4227 1 - protein_coding YES ENSP00000374273 - - - - - - -rs543 3:97949211 A ENSG00000170854 ENST00000394198 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000377748 - - - - - - -rs838 3:99075824 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs311 3:101580812 C ENSG00000081154 ENST00000265260 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000265260 - - - - - - -rs311 3:101580812 C ENSG00000242299 ENST00000496294 Transcript upstream_gene_variant - - - - - - MODIFIER 3865 -1 - processed_pseudogene YES - - - - - - - -rs382 3:103151123 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs179 3:103329532 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs19 3:103928516 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs341 3:105180981 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs470 3:111113126 G ENSG00000177707 ENST00000485303 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000418070 - - - - - - -rs467 3:111866541 A ENSG00000144824 ENST00000431670 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000405405 - - - - - - -rs718 3:117455785 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs506 3:120258434 C ENSG00000175697 ENST00000464295 Transcript intron_variant - - - - - rs1470110063 MODIFIER - -1 - protein_coding YES ENSP00000417261 - - - - - - -rs367 3:120364684 G ENSG00000240661 ENST00000634410 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - transcribed_unitary_pseudogene YES - - - - - - - -rs367 3:120364684 G ENSG00000282950 ENST00000634744 Transcript downstream_gene_variant - - - - - - MODIFIER 1309 -1 - lncRNA YES - - - - - - - -rs488 3:122803142 C ENSG00000138463 ENST00000261038 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000261038 - - - - - - -rs146 3:125013245 G ENSG00000173706 ENST00000311127 Transcript synonymous_variant 2441/9195 2334/4146 778/1381 L ctT/ctC - LOW - -1 - protein_coding YES ENSP00000311502 - - - - - - -rs318 3:127342540 T ENSG00000244215 ENST00000488425 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs104 3:133734681 A ENSG00000291042 ENST00000460564 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs665 3:139349025 C ENSG00000272656 ENST00000608472 Transcript non_coding_transcript_exon_variant 347/348 - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs665 3:139349025 C ENSG00000184432 ENST00000503326 Transcript downstream_gene_variant - - - - - - MODIFIER 4921 -1 - protein_coding - ENSP00000426682 - - - - - - -rs665 3:139349025 C ENSG00000175110 ENST00000680020 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000505414 - - - - - - -rs791 3:140275153 C ENSG00000158258 ENST00000458420 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000402460 - - - - - - -rs102 3:145304395 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs274 3:147901161 T - - - intergenic_variant - - - - - rs1305018800 MODIFIER - - - - - - - - - - - - -rs123 3:150051584 A ENSG00000243944 ENST00000487840 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs123 3:150051584 A ENSG00000070087 ENST00000497148 Transcript upstream_gene_variant - - - - - - MODIFIER 796 -1 - protein_coding - ENSP00000417817 - - - - - - -rs123 3:150051584 A ENSG00000240477 ENST00000466044 Transcript downstream_gene_variant - - - - - - MODIFIER 128 1 - processed_pseudogene YES - - - - - - - -rs648 3:150399452 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs748 3:158349305 A ENSG00000174891 ENST00000611884 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000481697 - - - - - - -rs408 3:158851780 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs963 3:160382108 C ENSG00000068885 ENST00000326448 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000312778 - - - - - - -rs751 3:168465216 C ENSG00000206120 ENST00000431685 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - transcribed_unitary_pseudogene YES - - - - - - - -rs197 3:171089322 T ENSG00000154310 ENST00000436636 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000399511 - - - - - - -rs376 3:177499702 C ENSG00000252028 ENST00000516219 Transcript downstream_gene_variant - - - - - - MODIFIER 3601 -1 - misc_RNA YES - - - - - - - -rs376 3:177499702 C ENSG00000228221 ENST00000656037 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs581 3:185836100 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs596 3:191856146 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs701 3:192824921 G ENSG00000180611 ENST00000392452 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000376246 - - - - - - -rs434 3:193390684 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs70 3:194577309 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs598 3:194762766 A ENSG00000237222 ENST00000667646 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs598 3:194762766 A ENSG00000230401 ENST00000422271 Transcript downstream_gene_variant - - - - - - MODIFIER 2472 -1 - lncRNA YES - - - - - - - -rs356 3:197345633 A ENSG00000286870 ENST00000669801 Transcript downstream_gene_variant - - - - - - MODIFIER 4927 1 - lncRNA YES - - - - - - - -rs693 3:197732094 T ENSG00000145016 ENST00000296343 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000296343 - - - - - - diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/variants.parquet b/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/variants.parquet deleted file mode 100644 index 35d9aaf3..00000000 Binary files a/tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/variants.parquet and /dev/null differ diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_small/expected/merged_annotations_expected.parquet b/tests/annotations/test_data/merge_annotations/merge_annotations_small/expected/merged_annotations_expected.parquet deleted file mode 100644 index 3e645640..00000000 Binary files a/tests/annotations/test_data/merge_annotations/merge_annotations_small/expected/merged_annotations_expected.parquet and /dev/null differ diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test.vcf b/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test.vcf deleted file mode 100644 index 357a3a89..00000000 --- a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test.vcf +++ /dev/null @@ -1,60 +0,0 @@ -chr3 3474106 rs111 C T -chr3 6134790 rs881 A G -chr3 6492413 rs94 A G -chr3 7479092 rs200 T A -chr3 10151779 rs337 G T -chr3 10963200 rs632 C A -chr3 13336897 rs178 T A -chr3 25565017 rs37 C G -chr3 28027872 rs721 T C -chr3 30429305 rs135 T C -chr3 39059372 rs23 A C -chr3 47378509 rs727 T A -chr3 47839379 rs268 C T -chr3 55062103 rs873 A G -chr3 56288165 rs664 G C -chr3 64813843 rs815 A G -chr3 70306576 rs107 C G -chr3 72140079 rs492 A T -chr3 72906610 rs930 T G -chr3 74562325 rs523 G T -chr3 78839934 rs583 G A -chr3 81414874 rs170 A T -chr3 97458263 rs548 A T -chr3 97649369 rs546 C G -chr3 97949211 rs543 G A -chr3 99075824 rs838 T C -chr3 101580812 rs311 A C -chr3 103151123 rs382 C A -chr3 103329532 rs179 T C -chr3 103928516 rs19 A T -chr3 105180981 rs341 A G -chr3 111113126 rs470 A G -chr3 111866541 rs467 T A -chr3 117455785 rs718 C A -chr3 120258434 rs506 A C -chr3 120364684 rs367 T G -chr3 122803142 rs488 A C -chr3 125013245 rs146 A G -chr3 127342540 rs318 G T -chr3 133734681 rs104 G A -chr3 139349025 rs665 T C -chr3 140275153 rs791 G C -chr3 145304395 rs102 C G -chr3 147901161 rs274 C T -chr3 150051584 rs123 C A -chr3 150399452 rs648 T A -chr3 158349305 rs748 T A -chr3 158851780 rs408 A T -chr3 160382108 rs963 A C -chr3 168465216 rs751 G C -chr3 171089322 rs197 A T -chr3 177499702 rs376 G C -chr3 185836100 rs581 G T -chr3 191856146 rs596 G C -chr3 192824921 rs701 C G -chr3 193390684 rs434 A C -chr3 194577309 rs70 T G -chr3 194762766 rs598 G A -chr3 197345633 rs356 T A -chr3 197732094 rs693 G T diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_hg2_deepripe.csv.gz b/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_hg2_deepripe.csv.gz deleted file mode 100644 index 69a44862..00000000 Binary files a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_hg2_deepripe.csv.gz and /dev/null differ diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_k5_deepripe.csv.gz b/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_k5_deepripe.csv.gz deleted file mode 100644 index cc970e2a..00000000 Binary files a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_k5_deepripe.csv.gz and /dev/null differ diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_parclip.csv.gz b/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_parclip.csv.gz deleted file mode 100644 index 271142ab..00000000 Binary files a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_parclip.csv.gz and /dev/null differ diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_vep.tsv b/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_vep.tsv deleted file mode 100644 index ef9eeab0..00000000 --- a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/test_vep.tsv +++ /dev/null @@ -1,122 +0,0 @@ -## ENSEMBL VARIANT EFFECT PREDICTOR v110.1 -## Output produced at 2024-04-24 15:05:38 -## Using cache in repo_dir/ensembl-vep/cache/homo_sapiens/110_GRCh38 -## Using API version 110, DB version ? -## ensembl-variation version 110.d34d25e -## ensembl-io version 110.b1a0d57 -## ensembl version 110.584a8f3 -## ensembl-funcgen version 110.24e6da6 -## dbSNP version 154 -## 1000genomes version phase3 -## gencode version GENCODE 44 -## polyphen version 2.2.3 -## sift version 6.2.1 -## gnomADe version r2.1.1 -## ClinVar version 202301 -## HGMD-PUBLIC version 20204 -## assembly version GRCh38.p14 -## COSMIC version 97 -## regbuild version 1.0 -## gnomADg version v3.1.2 -## genebuild version 2014-07 -## Column descriptions: -## Uploaded_variation : Identifier of uploaded variant -## Location : Location of variant in standard coordinate format (chr:start or chr:start-end) -## Allele : The variant allele used to calculate the consequence -## Gene : Stable ID of affected gene -## Feature : Stable ID of feature -## Feature_type : Type of feature - Transcript, RegulatoryFeature or MotifFeature -## Consequence : Consequence type -## cDNA_position : Relative position of base pair in cDNA sequence -## CDS_position : Relative position of base pair in coding sequence -## Protein_position : Relative position of amino acid in protein -## Amino_acids : Reference and variant amino acids -## Codons : Reference and variant codon sequence -## Existing_variation : Identifier(s) of co-located known variants -## IMPACT : Subjective impact classification of consequence type -## DISTANCE : Shortest distance from variant to transcript -## STRAND : Strand of the feature (1/-1) -## FLAGS : Transcript quality flags -## BIOTYPE : Biotype of transcript or regulatory feature -## CANONICAL : Indicates if transcript is canonical for this gene -## ENSP : Protein identifer -## SIFT : SIFT prediction and/or score -## PolyPhen : PolyPhen prediction and/or score -## AF : Frequency of existing variant in 1000 Genomes combined population -## CLIN_SIG : ClinVar clinical significance of the dbSNP variant -## SOMATIC : Somatic status of existing variant -## PHENO : Indicates if existing variant(s) is associated with a phenotype, disease or trait; multiple values correspond to multiple variants -## VEP command-line: vep --af --assembly GRCh38 --biotype --cache --canonical --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/Plugins --fasta [PATH]/GRCh38.primary_assembly.genome.fa --force_overwrite --fork 5 --format vcf --input_file [PATH]/chr3test_stripped.vcf.gz --no_escape --no_stats --offline --output_file [PATH]/chr3test_vep_anno.tsv --per_gene --pick_order biotype,mane_select,mane_plus_clinical,canonical,appris,tsl,ccds,rank,length,ensembl,refseq --polyphen s --protein --sift s --tab --total_length -#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS BIOTYPE CANONICAL ENSP SIFT PolyPhen AF CLIN_SIG SOMATIC PHENO -rs111 3:3474106 T ENSG00000223727 ENST00000420000 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs881 3:6134790 G - - - intergenic_variant - - - - - rs1007430246 MODIFIER - - - - - - - - - - - - -rs94 3:6492413 G ENSG00000189229 ENST00000655754 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs200 3:7479092 A ENSG00000196277 ENST00000357716 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000350348 - - - - - - -rs337 3:10151779 T ENSG00000287086 ENST00000660063 Transcript intron_variant,non_coding_transcript_variant - - - - - COSV56556349 MODIFIER - -1 - lncRNA YES - - - - - 1 1 -rs337 3:10151779 T ENSG00000134086 ENST00000256474 Transcript 3_prime_UTR_variant 2526/4414 - - - - COSV56556349 MODIFIER - 1 - protein_coding YES ENSP00000256474 - - - - 1 1 -rs632 3:10963200 A ENSG00000286962 ENST00000656787 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs178 3:13336897 A ENSG00000132182 ENST00000254508 Transcript missense_variant 3670/7206 3574/5664 1192/1887 I/F Atc/Ttc - MODERATE - -1 - protein_coding YES ENSP00000254508 0.01 0.712 - - - - -rs37 3:25565017 G ENSG00000077092 ENST00000330688 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000332296 - - - - - - -rs721 3:28027872 C ENSG00000235493 ENST00000356047 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA - - - - - - - - -rs135 3:30429305 C ENSG00000289450 ENST00000691186 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs23 3:39059372 C ENSG00000114742 ENST00000302313 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000307491 - - - - - - -rs727 3:47378509 A ENSG00000260236 ENST00000568593 Transcript downstream_gene_variant - - - - - - MODIFIER 580 -1 - lncRNA YES - - - - - - - -rs727 3:47378509 A ENSG00000076201 ENST00000265562 Transcript upstream_gene_variant - - - - - - MODIFIER 2512 1 - protein_coding YES ENSP00000265562 - - - - - - -rs268 3:47839379 T ENSG00000132153 ENST00000445061 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000405620 - - - - - - -rs873 3:55062103 G ENSG00000157445 ENST00000474759 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000419101 - - - - - - -rs664 3:56288165 C ENSG00000187672 ENST00000288221 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000288221 - - - - - - -rs815 3:64813843 G ENSG00000241684 ENST00000650103 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs107 3:70306576 G ENSG00000240405 ENST00000642114 Transcript intron_variant,non_coding_transcript_variant - - - - - rs536908099 MODIFIER - 1 - lncRNA YES - - - 0.0002 - - - -rs107 3:70306576 G ENSG00000242120 ENST00000567252 Transcript intron_variant - - - - - rs536908099 MODIFIER - -1 - protein_coding YES ENSP00000490638 - - 0.0002 - - - -rs492 3:72140079 T ENSG00000241163 ENST00000626474 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs930 3:72906610 G ENSG00000172986 ENST00000389617 Transcript intron_variant - - - - - COSV67474846 MODIFIER - 1 - protein_coding YES ENSP00000374268 - - - - 1 1 -rs523 3:74562325 T ENSG00000113805 ENST00000263665 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000263665 - - - - - - -rs583 3:78839934 A ENSG00000169855 ENST00000464233 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000420321 - - - - - - -rs170 3:81414874 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs548 3:97458263 T ENSG00000080224 ENST00000389672 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000374323 - - - - - - -rs546 3:97649369 G ENSG00000080224 ENST00000389672 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000374323 - - - - - - -rs543 3:97949211 A ENSG00000080200 ENST00000389622 Transcript downstream_gene_variant - - - - - - MODIFIER 4227 1 - protein_coding YES ENSP00000374273 - - - - - - -rs543 3:97949211 A ENSG00000170854 ENST00000394198 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000377748 - - - - - - -rs838 3:99075824 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs311 3:101580812 C ENSG00000081154 ENST00000265260 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000265260 - - - - - - -rs311 3:101580812 C ENSG00000242299 ENST00000496294 Transcript upstream_gene_variant - - - - - - MODIFIER 3865 -1 - processed_pseudogene YES - - - - - - - -rs382 3:103151123 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs179 3:103329532 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs19 3:103928516 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs341 3:105180981 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs470 3:111113126 G ENSG00000177707 ENST00000485303 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000418070 - - - - - - -rs467 3:111866541 A ENSG00000144824 ENST00000431670 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000405405 - - - - - - -rs718 3:117455785 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs506 3:120258434 C ENSG00000175697 ENST00000464295 Transcript intron_variant - - - - - rs1470110063 MODIFIER - -1 - protein_coding YES ENSP00000417261 - - - - - - -rs367 3:120364684 G ENSG00000240661 ENST00000634410 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - transcribed_unitary_pseudogene YES - - - - - - - -rs367 3:120364684 G ENSG00000282950 ENST00000634744 Transcript downstream_gene_variant - - - - - - MODIFIER 1309 -1 - lncRNA YES - - - - - - - -rs488 3:122803142 C ENSG00000138463 ENST00000261038 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000261038 - - - - - - -rs146 3:125013245 G ENSG00000173706 ENST00000311127 Transcript synonymous_variant 2441/9195 2334/4146 778/1381 L ctT/ctC - LOW - -1 - protein_coding YES ENSP00000311502 - - - - - - -rs318 3:127342540 T ENSG00000244215 ENST00000488425 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs104 3:133734681 A ENSG00000291042 ENST00000460564 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs665 3:139349025 C ENSG00000272656 ENST00000608472 Transcript non_coding_transcript_exon_variant 347/348 - - - - - MODIFIER - -1 - lncRNA YES - - - - - - - -rs665 3:139349025 C ENSG00000184432 ENST00000503326 Transcript downstream_gene_variant - - - - - - MODIFIER 4921 -1 - protein_coding - ENSP00000426682 - - - - - - -rs665 3:139349025 C ENSG00000175110 ENST00000680020 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000505414 - - - - - - -rs791 3:140275153 C ENSG00000158258 ENST00000458420 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000402460 - - - - - - -rs102 3:145304395 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs274 3:147901161 T - - - intergenic_variant - - - - - rs1305018800 MODIFIER - - - - - - - - - - - - -rs123 3:150051584 A ENSG00000243944 ENST00000487840 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs123 3:150051584 A ENSG00000070087 ENST00000497148 Transcript upstream_gene_variant - - - - - - MODIFIER 796 -1 - protein_coding - ENSP00000417817 - - - - - - -rs123 3:150051584 A ENSG00000240477 ENST00000466044 Transcript downstream_gene_variant - - - - - - MODIFIER 128 1 - processed_pseudogene YES - - - - - - - -rs648 3:150399452 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs748 3:158349305 A ENSG00000174891 ENST00000611884 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000481697 - - - - - - -rs408 3:158851780 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs963 3:160382108 C ENSG00000068885 ENST00000326448 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000312778 - - - - - - -rs751 3:168465216 C ENSG00000206120 ENST00000431685 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - transcribed_unitary_pseudogene YES - - - - - - - -rs197 3:171089322 T ENSG00000154310 ENST00000436636 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000399511 - - - - - - -rs376 3:177499702 C ENSG00000252028 ENST00000516219 Transcript downstream_gene_variant - - - - - - MODIFIER 3601 -1 - misc_RNA YES - - - - - - - -rs376 3:177499702 C ENSG00000228221 ENST00000656037 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs581 3:185836100 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs596 3:191856146 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs701 3:192824921 G ENSG00000180611 ENST00000392452 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000376246 - - - - - - -rs434 3:193390684 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs70 3:194577309 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - - -rs598 3:194762766 A ENSG00000237222 ENST00000667646 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - - -rs598 3:194762766 A ENSG00000230401 ENST00000422271 Transcript downstream_gene_variant - - - - - - MODIFIER 2472 -1 - lncRNA YES - - - - - - - -rs356 3:197345633 A ENSG00000286870 ENST00000669801 Transcript downstream_gene_variant - - - - - - MODIFIER 4927 1 - lncRNA YES - - - - - - - -rs693 3:197732094 T ENSG00000145016 ENST00000296343 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000296343 - - - - - - diff --git a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/variants.parquet b/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/variants.parquet deleted file mode 100644 index 35d9aaf3..00000000 Binary files a/tests/annotations/test_data/merge_annotations/merge_annotations_small/input/variants.parquet and /dev/null differ diff --git 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a/tests/annotations/test_data/merge_deepsea_pcas/merge_deepsea_pcas_small/input/all_variants.wID.deepSea.parquet/part.0.parquet and /dev/null differ diff --git a/tests/annotations/test_data/merge_deepsea_pcas/merge_deepsea_pcas_small/input/annotation_colnames_filling_values.yaml b/tests/annotations/test_data/merge_deepsea_pcas/merge_deepsea_pcas_small/input/annotation_colnames_filling_values.yaml deleted file mode 100644 index fe0c483b..00000000 --- a/tests/annotations/test_data/merge_deepsea_pcas/merge_deepsea_pcas_small/input/annotation_colnames_filling_values.yaml +++ /dev/null @@ -1,63 +0,0 @@ -annotation_column_names: - 'af' : - 'combined_UKB_NFE_AF' : 0 - 'maf_mb' : - 'combined_UKB_NFE_AF_MB' : 10000 - 'maf' : - 'combined_UKB_NFE_MAF' : 0 - 'PolyPhen' : - 'polyphen_score' : 0 - 'SIFT' : - 'sift_score' : 1 - 'QKI_hg2' : - 'DeepRipe_plus_QKI_lip_hg2' : 0 - 'QKI_k5' : - 'DeepRipe_plus_QKI_clip_k5' : 0 - 'KHDRBS1_k5' : - 'DeepRipe_plus_KHDRBS1_clip_k5' : 0 - 'ELAVL1_parclip' : - 'DeepRipe_plus_ELAVL1_parclip' : 0 - 'TARDBP_parclip' : - 'DeepRipe_plus_TARDBP_parclip' : 0 - 'HNRNPD_parclip' : - 'DeepRipe_plus_HNRNPD_parclip' : 0 - 'MBNL1_parclip' : - 'DeepRipe_plus_MBNL1_parclip' : 0 - 'QKI_parclip' : - 'DeepRipe_plus_QKI_parclip' : 0 - 'Consequence_splice_acceptor_variant' : - 'Consequence_splice_acceptor_variant' : 0 - 'Consequence_splice_donor_variant' : - 'Consequence_splice_donor_variant' : 0 - 'Consequence_stop_gained' : - 'Consequence_stop_gained' : 0 - 'Consequence_frameshift_variant' : - 'Consequence_frameshift_variant' : 0 - 'Consequence_stop_lost' : - 'Consequence_stop_lost' : 0 - 'Consequence_start_lost' : - 'Consequence_start_lost' : 0 - 'Consequence_inframe_insertion' : - 'Consequence_inframe_insertion' : 0 - 'Consequence_inframe_deletion' : - 'Consequence_inframe_deletion' : 0 - 'Consequence_missense_variant' : - 'Consequence_missense_variant' : 0 - 'Consequence_protein_altering_variant' : - 'Consequence_protein_altering_variant' : 0 - 'Consequence_splice_region_variant' : - 'Consequence_splice_region_variant' : 0 - 'DeepSEA_PC_1' : - 'DeepSEA_PC_1' : 0 - 'DeepSEA_PC_2' : - 'DeepSEA_PC_2' : 0 - 'DeepSEA_PC_3' : - 'DeepSEA_PC_3' : 0 - 'DeepSEA_PC_4' : - 'DeepSEA_PC_4' : 0 - 'DeepSEA_PC_5' : - 'DeepSEA_PC_5' : 0 - 'DeepSEA_PC_6' : - 'DeepSEA_PC_6' : 0 - 'AF' : - 'AF' : 0 diff --git a/tests/annotations/test_data/merge_deepsea_pcas/merge_deepsea_pcas_small/input/vep_deepripe.parquet b/tests/annotations/test_data/merge_deepsea_pcas/merge_deepsea_pcas_small/input/vep_deepripe.parquet deleted file mode 100644 index 715ee750..00000000 Binary files a/tests/annotations/test_data/merge_deepsea_pcas/merge_deepsea_pcas_small/input/vep_deepripe.parquet and /dev/null differ diff --git a/tests/annotations/test_data/process_annotations/process_annotations_small/expected_variants.parquet b/tests/annotations/test_data/process_annotations/process_annotations_small/expected_variants.parquet deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/annotations/test_data/process_annotations/process_annotations_small/in_variants.parquet b/tests/annotations/test_data/process_annotations/process_annotations_small/in_variants.parquet deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/expected/expected.parquet b/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/expected/expected.parquet deleted file mode 100644 index 710d4112..00000000 Binary files a/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/expected/expected.parquet and /dev/null differ diff --git a/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/input/annotation_colnames_filling_values.yaml b/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/input/annotation_colnames_filling_values.yaml deleted file mode 100644 index fe0c483b..00000000 --- a/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/input/annotation_colnames_filling_values.yaml +++ /dev/null @@ -1,63 +0,0 @@ -annotation_column_names: - 'af' : - 'combined_UKB_NFE_AF' : 0 - 'maf_mb' : - 'combined_UKB_NFE_AF_MB' : 10000 - 'maf' : - 'combined_UKB_NFE_MAF' : 0 - 'PolyPhen' : - 'polyphen_score' : 0 - 'SIFT' : - 'sift_score' : 1 - 'QKI_hg2' : - 'DeepRipe_plus_QKI_lip_hg2' : 0 - 'QKI_k5' : - 'DeepRipe_plus_QKI_clip_k5' : 0 - 'KHDRBS1_k5' : - 'DeepRipe_plus_KHDRBS1_clip_k5' : 0 - 'ELAVL1_parclip' : - 'DeepRipe_plus_ELAVL1_parclip' : 0 - 'TARDBP_parclip' : - 'DeepRipe_plus_TARDBP_parclip' : 0 - 'HNRNPD_parclip' : - 'DeepRipe_plus_HNRNPD_parclip' : 0 - 'MBNL1_parclip' : - 'DeepRipe_plus_MBNL1_parclip' : 0 - 'QKI_parclip' : - 'DeepRipe_plus_QKI_parclip' : 0 - 'Consequence_splice_acceptor_variant' : - 'Consequence_splice_acceptor_variant' : 0 - 'Consequence_splice_donor_variant' : - 'Consequence_splice_donor_variant' : 0 - 'Consequence_stop_gained' : - 'Consequence_stop_gained' : 0 - 'Consequence_frameshift_variant' : - 'Consequence_frameshift_variant' : 0 - 'Consequence_stop_lost' : - 'Consequence_stop_lost' : 0 - 'Consequence_start_lost' : - 'Consequence_start_lost' : 0 - 'Consequence_inframe_insertion' : - 'Consequence_inframe_insertion' : 0 - 'Consequence_inframe_deletion' : - 'Consequence_inframe_deletion' : 0 - 'Consequence_missense_variant' : - 'Consequence_missense_variant' : 0 - 'Consequence_protein_altering_variant' : - 'Consequence_protein_altering_variant' : 0 - 'Consequence_splice_region_variant' : - 'Consequence_splice_region_variant' : 0 - 'DeepSEA_PC_1' : - 'DeepSEA_PC_1' : 0 - 'DeepSEA_PC_2' : - 'DeepSEA_PC_2' : 0 - 'DeepSEA_PC_3' : - 'DeepSEA_PC_3' : 0 - 'DeepSEA_PC_4' : - 'DeepSEA_PC_4' : 0 - 'DeepSEA_PC_5' : - 'DeepSEA_PC_5' : 0 - 'DeepSEA_PC_6' : - 'DeepSEA_PC_6' : 0 - 'AF' : - 'AF' : 0 diff --git a/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/input/annotations.parquet b/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/input/annotations.parquet deleted file mode 100644 index cf3bad1a..00000000 Binary files a/tests/annotations/test_data/select_rename_fill_columns/select_rename_fill_columns_small/input/annotations.parquet and /dev/null differ