From 10cd9ac9ee410a71b7bf36d9c010847d8289e0d4 Mon Sep 17 00:00:00 2001 From: julesjacobsen Date: Thu, 25 Apr 2024 11:23:36 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20monarch-?= =?UTF-8?q?initiative/pheval@0310db7a20dd98a2b4b2875dc83a011af2643f81=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 14 + CODE_OF_CONDUCT/index.html | 14 + about/index.html | 14 + api/pheval/analyse/analysis/index.html | 14 + .../analyse/benchmark_generator/index.html | 14 + .../analyse/benchmarking_data/index.html | 14 + .../binary_classification_stats/index.html | 14 + .../index.html | 14 + .../gene_prioritisation_analysis/index.html | 14 + api/pheval/analyse/generate_plots/index.html | 14 + .../generate_summary_outputs/index.html | 14 + .../parse_benchmark_summary/index.html | 14 + .../analyse/parse_pheval_result/index.html | 14 + .../prioritisation_rank_recorder/index.html | 14 + .../prioritisation_result_types/index.html | 14 + api/pheval/analyse/rank_stats/index.html | 14 + api/pheval/analyse/run_data_parser/index.html | 14 + .../index.html | 14 + api/pheval/cli/index.html | 120 +- api/pheval/config_parser/index.html | 14 + api/pheval/constants/index.html | 14 + api/pheval/infra/exomiserdb/index.html | 14 + .../post_processing/index.html | 14 + .../create_noisy_phenopackets/index.html | 14 + .../prepare/create_spiked_vcf/index.html | 14 + .../prepare/custom_exceptions/index.html | 18 +- api/pheval/prepare/prepare_corpus/index.html | 1587 +++++++++++++++++ .../prepare/update_phenopacket/index.html | 42 +- api/pheval/run_metadata/index.html | 14 + api/pheval/runners/runner/index.html | 14 + api/pheval/utils/exomiser/index.html | 14 + api/pheval/utils/file_utils/index.html | 14 + api/pheval/utils/phenopacket_utils/index.html | 1110 ++++++++---- api/pheval/utils/semsim_utils/index.html | 14 + api/pheval/utils/utils/index.html | 14 + contact/index.html | 14 + contributing/index.html | 14 + developing_a_pheval_plugin/index.html | 126 +- exomiser_pipeline/index.html | 14 + index.html | 14 + objects.inv | Bin 2714 -> 2761 bytes pipeline/index.html | 14 + plugins/index.html | 14 + roadmap/index.html | 14 + search/search_index.json | 2 +- sitemap.xml | 89 +- sitemap.xml.gz | Bin 627 -> 636 bytes styleguide/index.html | 14 + 48 files changed, 3210 insertions(+), 416 deletions(-) create mode 100644 api/pheval/prepare/prepare_corpus/index.html diff --git a/404.html b/404.html index fe810e38d..5ec9cfd56 100644 --- a/404.html +++ b/404.html @@ -827,6 +827,20 @@ +
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    pheval-utils
  • benchmark-comparison: Benchmark the gene/variant/disease prioritisation performance for two runs.
  • create-spiked-vcfs:
  • generate-stats-plot: Generate bar plot from benchmark stats summary tsv.
    • +
  • prepare-corpus:
  • scramble-phenopackets: Generate noisy phenopackets from existing ones.
  • semsim-scramble: Scrambles semsim profile multiplying score value by scramble factor
  • semsim-to-exomiserdb: ingests semsim file into exomiser phenotypic database
    • @@ -1807,19 +1836,19 @@
    generate-stats-plot
    --gene-analysis / --no-gene-analysis boolean -Specify analysis for gene prioritisation NOTE: This argument is mutually exclusive with arguments: [disease_analysis, variant_analysis]. +Specify analysis for gene prioritisation NOTE: This argument is mutually exclusive with arguments: [variant_analysis, disease_analysis]. False --variant-analysis / --no-variant-analysis boolean -Specify analysis for variant prioritisation NOTE: This argument is mutually exclusive with arguments: [gene_analysis, disease_analysis]. +Specify analysis for variant prioritisation NOTE: This argument is mutually exclusive with arguments: [disease_analysis, gene_analysis]. False --disease-analysis / --no-disease-analysis boolean -Specify analysis for disease prioritisation NOTE: This argument is mutually exclusive with arguments: [gene_analysis, variant_analysis]. +Specify analysis for disease prioritisation NOTE: This argument is mutually exclusive with arguments: [variant_analysis, gene_analysis]. False @@ -1842,6 +1871,91 @@
    generate-stats-plot
    +
    prepare-corpus
    +

    Prepare a corpus of Phenopackets for analysis, optionally checking for complete variant records and updating +gene identifiers.

    +
    Args:
+    phenopacket_dir (Path): The path to the directory containing Phenopackets.
+    variant_analysis (bool): If True, check for complete variant records in the Phenopackets.
+    gene_analysis (bool): If True, check for complete gene records in the Phenopackets.
+    disease_analysis (bool): If True, check for complete disease records in the Phenopackets.
+    gene_identifier (str): Identifier for updating gene identifiers, if applicable.
+    hg19_template_vcf (Path): Path to the hg19 template VCF file (optional), to spike variants into
+    VCFs for variant-based analysis at least one of hg19_template_vcf or hg38_template_vcf is required.
+    hg38_template_vcf (Path): Path to the hg38 template VCF file (optional), to spike variants into
+    VCFs for variant-based analysis at least one of hg19_template_vcf or hg38_template_vcf is required.
+    output_dir (Path): The directory to save the prepared Phenopackets and, optionally, VCF files.
+
    +

    Usage:

    +
    pheval-utils prepare-corpus [OPTIONS]
+
    +

    Options:

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameTypeDescriptionDefault
    --phenopacket-dir, -pPathPath to phenopacket corpus directory.._required
    --variant-analysis / --no-variant-analysisbooleanSpecify whether to check for complete variant records in the phenopackets.False
    --gene-analysis / --no-gene-analysisbooleanSpecify whether to check for complete gene records in the phenopackets.False
    --disease-analysis / --no-disease-analysisbooleanSpecify whether to check for complete disease records in the phenopackets.False
    --gene-identifier, -gchoice (ensembl_id | entrez_id | hgnc_id)Gene identifier to update in phenopacketNone
    --hg19-template-vcf, -hg19PathTemplate hg19 VCF fileNone
    --hg38-template-vcf, -hg38PathTemplate hg38 VCF fileNone
    --output-dir, -oPathPath to output prepared corpus.prepared_corpus
    --helpbooleanShow this message and exit.False
    scramble-phenopackets

    Generate noisy phenopackets from existing ones.

    Usage:

    diff --git a/api/pheval/config_parser/index.html b/api/pheval/config_parser/index.html index e36f9372f..8c7dec36b 100644 --- a/api/pheval/config_parser/index.html +++ b/api/pheval/config_parser/index.html @@ -887,6 +887,20 @@ +
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