Cli
main
main CLI method for PhEval
Args: verbose (int, optional): Verbose flag. quiet (bool, optional): Queit Flag.
Usage:
main [OPTIONS] COMMAND [ARGS]...
Options:
| Name | Type | Description | Default |
|---|---|---|---|
-v, --verbose |
integer range (0 and above) |
N/A | 0 |
-q, --quiet |
text | N/A | None |
--help |
boolean | Show this message and exit. | False |
pheval
pheval
Usage:
pheval [OPTIONS] COMMAND [ARGS]...
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--help |
boolean | Show this message and exit. | False |
Subcommands
- run: PhEval Runner Command Line Interface
run
PhEval Runner Command Line Interface Args: input_dir (Path): The input directory (relative path: e.g exomiser-13.11) testdata_dir (Path): The input directory (relative path: e.g ./data runner (str): Runner implementation (e.g exomiser-13.11) tmp_dir (Path): The path of the temporary directory (optional) output_dir (Path): The path of the output directory config (Path): The path of the configuration file (optional e.g., config.yaml) version (str): The version of the tool implementation
Usage:
pheval run [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--input-dir, -i |
Path | The input directory (relative path: e.g exomiser-13.11) | _required |
--testdata-dir, -t |
Path | The input directory (relative path: e.g ./data) | _required |
--runner, -r |
text | Runner implementation (e.g exomiser-13.11) | _required |
--tmp-dir, -m |
Path | The path of the temporary directory (optional) | None |
--output-dir, -o |
Path | The path of the output directory | _required |
--config, -c |
Path | The path of the configuration file (optional e.g config.yaml) | None |
--version, -v |
text | Version of the tool implementation. | None |
--help |
boolean | Show this message and exit. | False |
pheval-utils
pheval_utils
Usage:
pheval-utils [OPTIONS] COMMAND [ARGS]...
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--help |
boolean | Show this message and exit. | False |
Subcommands
- benchmark: Benchmark the gene/variant/disease prioritisation performance for a single run.
- 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
- update-phenopackets: Update gene symbols and identifiers for phenopackets.
benchmark
Benchmark the gene/variant/disease prioritisation performance for a single run.
Usage:
pheval-utils benchmark [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--directory, -d |
Path | General results directory to be benchmarked, assumes contains subdirectories of pheval_gene_results/,pheval_variant_results/ or pheval_disease_results/. | _required |
--phenopacket-dir, -p |
Path | Full path to directory containing input phenopackets. | _required |
--output-prefix, -o |
text | Output file prefix. | _required |
--score-order, -so |
choice (ascending | descending) |
Ordering of results for ranking. | descending |
--threshold, -t |
float | Score threshold. | 0.0 |
--gene-analysis / --no-gene-analysis |
boolean | Specify analysis for gene prioritisation | False |
--variant-analysis / --no-variant-analysis |
boolean | Specify analysis for variant prioritisation | False |
--disease-analysis / --no-disease-analysis |
boolean | Specify analysis for disease prioritisation | False |
--plot-type, -y |
choice (bar_stacked | bar_cumulative | bar_non_cumulative) |
Bar chart type to output. | bar_stacked |
--help |
boolean | Show this message and exit. | False |
benchmark-comparison
Benchmark the gene/variant/disease prioritisation performance for two runs.
Usage:
pheval-utils benchmark-comparison [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--run-data, -r |
Path | Path to .txt file containing testdata phenopacket directory and corresponding results directory separated by tab.Each run contained to a new line with the input testdata listed first and on the same line separated by a tabthe results directory. | _required |
--output-prefix, -o |
text | Output file prefix. | _required |
--score-order, -so |
choice (ascending | descending) |
Ordering of results for ranking. | descending |
--threshold, -t |
float | Score threshold. | 0.0 |
--gene-analysis / --no-gene-analysis |
boolean | Specify analysis for gene prioritisation | False |
--variant-analysis / --no-variant-analysis |
boolean | Specify analysis for variant prioritisation | False |
--disease-analysis / --no-disease-analysis |
boolean | Specify analysis for disease prioritisation | False |
--plot-type, -y |
choice (bar_stacked | bar_cumulative | bar_non_cumulative) |
Bar chart type to output. | bar_cumulative |
--help |
boolean | Show this message and exit. | False |
create-spiked-vcfs
Create spiked VCF from either a Phenopacket or a Phenopacket directory.
Args: phenopacket_path (Path): Path to a single Phenopacket file (optional). phenopacket_dir (Path): Path to a directory containing Phenopacket files (optional). output_dir (Path): The directory to store the generated spiked VCF file(s). hg19_template_vcf (Path): Path to the hg19 template VCF file (optional). hg38_template_vcf (Path): Path to the hg38 template VCF file (optional). hg19_vcf_dir (Path): Path to the directory containing the hg19 VCF files (optional). hg38_vcf_dir (Path): Path to the directory containing the hg38 VCF files (optional).
Usage:
pheval-utils create-spiked-vcfs [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--phenopacket-path, -p |
Path | Path to phenopacket. NOTE: This argument is mutually exclusive with arguments: [phenopacket_dir]. | None |
--phenopacket-dir, -P |
Path | Path to phenopacket directory for updating. NOTE: This argument is mutually exclusive with arguments: [phenopacket_path]. | None |
--hg19-template-vcf, -hg19 |
Path | Template hg19 VCF file NOTE: This argument is mutually exclusive with arguments: [hg19_vcf_dir]. | None |
--hg38-template-vcf, -hg38 |
Path | Template hg38 VCF file NOTE: This argument is mutually exclusive with arguments: [hg38_vcf_dir]. | None |
--hg19-vcf-dir, -hg19-dir |
Path | Path to directory containing hg19 VCF templates. NOTE: This argument is mutually exclusive with arguments: [hg19_template_vcf]. | None |
--hg38-vcf-dir, -hg38-dir |
Path | Path to directory containing hg38 VCF templates. NOTE: This argument is mutually exclusive with arguments: [hg38_template_vcf]. | None |
--output-dir, -O |
Path | Path for creation of output directory | vcf |
--help |
boolean | Show this message and exit. | False |
generate-stats-plot
Generate bar plot from benchmark stats summary tsv.
Usage:
pheval-utils generate-stats-plot [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--benchmarking-tsv, -b |
Path | Path to benchmark summary tsv output by PhEval benchmark commands. | _required |
--gene-analysis / --no-gene-analysis |
boolean | Specify analysis for gene prioritisation NOTE: This argument is mutually exclusive with arguments: [disease_analysis, variant_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]. | False |
--disease-analysis / --no-disease-analysis |
boolean | Specify analysis for disease prioritisation NOTE: This argument is mutually exclusive with arguments: [gene_analysis, variant_analysis]. | False |
--plot-type, -y |
choice (bar_stacked | bar_cumulative | bar_non_cumulative) |
Bar chart type to output. | bar_cumulative |
--title, -t |
text | Title for plot, specify the title on the CLI enclosed with "" | None |
--help |
boolean | Show this message and exit. | False |
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). hg38_template_vcf (Path): Path to the hg38 template VCF file (optional). hg19_vcf_dir (Path): Path to the directory containing the hg19 VCF files (optional). hg38_vcf_dir (Path): Path to the directory containing the hg38 VCF files (optional). output_dir (Path): The directory to save the prepared Phenopackets and, optionally, VCF files. Notes: To spike variants into VCFs for variant-based analysis at least one of hg19_template_vcf, hg38_template_vcf, hg19_vcf_dir or hg38_vcf_dir is required.
Usage:
pheval-utils prepare-corpus [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--phenopacket-dir, -p |
Path | Path to phenopacket corpus directory.. | _required |
--variant-analysis / --no-variant-analysis |
boolean | Specify whether to check for complete variant records in the phenopackets. | False |
--gene-analysis / --no-gene-analysis |
boolean | Specify whether to check for complete gene records in the phenopackets. | False |
--disease-analysis / --no-disease-analysis |
boolean | Specify whether to check for complete disease records in the phenopackets. | False |
--gene-identifier, -g |
choice (ensembl_id | entrez_id | hgnc_id) |
Gene identifier to update in phenopacket | None |
--hg19-template-vcf, -hg19 |
Path | Template hg19 VCF file NOTE: This argument is mutually exclusive with arguments: [hg19_vcf_dir]. | None |
--hg38-template-vcf, -hg38 |
Path | Template hg38 VCF file NOTE: This argument is mutually exclusive with arguments: [hg38_vcf_dir]. | None |
--hg19-vcf-dir, -hg19-dir |
Path | Path to directory containing hg19 VCF templates. NOTE: This argument is mutually exclusive with arguments: [hg19_template_vcf]. | None |
--hg38-vcf-dir, -hg38-dir |
Path | Path to directory containing hg38 VCF templates. NOTE: This argument is mutually exclusive with arguments: [hg38_template_vcf]. | None |
--output-dir, -o |
Path | Path to output prepared corpus. | prepared_corpus |
--help |
boolean | Show this message and exit. | False |
scramble-phenopackets
Generate noisy phenopackets from existing ones.
Usage:
pheval-utils scramble-phenopackets [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--phenopacket-path, -p |
Path | Path to phenopacket. NOTE: This argument is mutually exclusive with arguments: [phenopacket_dir]. | None |
--phenopacket-dir, -P |
Path | Path to phenopackets directory. NOTE: This argument is mutually exclusive with arguments: [phenopacket_path]. | None |
--scramble-factor, -s |
float | Scramble factor for randomising phenopacket phenotypic profiles. | 0.5 |
--output-dir, -O |
Path | Path for creation of output directory | noisy_phenopackets |
--help |
boolean | Show this message and exit. | False |
semsim-scramble
Scrambles semsim profile multiplying score value by scramble factor Args: input (Path): Path file that points out to the semsim profile output (Path): Path file that points out to the output file score_column (List[str]): Score column(s) that will be scrambled scramble_factor (float): Scramble Magnitude
Usage:
pheval-utils semsim-scramble [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--input, -i |
Path | Path to the semantic similarity profile to be scrambled. | _required |
--output, -o |
Path | Path where the scrambled semsim file will be written. | _required |
--score-column, -c |
choice (jaccard_similarity | dice_similarity | phenodigm_score) |
Score column that will be scrambled | _required |
--scramble-factor, -s |
float | Scramble Magnitude (noise) | |
| that will be applied to semantic similarity score column (e.g. jaccard similarity). | 0.5 |
||
--help |
boolean | Show this message and exit. | False |
semsim-to-exomiserdb
ingests semsim file into exomiser phenotypic database
Args: input_file (Path): semsim input file. e.g phenio-plus-hp-mp.0.semsimian.tsv object_prefix (str): object prefix. e.g. MP subject_prefix (str): subject prefix e.g HP db_path (Path): Exomiser Phenotypic Database Folder Path. (e.g. /exomiser_folder/2209_phenotype/2209_phenotype/)
Usage:
pheval-utils semsim-to-exomiserdb [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--input-file, -i |
Path | Semsim input file. | _required |
--object-prefix |
text | Object Prefix. e.g. MP | _required |
--subject-prefix |
text | Subject Prefix. e.g. HP | _required |
--db-path, -d |
Path | Exomiser Phenotypic Database Folder Path. | |
| (e.g. /exomiser_folder/2209_phenotype/2209_phenotype/). | |||
| This is the path where the phenotypic database folder will be written out. | _required | ||
--help |
boolean | Show this message and exit. | False |
update-phenopackets
Update gene symbols and identifiers for phenopackets.
Usage:
pheval-utils update-phenopackets [OPTIONS]
Options:
| Name | Type | Description | Default |
|---|---|---|---|
--phenopacket-path, -p |
Path | Path to phenopacket. NOTE: This argument is mutually exclusive with arguments: [phenopacket_dir]. | None |
--phenopacket-dir, -P |
Path | Path to phenopacket directory for updating. NOTE: This argument is mutually exclusive with arguments: [phenopacket_path]. | None |
--output-dir, -o |
Path | Path to write phenopacket. | _required |
--gene-identifier, -g |
choice (ensembl_id | entrez_id | hgnc_id) |
Gene identifier to add to phenopacket | ensembl_id |
--help |
boolean | Show this message and exit. | False |