dae.gene_scores package

Subpackages

• dae.gene_scores.implementations package
  • Submodules
  • dae.gene_scores.implementations.gene_scores_impl module
    • GeneScoreImplementation
      • GeneScoreImplementation.add_statistics_build_tasks()
      • GeneScoreImplementation.calc_info_hash()
      • GeneScoreImplementation.calc_statistics_hash()
      • GeneScoreImplementation.get_info()
      • GeneScoreImplementation.get_statistics_info()
      • GeneScoreImplementation.get_template()
    • build_gene_score_implementation_from_resource()
  • Module contents

Submodules

dae.gene_scores.gene_scores module

class dae.gene_scores.gene_scores.GeneScore(resource: GenomicResource)

Bases: ResourceConfigValidationMixin

Class used to represent gene scores.

property files: set[str]

get_all_scores() → list[str]

get_gene_value(score_id: str, gene_symbol: str) → float | None

Return the value for a given gene symbol.

get_genes(score_id: str, score_min: float | None = None, score_max: float | None = None, values: list[str] | None = None) → set[str]

Return set of genes for a score between a min and max value or genes with certain gene score values.

get_histogram_filename(score_id: str) → str

Return the histogram filename for a gene score.

get_histogram_image_filename(score_id: str) → str

get_histogram_image_url(score_id: str) → str | None

get_max(score_id: str) → float

Return maximal score value.

get_min(score_id: str) → float

Return minimal score value.

get_number_range(score_id: str) → tuple[float, float] | None

Return the value range for a number score.

static get_schema() → dict[str, Any]

Return schema to be used for config validation.

get_score_df(score_id: str) → DataFrame

get_score_histogram(score_id: str) → NumberHistogram

Return defined histogram for a score.

get_scores() → list[str]

get_values(score_id: str) → list[float]

Return a list of score values.

get_x_scale(score_id: str) → str | None

Return the scale type of the X axis.

get_y_scale(score_id: str) → str | None

Return the scale type of the Y axis.

to_tsv(score_id: str | None = None) → list[str]

Return a TSV version of the gene score data.

class dae.gene_scores.gene_scores.GeneScoresDb(gene_scores: list[GeneScore])

Bases: object

Helper class used to load all defined gene scores.

Used by Web interface.

static build_descs_from_score(gene_score: GeneScore) → list[ScoreDesc]

Build score descriptions from score.

get_gene_score(score_id: str) → GeneScore | None

Return a given gene score.

get_gene_score_ids() → list[str]

Return a list of the IDs of all the gene scores contained.

get_gene_scores() → list[GeneScore]

Return a list of all the gene scores contained in the DB.

get_score_desc(score_id: str) → ScoreDesc | None

get_score_ids() → list[str]

Return a list of the IDs of all the gene scores contained.

get_scores() → list[ScoreDesc]

class dae.gene_scores.gene_scores.ScoreDef(score_id: str, name: str, desc: str, hist_conf: NumberHistogramConfig | CategoricalHistogramConfig | None, small_values_desc: str | None, large_values_desc: str | None)

Bases: object

Class used to represent a gene score definition.

desc: str

hist_conf: NumberHistogramConfig | CategoricalHistogramConfig | None

large_values_desc: str | None

name: str

score_id: str

small_values_desc: str | None

class dae.gene_scores.gene_scores.ScoreDesc(resource_id: str, score_id: str, name: str, hist: NumberHistogram, description: str, help: str, small_values_desc: str | None, large_values_desc: str | None)

Bases: object

Class used to represent a score description.

description: str

help: str

hist: NumberHistogram

large_values_desc: str | None

name: str

resource_id: str

score_id: str

small_values_desc: str | None

dae.gene_scores.gene_scores.build_gene_score_from_resource(resource: GenomicResource) → GeneScore

dae.gene_scores.gene_scores.build_gene_score_from_resource_id(resource_id: str, grr: GenomicResourceRepo | None = None) → GeneScore

Module contents