Source code for modalysis.server.models

from pydantic import BaseModel




class GffFormatRequest(BaseModel):
    input_path: str
    output_path: str
    output_name: str
    allowed_chromosomes: list[str]





class GffAnnotateRequest(BaseModel):
    gff_path: str
    expression_paths: list[str]
    expression_labels: list[str]
    output_path: str
    output_name: str





class PileupFormatRequest(BaseModel):
    input_path: str
    output_path: str
    output_name: str
    allowed_chromosomes: list[str]





class PileupMergeRequest(BaseModel):
    pileup_paths: list[str]
    output_path: str
    output_name: str
    min_files: int = 2
    min_file_coverage: float = 50.0
    min_reads: int = 5





class DmrFormatRequest(BaseModel):
    input_path: str
    output_path: str
    output_name: str
    allowed_chromosomes: list[str]
    min_score: float = 5
    max_p_value: float = 0.05
    min_pct_a_samples: float = 50.0
    min_pct_b_samples: float = 50.0
    min_reads: int = 5





class DmrAnnotateRequest(BaseModel):
    dmr_path: str
    gff_path: str
    output_path: str
    output_name: str





class DmrGeneCountsRequest(BaseModel):
    annotated_dmr_paths: list[str]
    manifestations: list[str]
    modifications: list[str]
    manifestation_labels: list[str]
    expression_labels: list[str]
    annotated_gff_path: str
    output_path: str
    output_name: str
    output_excel: bool = False





class DmrCommonGenesRequest(BaseModel):
    annotated_dmr_paths: list[str]
    manifestations: list[str]
    modifications: list[str]
    manifestation_labels: list[str]
    expression_labels: list[str]
    modification_a: str
    modification_b: str
    annotated_gff_path: str
    output_path: str
    output_name: str





class PlotMeanMethylationRequest(BaseModel):
    gff_path: str
    merged_pileup_paths: list[str]
    labels: list[str]
    output_path: str
    output_name: str
    y_min: float = 0.0
    y_max: float = 0.1
    chromosome_order: list[str] | None = None
    plot_title: str | None = None





class PlotGeneHeatmapRequest(BaseModel):
    annotated_dmr_paths: list[str]
    manifestations: list[str]
    modifications: list[str]
    manifestation_labels: list[str]
    expression_labels: list[str]
    annotated_gff_path: str
    gff_path: str
    merged_pileup_paths: list[str]
    pileup_manifestations: list[str]
    pileup_modifications: list[str]
    output_path: str
    output_name: str
    show_gene_labels: bool = False
    effect_signs: list[str] | None = None





class PlotDmrDotplotRequest(BaseModel):
    annotated_dmr_paths: list[str]
    manifestations: list[str]
    modifications: list[str]
    manifestation_labels: list[str]
    expression_labels: list[str]
    annotated_gff_path: str
    gff_path: str
    output_path: str
    output_name: str
    show_gene_labels: bool = False
    effect_signs: list[str] | None = None





class PlotCommonGenesVennRequest(BaseModel):
    annotated_dmr_paths: list[str]
    manifestations: list[str]
    modifications: list[str]
    modification_a: str
    modification_b: str
    output_path: str
    output_name: str