Server Modules

class modalysis.server.models.GffFormatRequest(*, input_path: str, output_path: str, output_name: str, allowed_chromosomes: list[str])[source]

Bases: BaseModel

Parameters:

  • input_path (str)

  • output_path (str)

  • output_name (str)

  • allowed_chromosomes (list[str])

input_path: str
output_path: str
output_name: str
allowed_chromosomes: list[str]
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.GffAnnotateRequest(*, gff_path: str, expression_paths: list[str], expression_labels: list[str], output_path: str, output_name: str)[source]

Bases: BaseModel

Parameters:

  • gff_path (str)

  • expression_paths (list[str])

  • expression_labels (list[str])

  • output_path (str)

  • output_name (str)

gff_path: str
expression_paths: list[str]
expression_labels: list[str]
output_path: str
output_name: str
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.PileupFormatRequest(*, input_path: str, output_path: str, output_name: str, allowed_chromosomes: list[str])[source]

Bases: BaseModel

Parameters:

  • input_path (str)

  • output_path (str)

  • output_name (str)

  • allowed_chromosomes (list[str])

input_path: str
output_path: str
output_name: str
allowed_chromosomes: list[str]
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.PileupMergeRequest(*, pileup_paths: list[str], output_path: str, output_name: str, min_files: int = 2, min_file_coverage: float = 50.0, min_reads: int = 5)[source]

Bases: BaseModel

Parameters:

  • pileup_paths (list[str])

  • output_path (str)

  • output_name (str)

  • min_files (int)

  • min_file_coverage (float)

  • min_reads (int)

pileup_paths: list[str]
output_path: str
output_name: str
min_files: int
min_file_coverage: float
min_reads: int
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.DmrFormatRequest(*, 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)[source]

Bases: BaseModel

Parameters:

  • input_path (str)

  • output_path (str)

  • output_name (str)

  • allowed_chromosomes (list[str])

  • min_score (float)

  • max_p_value (float)

  • min_pct_a_samples (float)

  • min_pct_b_samples (float)

  • min_reads (int)

input_path: str
output_path: str
output_name: str
allowed_chromosomes: list[str]
min_score: float
max_p_value: float
min_pct_a_samples: float
min_pct_b_samples: float
min_reads: int
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.DmrAnnotateRequest(*, dmr_path: str, gff_path: str, output_path: str, output_name: str)[source]

Bases: BaseModel

Parameters:

  • dmr_path (str)

  • gff_path (str)

  • output_path (str)

  • output_name (str)

dmr_path: str
gff_path: str
output_path: str
output_name: str
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.DmrGeneCountsRequest(*, 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)[source]

Bases: BaseModel

Parameters:

  • 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)

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
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.DmrCommonGenesRequest(*, 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)[source]

Bases: BaseModel

Parameters:

  • 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)

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
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.PlotMeanMethylationRequest(*, 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)[source]

Bases: BaseModel

Parameters:

  • gff_path (str)

  • merged_pileup_paths (list[str])

  • labels (list[str])

  • output_path (str)

  • output_name (str)

  • y_min (float)

  • y_max (float)

  • chromosome_order (list[str] | None)

  • plot_title (str | None)

gff_path: str
merged_pileup_paths: list[str]
labels: list[str]
output_path: str
output_name: str
y_min: float
y_max: float
chromosome_order: list[str] | None
plot_title: str | None
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.PlotGeneHeatmapRequest(*, 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)[source]

Bases: BaseModel

Parameters:

  • 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)

  • effect_signs (list[str] | None)

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
effect_signs: list[str] | None
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.PlotDmrDotplotRequest(*, 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)[source]

Bases: BaseModel

Parameters:

  • 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)

  • effect_signs (list[str] | None)

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
effect_signs: list[str] | None
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class modalysis.server.models.PlotCommonGenesVennRequest(*, annotated_dmr_paths: list[str], manifestations: list[str], modifications: list[str], modification_a: str, modification_b: str, output_path: str, output_name: str)[source]

Bases: BaseModel

Parameters:

  • annotated_dmr_paths (list[str])

  • manifestations (list[str])

  • modifications (list[str])

  • modification_a (str)

  • modification_b (str)

  • output_path (str)

  • output_name (str)

annotated_dmr_paths: list[str]
manifestations: list[str]
modifications: list[str]
modification_a: str
modification_b: str
output_path: str
output_name: str
_abc_impl = <_abc._abc_data object>
model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

FastAPI application entrypoint for modalysis.

modalysis.server.main.lifespan(app: FastAPI) → AsyncIterator[None][source]

Configure logging when the FastAPI application starts.

Parameters:

app (FastAPI)

Return type:

AsyncIterator[None]

FastAPI routes for GFF operations.

modalysis.server.gff.gff_format(request: GffFormatRequest) → dict[str, str][source]

Handle POST /gff/format and run core GFF formatting.

Parameters:

request (GffFormatRequest)

Return type:

dict[str, str]

modalysis.server.gff.gff_annotate(request: GffAnnotateRequest) → dict[str, str][source]

Handle POST /gff/annotate and run core GFF annotation.

Parameters:

request (GffAnnotateRequest)

Return type:

dict[str, str]

FastAPI routes for pileup operations.

modalysis.server.pileup.pileup_format(request: PileupFormatRequest) → dict[str, str][source]

Handle POST /pileup/format and run core pileup formatting.

Parameters:

request (PileupFormatRequest)

Return type:

dict[str, str]

modalysis.server.pileup.pileup_merge(request: PileupMergeRequest) → dict[str, str][source]

Handle POST /pileup/merge and run core pileup merging.

Parameters:

request (PileupMergeRequest)

Return type:

dict[str, str]

FastAPI routes for DMR operations.

modalysis.server.dmr.dmr_format(request: DmrFormatRequest) → dict[str, str][source]

Handle POST /dmr/format and run core DMR formatting.

Parameters:

request (DmrFormatRequest)

Return type:

dict[str, str]

modalysis.server.dmr.dmr_annotate(request: DmrAnnotateRequest) → dict[str, str][source]

Handle POST /dmr/annotate and run core DMR interval annotation.

Parameters:

request (DmrAnnotateRequest)

Return type:

dict[str, str]

modalysis.server.dmr.dmr_gene_counts(request: DmrGeneCountsRequest) → dict[str, str][source]

Handle POST /dmr/gene-counts and run gene-count aggregation.

Parameters:

request (DmrGeneCountsRequest)

Return type:

dict[str, str]

modalysis.server.dmr.dmr_common_genes(request: DmrCommonGenesRequest) → dict[str, str][source]

Handle POST /dmr/common-genes and run overlap aggregation.

Parameters:

request (DmrCommonGenesRequest)

Return type:

dict[str, str]

FastAPI routes for plot generation operations.

modalysis.server.plot.plot_mean_methylation(request: PlotMeanMethylationRequest) → dict[str, str][source]

Handle POST /plot/mean-methylation and generate mean methylation plot.

Parameters:

request (PlotMeanMethylationRequest)

Return type:

dict[str, str]

modalysis.server.plot.plot_gene_heatmap(request: PlotGeneHeatmapRequest) → dict[str, str][source]

Handle POST /plot/gene-heatmap and generate heatmap plots.

Parameters:

request (PlotGeneHeatmapRequest)

Return type:

dict[str, str]

modalysis.server.plot.plot_dmr_dotplot(request: PlotDmrDotplotRequest) → dict[str, str][source]

Handle POST /plot/dmr-dotplot and generate dotplot panels.

Parameters:

request (PlotDmrDotplotRequest)

Return type:

dict[str, str]

modalysis.server.plot.plot_common_genes_venn(request: PlotCommonGenesVennRequest) → dict[str, str][source]

Handle POST /plot/common-genes-venn and generate Venn figure.

Parameters:

request (PlotCommonGenesVennRequest)

Return type:

dict[str, str]