Client Modules

HTTP client calls for GFF endpoints.

modalysis.client.gff.gff_format(input_path: str, output_path: str, output_name: str, allowed_chromosomes: list[str], base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a GFF format request to the server.

Parameters:

  • input_path (str)

  • output_path (str)

  • output_name (str)

  • allowed_chromosomes (list[str])

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.gff.gff_annotate(gff_path: str, expression_paths: list[str], expression_labels: list[str], output_path: str, output_name: str, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a GFF annotate request to the server.

Parameters:

  • gff_path (str)

  • expression_paths (list[str])

  • expression_labels (list[str])

  • output_path (str)

  • output_name (str)

  • base_url (str)

Return type:

dict[str, str]

HTTP client calls for pileup endpoints.

modalysis.client.pileup.pileup_merge(pileup_paths: list[str], output_path: str, output_name: str, min_files: int = 2, min_file_coverage: float = 50.0, min_reads: int = 5, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a pileup merge request to the server.

Parameters:

  • pileup_paths (list[str])

  • output_path (str)

  • output_name (str)

  • min_files (int)

  • min_file_coverage (float)

  • min_reads (int)

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.pileup.pileup_format(input_path: str, output_path: str, output_name: str, allowed_chromosomes: list[str], base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a pileup format request to the server.

Parameters:

  • input_path (str)

  • output_path (str)

  • output_name (str)

  • allowed_chromosomes (list[str])

  • base_url (str)

Return type:

dict[str, str]

HTTP client calls for DMR endpoints.

modalysis.client.dmr.dmr_format(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, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a DMR format request to the server.

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)

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.dmr.dmr_annotate(dmr_path: str, gff_path: str, output_path: str, output_name: str, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a DMR annotate request to the server.

Parameters:

  • dmr_path (str)

  • gff_path (str)

  • output_path (str)

  • output_name (str)

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.dmr.dmr_gene_counts(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, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a DMR gene-count aggregation request to the server.

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)

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.dmr.dmr_common_genes(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, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a DMR common-genes aggregation request to the server.

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)

  • base_url (str)

Return type:

dict[str, str]

HTTP client calls for plot endpoints.

modalysis.client.plot.plot_mean_methylation(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, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a mean-methylation plotting request to the server.

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)

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.plot.plot_gene_heatmap(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, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a gene-heatmap plotting request to the server.

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)

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.plot.plot_dmr_dotplot(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, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a DMR dotplot request to the server.

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)

  • base_url (str)

Return type:

dict[str, str]

modalysis.client.plot.plot_common_genes_venn(annotated_dmr_paths: list[str], manifestations: list[str], modifications: list[str], modification_a: str, modification_b: str, output_path: str, output_name: str, base_url: str = 'http://localhost:8000') → dict[str, str][source]

POST a common-genes Venn plotting request to the server.

Parameters:

  • annotated_dmr_paths (list[str])

  • manifestations (list[str])

  • modifications (list[str])

  • modification_a (str)

  • modification_b (str)

  • output_path (str)

  • output_name (str)

  • base_url (str)

Return type:

dict[str, str]