tfmindi.load_motif_annotations

tfmindi.load_motif_annotations(annotations_file, motif_similarity_fdr=0.001, orthologous_identity_threshold=0.0, column_names=('#motif_id', 'gene_name', 'motif_similarity_qvalue', 'orthologous_identity', 'description'))

Load motif annotations from a motif2TF TSV file with filtering and categorization.

Parameters:

• annotations_file (str) – Path to the annotations TSV file

• motif_similarity_fdr (float (default: 0.001)) – Maximum False Discovery Rate for enriched motifs (default: 0.001)

• orthologous_identity_threshold (float (default: 0.0)) – Minimum orthologous identity for enriched motifs (default: 0.0)

• column_names (tuple[str, ...] (default: ('#motif_id', 'gene_name', 'motif_similarity_qvalue', 'orthologous_identity', 'description'))) – Column names to load from the TSV file

Return type:

DataFrame

Returns:

DataFrame with motif annotations categorized by annotation type: - Direct_annot: Direct gene annotations - Motif_similarity_annot: Annotations by motif similarity - Orthology_annot: Annotations by orthology - Motif_similarity_and_Orthology_annot: Combined annotations

Examples

>>> annotations = load_motif_annotations("./annotations.tbl")
>>> print(annotations.columns.tolist())
['Direct_annot', 'Motif_similarity_annot', 'Orthology_annot', 'Motif_similarity_and_Orthology_annot']