DDOT Converters

DDOT converters facilitate the transformation between CX2 and DDOT formats for both interaction networks and hierarchical networks. The DDOT format is structurally similar to HiDeF but is commonly used for representing interactomes and ontologies.

Example 1: Converting a CX2 Interaction Network to DDOT Format

To convert a CX2 interactome into a DDOT file, use the InteractomeToDDOTConverter class:

from cellmaps_utils.ddotconverter import InteractomeToDDOTConverter

converter = InteractomeToDDOTConverter(
    output_dir="path/to/output",
    interactome_path="path/to/interactome.cx2"
)
converter.generate_ddot_format_file()

Expected Output: interactome_ddot.txt

GeneA    GeneB    interaction_type
GeneC    GeneD    interaction_type

Example 2: Converting a DDOT Interaction Network Back to CX2

To convert a DDOT interactome into a CX2 format, use the DDOTToInteractomeConverter class:

from cellmaps_utils.ddotconverter import DDOTToInteractomeConverter

converter = DDOTToInteractomeConverter(
    output_dir="path/to/output",
    interactome_ddot_path="path/to/interactome_ddot.txt"
)
converter.generate_interactome_file()

Expected Output: interactome.cx2

Example 3: Converting a CX2 Hierarchical Network to DDOT Ontology Format

To convert a hierarchical network (CX2) into DDOT ontology format, use HierarchyToDDOTConverter:

from cellmaps_utils.ddotconverter import HierarchyToDDOTConverter

converter = HierarchyToDDOTConverter(
    output_dir="path/to/output",
    hierarchy_path="path/to/hierarchy.cx2"
)
converter.generate_ontology_ddot_file()

Expected Output: ontology.ont

Cluster1    Cluster2    default
Cluster1    GeneA    gene

Example 4: Converting a DDOT Ontology Back to a CX2 Hierarchical Network

To convert a DDOT ontology into CX2 hierarchical format (HCX), use DDOTToHierarchyConverter:

from cellmaps_utils.ddotconverter import DDOTToHierarchyConverter

converter = DDOTToHierarchyConverter(
    output_dir="path/to/output",
    ontology_ddot_path="path/to/ontology.ont",
    parent_ddot_path="path/to/interactome_ddot.txt"  # Optional: Parent interactome
)
converter.generate_hierarchy_hcx_file()

Expected Output:

• hierarchy.cx2 – The reconstructed hierarchical network.

• hierarchy_parent.cx2 (if parent interactome was used).