python API

class odgi.edge

edges link two handles together

class odgi.graph

the odgi graph type

append_step(self: odgi.graph, arg0: odgi.path_handle, arg1: odgi.handle) → odgi.step_handle

Append a visit to a node to the given path. Returns a handle to the new final step on the path which is appended.

apply_ordering(self: odgi.graph, order: List[odgi.handle], compact_ids: bool = False) → None

Reorder the graph’s internal structure to match that given. Optionally compact the id space of the graph to match the ordering, from 1->|ordering|.

apply_orientation(self: odgi.graph, arg0: odgi.handle) → odgi.handle

Alter the node that the given handle corresponds to so the orientation indicated by the handle becomes the node’s local forward orientation. Updates all links and path steps to match the new orientation.

apply_path_ordering(self: odgi.graph, arg0: List[odgi.path_handle]) → None

Reorder the graph’s paths as given.

clear(self: odgi.graph) → None

Remove all nodes and edges. Does not update any stored paths.

clear_paths(self: odgi.graph) → None

Remove all stored paths.

combine_handles(self: odgi.graph, arg0: List[odgi.handle]) → odgi.handle

Join handles into a new node, returning the handle of the new node.

create_edge(*args, **kwargs)

Overloaded function.

1. create_edge(self: odgi.graph, arg0: odgi.handle, arg1: odgi.handle) -> None

Create an edge connecting the given handles in the given order and orientations.

2. create_edge(self: odgi.graph, arg0: Tuple[odgi.handle, odgi.handle]) -> None

Create an edge connecting the given handles in the given order and orientations.

create_handle(*args, **kwargs)

Overloaded function.

1. create_handle(self: odgi.graph, arg0: str) -> odgi.handle

Create a new node with the given sequence and return the handle.

2. create_handle(self: odgi.graph, arg0: str, arg1: int) -> odgi.handle

Create a new node with the given sequence and return the handle.

create_path_handle(self: odgi.graph, name: str, is_circular: bool = False) → odgi.path_handle

Create a path with the given name. The caller must ensure that no path with the given name already exists.

destroy_edge(*args, **kwargs)

Overloaded function.

1. destroy_edge(self: odgi.graph, arg0: Tuple[odgi.handle, odgi.handle]) -> None

Remove the edge connecting the given handles in the given order and orientations.

2. destroy_edge(self: odgi.graph, arg0: odgi.handle, arg1: odgi.handle) -> None

Remove the edge connecting the given handles in the given order and orientations.

destroy_handle(self: odgi.graph, arg0: odgi.handle) → None

Remove the node belonging to the given handle and all of its edges. Does not update any stored paths. Invalidates the destroyed handle.

destroy_path(self: odgi.graph, arg0: odgi.path_handle) → None

Destroy the given path. Invalidates handles to the path and its node steps.

divide_handle(*args, **kwargs)

Overloaded function.

1. divide_handle(self: odgi.graph, arg0: odgi.handle, arg1: List[int]) -> List[odgi.handle]

Split a handle’s underlying node at the given offsets in the handle’s orientation. Returns the handles to the new parts.

2. divide_handle(self: odgi.graph, arg0: odgi.handle, arg1: int) -> Tuple[odgi.handle, odgi.handle]

Split a handle’s underlying node at the given offset in the handle’s orientation. Returns the handles to the new parts.

edge_handle(self: odgi.graph, arg0: odgi.handle, arg1: odgi.handle) → Tuple[odgi.handle, odgi.handle]

Return the edge handle for the given pair of handles.

flip(self: odgi.graph, handle: odgi.handle) → odgi.handle

Flip the handle to the opposite orientation.

follow_edges(self: odgi.graph, arg0: odgi.handle, arg1: bool, arg2: Callable[[odgi.handle], bool]) → bool

Follow edges starting at a given node.

for_each_handle(self: odgi.graph, iteratee: Callable[[odgi.handle], bool], parallel: bool = False) → bool

Iterate over all the nodes in the graph.

for_each_path_handle(self: odgi.graph, arg0: Callable[[odgi.path_handle], bool]) → bool

Invoke the callback for each path in the graph.

for_each_step_in_path(self: odgi.graph, arg0: odgi.path_handle, arg1: Callable[[odgi.step_handle], None]) → None

Invoke the callback for each step in a given path.

for_each_step_on_handle(self: odgi.graph, arg0: odgi.handle, arg1: Callable[[odgi.step_handle], bool]) → bool

Invoke the callback for each of the steps on a given handle.

forward(self: odgi.graph, arg0: odgi.handle) → odgi.handle

Return the forward version of the handle.

get_degree(self: odgi.graph, arg0: odgi.handle, arg1: bool) → int

Return the degree of the given node.

get_handle(self: odgi.graph, node_id: int, is_reverse: bool = False) → odgi.handle

Return the handle for the given node id.

get_handle_of_step(self: odgi.graph, arg0: odgi.step_handle) → odgi.handle

Return the handle that a given step occurs on.

get_id(self: odgi.graph, handle: odgi.handle) → int

Return the id of the given handle.

get_is_circular(self: odgi.graph, arg0: odgi.path_handle) → bool

Returns true if the path is circular.

get_is_reverse(self: odgi.graph, handle: odgi.handle) → bool

Return true if the handle refers to the node reverse complement.

get_length(self: odgi.graph, handle: odgi.handle) → int

Return the length of the node referred to by the handle.

get_next_step(self: odgi.graph, arg0: odgi.step_handle) → odgi.step_handle

Returns a handle to the next step on the path. Calling on an end marker step returns the same end marker.

get_node_count(self: odgi.graph) → int

Return the number of nodes in the graph.

get_path(self: odgi.graph, arg0: odgi.step_handle) → odgi.path_handle

Return the path of a given step handle.

get_path_count(self: odgi.graph) → int

Return the path count of the graph

get_path_handle(self: odgi.graph, arg0: str) → odgi.path_handle

Return the path handle for the named path.

get_path_handle_of_step(self: odgi.graph, arg0: odgi.step_handle) → odgi.path_handle

Returns a handle to the path that an step is on.

get_path_name(self: odgi.graph, arg0: odgi.path_handle) → str

Return the path name for a given path handle.

get_previous_step(self: odgi.graph, arg0: odgi.step_handle) → odgi.step_handle

Returns a handle to the previous step on the path. Calling on a front end marker step returns the same end marker.

get_sequence(self: odgi.graph, handle: odgi.handle) → str

get_step_count(*args, **kwargs)

Overloaded function.

1. get_step_count(self: odgi.graph, arg0: odgi.path_handle) -> int

Return the step count of a given path.

2. get_step_count(self: odgi.graph, arg0: odgi.handle) -> int

Return the number of steps on the given handle.

has_edge(self: odgi.graph, arg0: odgi.handle, arg1: odgi.handle) → bool

Returns true if the given edge exists

has_next_step(self: odgi.graph, arg0: odgi.step_handle) → bool

Returns true if the step is not the last step on the path, else false.

has_node(self: odgi.graph, node_id: int) → bool

Return true if the given node is in the graph.

has_path(self: odgi.graph, arg0: str) → bool

Return if a path with the givenv name exists in the graph.

has_previous_step(self: odgi.graph, arg0: odgi.step_handle) → bool

Returns true if the step is not the first step on the path, else false.

insert_step(self: odgi.graph, arg0: odgi.step_handle, arg1: odgi.step_handle, arg2: odgi.handle) → odgi.step_handle

Insert a visit to a node to the given path between the given steps. Returns a handle to the new step on the path which is appended.

is_empty(self: odgi.graph, arg0: odgi.path_handle) → bool

Returns true if the given path is empty, and false otherwise.

is_path_end(self: odgi.graph, arg0: odgi.step_handle) → bool

Returns true if the step handle is an end magic handle.

is_path_front_end(self: odgi.graph, arg0: odgi.step_handle) → bool

Returns true if the step handle is a front end magic handle.

load(self: odgi.graph, arg0: str) → None

Load the graph from the given file.

max_node_id(self: odgi.graph) → int

Return the maximum node id in the graph.

min_node_id(self: odgi.graph) → int

Return the minimum node id in the graph.

optimize(self: odgi.graph, allow_id_reassignment: bool = False) → None

Organize the graph for better performance and memory use.

path_back(self: odgi.graph, arg0: odgi.path_handle) → odgi.step_handle

Return a step handle to the last step, which is arbitrary in the case of a circular path.

path_begin(self: odgi.graph, arg0: odgi.path_handle) → odgi.step_handle

Return the step handle for the first step in the given path.

path_end(self: odgi.graph, arg0: odgi.path_handle) → odgi.step_handle

Return a step handle to a fictitious handle one past the end of the path.

path_front_end(self: odgi.graph, arg0: odgi.path_handle) → odgi.step_handle

Return a step handle to a fictitious handle one past the start of the path.

prepend_step(self: odgi.graph, arg0: odgi.path_handle, arg1: odgi.handle) → odgi.step_handle

Append a visit to a node to the given path. Returns a handle to the new final step on the path which is appended.

rewrite_segment(self: odgi.graph, arg0: odgi.step_handle, arg1: odgi.step_handle, arg2: List[odgi.handle]) → Tuple[odgi.step_handle, odgi.step_handle]

Replace the path range with the new segment, returning the new start and end step handles for the segment.

serialize(self: odgi.graph, arg0: str) → None

Save the graph to the given file, returning the number of bytes written.

set_circularity(self: odgi.graph, arg0: odgi.path_handle, arg1: bool) → None

Set if the path is circular or not.

set_step(self: odgi.graph, arg0: odgi.step_handle, arg1: odgi.handle) → odgi.step_handle

Set the step to the given handle, possibly re-linking and cleaning up if needed.

steps_of_handle(self: odgi.graph, arg0: odgi.handle, arg1: bool) → List[odgi.step_handle]

Obtain the steps on a given handle.

to_gfa(self: odgi.graph) → None

Display as GFA

class odgi.handle

the handle, which refers to oriented nodes

class odgi.path_handle

the path handle type, which refers to paths

class odgi.step_handle

the step handle type, which refers to path paths