Defining reference path on graph

[ManuelTgn]

Hi team,

thank you for developing this amazing tool!

I have a couple of questions regarding odgi graphs manipulation through the Python API.

I created an odgi graph from a gfa containing > 1000 haplotypes + 1 reference sequence. Is there a way to understand which path belongs to the reference sequence? All paths seem to point to an haplotype.

While traversing the paths embedded in the graph, is it possible to understand to which position correspond a nucleotide in a node, using the reference coordinates space?

Thanks for the help!

[subwaystation]

Hi @ManuelTgn,

since I don't know in detail how you created the graphs, it is hard to tell. In ODGI's variation graph model all paths are equal, there is no sense of a reference path.

If you want to use ODGI to translate path positions to your path of choice, please take a look at https://odgi.readthedocs.io/en/latest/rst/tutorials/navigating_and_annotating_graphs.html#path-to-path-position-mapping.

[ManuelTgn]

Hi @subwaystation,

thank you for the reply. That was very helpful!

I created my input graph using the vg toolkit, enriching a chromosome with some variants stored in a phased VCF. Are there python functions in ODGI's API to replicate the command line functionalities showed in the documentation page you shared?

[subwaystation]

Hi @ManuelTgn,

I see, so no crazy variants with crazy repeats. That's good :)

As far as I know, the Python API only exposes basic ODGI functionality. You would have to build such code on your own. Take a look at

odgi/src/subcommand/position_main.cpp

Lines 794 to 840 in de70fcd

	#pragma omp parallel for schedule(dynamic,1)
	for (auto& path_pos : path_positions) {
	// TODO we need a better input format
	pos_t pos;
	step_handle_t step_handle_graph_pos;
	// handle the lift into the target graph
	if (lifting) {
	lift_result_t source_result;
	pos_t _pos = get_graph_pos(source_graph, path_pos, step_handle_graph_pos);
	if (id(_pos) && get_position(source_graph, lift_path_set_source, _pos, source_result, step_handle_graph_pos, true)) {
	pos = get_graph_pos(target_graph,
	{ target_graph.get_path_handle(
	source_graph.get_path_name(
	source_graph.get_path_handle_of_step(
	source_result.ref_hit))),
	(uint64_t)source_result.path_offset,
	source_result.is_rev_vs_ref },
	step_handle_graph_pos);
	} else {
	pos = make_pos_t(0,false,0); // couldn't lift
	}
	} else {
	//path_pos = _path_pos;
	pos = get_graph_pos(target_graph, path_pos, step_handle_graph_pos);
	}
	lift_result_t result;
	//std::cerr << "Got graph pos " << id(pos) << std::endl;
	if (id(pos)) {
	if (give_graph_pos) {
	#pragma omp critical (cout)
	std::cout << "#source.path.pos\ttarget.graph.pos" << std::endl
	<< (lifting ? source_graph.get_path_name(path_pos.path) : target_graph.get_path_name(path_pos.path))
	<< "," << path_pos.offset << "," << (path_pos.is_rev ? "-" : "+")
	<< "\t" << id(pos) << "," << offset(pos) << "," << (is_rev(pos) ? "-" : "+") << std::endl;
	} else if (get_position(target_graph, ref_path_set, pos, result, step_handle_graph_pos, true)) {
	bool ref_is_rev = false;
	path_handle_t p = target_graph.get_path_handle_of_step(result.ref_hit);
	#pragma omp critical (cout)
	std::cout << "#source.path.pos\ttarget.path.pos\tdist.to.ref\tstrand.vs.ref" << std::endl
	<< (lifting ? source_graph.get_path_name(path_pos.path) : target_graph.get_path_name(path_pos.path)) << ","
	<< path_pos.offset << "," << (path_pos.is_rev ? "-" : "+") << "\t"
	<< target_graph.get_path_name(p) << "," << result.path_offset << "," << (ref_is_rev ? "-" : "+") << "\t"
	<< result.walked_to_hit_ref << "\t" << (result.is_rev_vs_ref ? "-" : "+") << std::endl;
	}
	}
	}

as in inspiration.

Best,
Simon