BioGraph Function

read_from_gfa(filename::String; weight_file::String)

Read graph from GFA file and optional weight_file (contains two column node and weight) and return GFAResult struct which has g - the graph, w - weight array, l - node label array, e - edge label array and p - path array.

find_graph_component(gfa_result::BioGraph.GFAResult)

Return graph components of GFAResult:

• Simple Graphs
• Lone Cycles
• Lone Nodes

get_summary(g_coms::BioGraph.GraphComponent)

Summary of GraphComponent.

get_summary(g_coms::BioGraph.GraphResult)

Summary of GraphResult:

• No of vertices
• No of edges
• No of source nodes
• No of end nodes
• No of path

get_terminus(g_result::BioGraph.GraphResult; outfile::String)

Get all source and sink nodes of GraphResult. Write to CSV, including data from GFA.

get_gfa(g_result::BioGraph.GraphResult; outfile::String)

Get GFA output of GraphResult.

find_longest_path(graph_result::BioGraph.GraphResult, optimizer_factory; is_weighted::Bool, source_node::Int64, sink_node::Int64, has_path::String)

Find longest path in graph. Input:

• GraphResult
• JuMP optimizer_factory such as CPLEX.Optimizer
• has_path: optional string that indicates the path must have in longest path.
• is_weighted: if true find shortest path which is weighted
• source_node, sink_node: find longest path which has source and sink nodes.

get_gfa(g_result::BioGraph.LongestPath; outfile::String)

Get GFA output of LongestPath.

get_fasta(g_result::BioGraph.LongestPath; header::String="linear_path", outdir::String="")

Get FastA and Bed output of LongestPath. Will not generate files if outdir was not specified.