{"action":"created","issue":{"url":"https://api.github.com/repos/crsl4/PhyloNetworks.jl/issues/70","repository_url":"https://api.github.com/repos/crsl4/PhyloNetworks.jl","labels_url":"https://api.github.com/repos/crsl4/PhyloNetworks.jl/issues/70/labels{/name}","comments_url":"https://api.github.com/repos/crsl4/PhyloNetworks.jl/issues/70/comments","events_url":"https://api.github.com/repos/crsl4/PhyloNetworks.jl/issues/70/events","html_url":"https://github.com/crsl4/PhyloNetworks.jl/issues/70","id":287836528,"number":70,"title":"phylogeny parsing: error when a hybrid node has hybrid child","user":{"login":"cecileane","id":9857294,"avatar_url":"https://avatars1.githubusercontent.com/u/9857294?v=4","gravatar_id":"","url":"https://api.github.com/users/cecileane","html_url":"https://github.com/cecileane","followers_url":"https://api.github.com/users/cecileane/followers","following_url":"https://api.github.com/users/cecileane/following{/other_user}","gists_url":"https://api.github.com/users/cecileane/gists{/gist_id}","starred_url":"https://api.github.com/users/cecileane/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cecileane/subscriptions","organizations_url":"https://api.github.com/users/cecileane/orgs","repos_url":"https://api.github.com/users/cecileane/repos","events_url":"https://api.github.com/users/cecileane/events{/privacy}","received_events_url":"https://api.github.com/users/cecileane/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-01-11T16:11:37Z","updated_at":"2018-04-20T18:52:23Z","closed_at":null,"author_association":"COLLABORATOR","body":"In this situation, the network is not of level 1, but the `readTopology` function should still be able to parse the network. The issue was reported on the [google group](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/phylonetworks-users/2GWULTOcF9U). Examples:\r\n```julia\r\nnet = readTopology(\"((((B)#H1)#H2,((C,#H2)S1,(#H1,A)S2)S3)S4);\")\r\n```\r\n    ERROR: hybrid node 3 has more than two hybrid edges attached to it: polytomy that cannot be resolved without intersecting cycles.\r\n\r\ndoing this helps to see that the parenthetical description is just fine (the # signs were taken out to mean that node names are just normal names):\r\n\r\n```julia\r\nnet = readTopology(\"((((B)H1)H2,((C,H2)S1,(H1,A)S2)S3)S4);\")\r\nplot(net, showNodeNumber=true)\r\nnet.node\r\n```\r\n\r\nAnother example:\r\n\r\n```julia\r\nnet = readTopology(\"((A,(((B,C))#H1)#H2),(#H2,((#H1,D),E)));\") # error: node 5 has >2 hybrid edges\r\nnet = readTopology(\"((A,(((B,C))H1)H2),(H2,((H1,D),E)));\")   # just fine\r\nplot(net, showNodeNumber=true) # to see what the network was supposed to be\r\nnet.node\r\n```\r\n\r\n@ChristianBorst: we can work on this after your improvements to the parsing functions are merged into the master version."},"comment":{"url":"https://api.github.com/repos/crsl4/PhyloNetworks.jl/issues/comments/383189506","html_url":"https://github.com/crsl4/PhyloNetworks.jl/issues/70#issuecomment-383189506","issue_url":"https://api.github.com/repos/crsl4/PhyloNetworks.jl/issues/70","id":383189506,"user":{"login":"ujain6","id":14304430,"avatar_url":"https://avatars1.githubusercontent.com/u/14304430?v=4","gravatar_id":"","url":"https://api.github.com/users/ujain6","html_url":"https://github.com/ujain6","followers_url":"https://api.github.com/users/ujain6/followers","following_url":"https://api.github.com/users/ujain6/following{/other_user}","gists_url":"https://api.github.com/users/ujain6/gists{/gist_id}","starred_url":"https://api.github.com/users/ujain6/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ujain6/subscriptions","organizations_url":"https://api.github.com/users/ujain6/orgs","repos_url":"https://api.github.com/users/ujain6/repos","events_url":"https://api.github.com/users/ujain6/events{/privacy}","received_events_url":"https://api.github.com/users/ujain6/received_events","type":"User","site_admin":false},"created_at":"2018-04-20T18:52:23Z","updated_at":"2018-04-20T18:52:23Z","author_association":"NONE","body":"Hi Cecile,\r\n\r\nin net1, (sp)#H3 means that H3 has a single child that is \"sp\"? Right?"}}
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