{"action":"created","issue":{"url":"https://api.github.com/repos/soedinglab/prosstt/issues/6","repository_url":"https://api.github.com/repos/soedinglab/prosstt","labels_url":"https://api.github.com/repos/soedinglab/prosstt/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/soedinglab/prosstt/issues/6/comments","events_url":"https://api.github.com/repos/soedinglab/prosstt/issues/6/events","html_url":"https://github.com/soedinglab/prosstt/issues/6","id":341647975,"node_id":"MDU6SXNzdWUzNDE2NDc5NzU=","number":6,"title":"Simulating tree from newick: the parameters are not enough for [n] branches","user":{"login":"scottgigante","id":8499679,"node_id":"MDQ6VXNlcjg0OTk2Nzk=","avatar_url":"https://avatars3.githubusercontent.com/u/8499679?v=4","gravatar_id":"","url":"https://api.github.com/users/scottgigante","html_url":"https://github.com/scottgigante","followers_url":"https://api.github.com/users/scottgigante/followers","following_url":"https://api.github.com/users/scottgigante/following{/other_user}","gists_url":"https://api.github.com/users/scottgigante/gists{/gist_id}","starred_url":"https://api.github.com/users/scottgigante/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/scottgigante/subscriptions","organizations_url":"https://api.github.com/users/scottgigante/orgs","repos_url":"https://api.github.com/users/scottgigante/repos","events_url":"https://api.github.com/users/scottgigante/events{/privacy}","received_events_url":"https://api.github.com/users/scottgigante/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-07-16T19:30:29Z","updated_at":"2018-07-25T10:45:49Z","closed_at":"2018-07-25T10:45:49Z","author_association":"CONTRIBUTOR","body":"Hi,\r\n\r\nThanks for providing a great tool! I'm trying to generate a tree following your `sample_pseudotime_series.ipynb` and came across the following error.\r\n\r\n```\r\n>>> import prosstt.simulation as sim\r\n>>> import prosstt.sim_utils as sut\r\n>>> from prosstt import tree\r\n>>> import numpy as np\r\n>>> import newick\r\n>>> np.random.seed(42)\r\n>>> newick1 = \"((A:170,B:170),(C:170,D:170))E:170;\"\r\n>>> tree1 = newick.loads(newick1)\r\n>>> lineage = tree.Tree.from_newick(newick1, genes=1000)\r\n>>> uMs, Ws, Hs = sim.simulate_lineage(lineage, a=0.05)\r\nTraceback (most recent call last):\r\n  File \"<stdin>\", line 1, in <module>\r\n  File \"/old/home/scottgigante/sync/1_soft/prosstt/prosstt/simulation.py\", line 252, in simulate_lineage\r\n    tree.num_branches)\r\nValueError: the parameters are not enough for 7 branches\r\n```\r\n\r\nI'm pretty sure my Newick representation is correct as otherwise the `newick` package throws an error. Any ideas as to what I'm doing wrong?\r\n\r\nThanks again!"},"comment":{"url":"https://api.github.com/repos/soedinglab/prosstt/issues/comments/407713331","html_url":"https://github.com/soedinglab/prosstt/issues/6#issuecomment-407713331","issue_url":"https://api.github.com/repos/soedinglab/prosstt/issues/6","id":407713331,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNzcxMzMzMQ==","user":{"login":"galicae","id":1651067,"node_id":"MDQ6VXNlcjE2NTEwNjc=","avatar_url":"https://avatars0.githubusercontent.com/u/1651067?v=4","gravatar_id":"","url":"https://api.github.com/users/galicae","html_url":"https://github.com/galicae","followers_url":"https://api.github.com/users/galicae/followers","following_url":"https://api.github.com/users/galicae/following{/other_user}","gists_url":"https://api.github.com/users/galicae/gists{/gist_id}","starred_url":"https://api.github.com/users/galicae/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/galicae/subscriptions","organizations_url":"https://api.github.com/users/galicae/orgs","repos_url":"https://api.github.com/users/galicae/repos","events_url":"https://api.github.com/users/galicae/events{/privacy}","received_events_url":"https://api.github.com/users/galicae/received_events","type":"User","site_admin":false},"created_at":"2018-07-25T10:45:49Z","updated_at":"2018-07-25T10:45:49Z","author_association":"MEMBER","body":"Addressed in #8 :)"}}
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