{"action":"created","issue":{"url":"https://api.github.com/repos/endrebak/kg/issues/1","labels_url":"https://api.github.com/repos/endrebak/kg/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/endrebak/kg/issues/1/comments","events_url":"https://api.github.com/repos/endrebak/kg/issues/1/events","html_url":"https://github.com/endrebak/kg/issues/1","id":114060895,"number":1,"title":"Choose type of gene ID","user":{"login":"slowkow","id":209714,"avatar_url":"https://avatars.githubusercontent.com/u/209714?v=3","gravatar_id":"","url":"https://api.github.com/users/slowkow","html_url":"https://github.com/slowkow","followers_url":"https://api.github.com/users/slowkow/followers","following_url":"https://api.github.com/users/slowkow/following{/other_user}","gists_url":"https://api.github.com/users/slowkow/gists{/gist_id}","starred_url":"https://api.github.com/users/slowkow/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/slowkow/subscriptions","organizations_url":"https://api.github.com/users/slowkow/orgs","repos_url":"https://api.github.com/users/slowkow/repos","events_url":"https://api.github.com/users/slowkow/events{/privacy}","received_events_url":"https://api.github.com/users/slowkow/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-10-29T14:25:32Z","updated_at":"2015-10-29T18:06:41Z","closed_at":null,"body":"Thanks for the great package! It just works, and I'm very impressed with the effective use of joblib and other packages. I could definitely learn a few things about making Python packages from your code.\r\n\r\nHowever, I'd like to ask if you could support several gene identifiers like Entrez ID or Ensembl. The command below outputs gene symbols, but it is not clear to me if these gene symbols are HGNC names or some other names. Could you please clarify? Could you add an option to output other types of identifiers?\r\n\r\n```\r\nkg --mergecol=0 --noheader --genes --definition --species=hsa <(echo 01200)\r\n```\r\n\r\n```\r\nCache path is: /Users/slowikow/.kegg/ (Time:  Thu, 29 Oct 2015 10:10:24 )\r\nGet KEGG gene to external gene map. (Time:  Thu, 29 Oct 2015 10:10:24 )\r\nGet KEGG path to gene map. (Time:  Thu, 29 Oct 2015 10:10:25 )\r\nGet KEGG pathway to definition map. (Time:  Thu, 29 Oct 2015 10:10:25 )\r\nConnect KEGG gene map and KEGG pathway map. (Time:  Thu, 29 Oct 2015 10:10:26 )\r\n/Users/slowikow/anaconda/lib/python2.7/site-packages/ebs/merge_cols.py:74: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)\r\n  in_df = in_df.sort(pre_merge_sort_order_col)\r\nAttaching pathway definitions. (Time:  Thu, 29 Oct 2015 10:10:26 )\r\n01200   ME3     Carbon metabolism\r\n01200   PGAMA   Carbon metabolism\r\n01200   PGAM-B  Carbon metabolism\r\n01200   HEL-S-35        Carbon metabolism\r\n01200   PGAM1   Carbon metabolism\r\n01200   PFKF    Carbon metabolism\r\n```"},"comment":{"url":"https://api.github.com/repos/endrebak/kg/issues/comments/152268776","html_url":"https://github.com/endrebak/kg/issues/1#issuecomment-152268776","issue_url":"https://api.github.com/repos/endrebak/kg/issues/1","id":152268776,"user":{"login":"endrebak","id":5526486,"avatar_url":"https://avatars.githubusercontent.com/u/5526486?v=3","gravatar_id":"","url":"https://api.github.com/users/endrebak","html_url":"https://github.com/endrebak","followers_url":"https://api.github.com/users/endrebak/followers","following_url":"https://api.github.com/users/endrebak/following{/other_user}","gists_url":"https://api.github.com/users/endrebak/gists{/gist_id}","starred_url":"https://api.github.com/users/endrebak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/endrebak/subscriptions","organizations_url":"https://api.github.com/users/endrebak/orgs","repos_url":"https://api.github.com/users/endrebak/repos","events_url":"https://api.github.com/users/endrebak/events{/privacy}","received_events_url":"https://api.github.com/users/endrebak/received_events","type":"User","site_admin":false},"created_at":"2015-10-29T18:06:41Z","updated_at":"2015-10-29T18:06:41Z","body":"I try to use the gene ids called `external_gene_name`, because they seem like the most common ones.\r\n\r\n```shell\r\npip install biomartian==0.0.18\r\nbiomartian -d hsap -i external_gene_name -o entrezgene | grep ME3\r\n10873.0\tME3\r\n10197.0\tPSME3\r\n4832.0\tNME3\r\n```\r\n\r\nI am trying to keep this library minimal, only the stuff you can't do anywhere else. This is to avoid duplication, but also the `rest/KEGG` I use only has funding til 2016 sometime, IIRC, so I might have to rewrite the code then. \r\n\r\nMost conversions can be done in `biomartian`, like shown above. Ps. the `.0` are a bug I'll get around to fixing; entrez_ids are ints.\r\n\r\nYou are right that lots of info is lacking though. I'll update the docs, and please tell me if you see something you'd want added.\r\n\r\nAlso feel free to suggest other sources for kegg conversions and I'll add them to the README. If there are better ways of getting KEGG data, I'd like to know and let others know. "}}