{"action":"created","issue":{"url":"https://api.github.com/repos/khyox/recentrifuge/issues/2","repository_url":"https://api.github.com/repos/khyox/recentrifuge","labels_url":"https://api.github.com/repos/khyox/recentrifuge/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/khyox/recentrifuge/issues/2/comments","events_url":"https://api.github.com/repos/khyox/recentrifuge/issues/2/events","html_url":"https://github.com/khyox/recentrifuge/issues/2","id":322329686,"number":2,"title":"pandas and Excel output","user":{"login":"devonorourke","id":11182172,"avatar_url":"https://avatars0.githubusercontent.com/u/11182172?v=4","gravatar_id":"","url":"https://api.github.com/users/devonorourke","html_url":"https://github.com/devonorourke","followers_url":"https://api.github.com/users/devonorourke/followers","following_url":"https://api.github.com/users/devonorourke/following{/other_user}","gists_url":"https://api.github.com/users/devonorourke/gists{/gist_id}","starred_url":"https://api.github.com/users/devonorourke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/devonorourke/subscriptions","organizations_url":"https://api.github.com/users/devonorourke/orgs","repos_url":"https://api.github.com/users/devonorourke/repos","events_url":"https://api.github.com/users/devonorourke/events{/privacy}","received_events_url":"https://api.github.com/users/devonorourke/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2018-05-11T15:02:29Z","updated_at":"2018-05-11T17:28:54Z","closed_at":null,"author_association":"NONE","body":"Hi Jose,\r\nI'm running `recentrifuge` in a virtual environment created as follows:\r\n```\r\nconda create -n py36 python=3.6 openpyxl biopython pandas\r\n```\r\n\r\nHowever, the `recentrifuge` program throws an error at the final step where it would generate an Excel file because it does not recognize Pandas as being installed.\r\n\r\nThe error:\r\n\r\n```\r\nBuilding the taxonomy multiple tree... OK!\r\nGenerating final plot (/mnt/lustre/macmaneslab/devon/pore604/centrifuge/pore604_results_unclassified.rcf.html)... OK!\r\nWARNING! Pandas not installed: Excel cannot be created.\r\n```\r\n\r\nThis is odd to me because that virtual environment suggests panadas is indeed present:\r\n```\r\n(py36) [devon@premise]$ pip freeze\r\nbiopython==1.70\r\ncertifi==2018.4.16\r\net-xmlfile==1.0.1\r\njdcal==1.4\r\nmmtf-python==1.1.0\r\nmsgpack==0.5.6\r\nnumpy==1.12.1\r\nolefile==0.45.1\r\nont-fast5-api==0.4.1\r\nopenpyxl==2.4.0b1\r\npandas==0.22.0\r\nPillow==4.2.1\r\nprogressbar33==2.4\r\npython-dateutil==2.7.2\r\npytz==2018.4\r\nreportlab==3.4.0\r\nsix==1.11.0\r\n```\r\n\r\nI thought maybe Panads was too new, so I downgraded to an older version (`0.20.3`) and the issue is the same. Do you have any suggestions on how to troubleshoot further?\r\n\r\nThanks!\r\n\r\n\r\n### Versions \r\n<!--Please specify your platform and versions of the relevant libraries you are using:-->\r\n  * Operating system: x86_64 GNU/Linux; Scientific Linux release 7.3 (Nitrogen)\r\n  * Python version: Python 3.6.5\r\n  * Recentrifuge version: v0.18.6\r\n  * Centrifuge or LMAT version used to generate the input data: 1.0.3-beta\r\n  * Pandas version (if applicable): 0.20.3\r\n  * Other libraries (if applicable): see above\r\n"},"comment":{"url":"https://api.github.com/repos/khyox/recentrifuge/issues/comments/388431147","html_url":"https://github.com/khyox/recentrifuge/issues/2#issuecomment-388431147","issue_url":"https://api.github.com/repos/khyox/recentrifuge/issues/2","id":388431147,"user":{"login":"devonorourke","id":11182172,"avatar_url":"https://avatars0.githubusercontent.com/u/11182172?v=4","gravatar_id":"","url":"https://api.github.com/users/devonorourke","html_url":"https://github.com/devonorourke","followers_url":"https://api.github.com/users/devonorourke/followers","following_url":"https://api.github.com/users/devonorourke/following{/other_user}","gists_url":"https://api.github.com/users/devonorourke/gists{/gist_id}","starred_url":"https://api.github.com/users/devonorourke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/devonorourke/subscriptions","organizations_url":"https://api.github.com/users/devonorourke/orgs","repos_url":"https://api.github.com/users/devonorourke/repos","events_url":"https://api.github.com/users/devonorourke/events{/privacy}","received_events_url":"https://api.github.com/users/devonorourke/received_events","type":"User","site_admin":false},"created_at":"2018-05-11T17:28:54Z","updated_at":"2018-05-11T17:28:54Z","author_association":"NONE","body":"One final thought - why not add an option for this output file to be formatted via pandas as either an Excel sheet, or a tsv or can file?\r\nI'm sure many people could benefit from those delimited formats also."}}
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