{"action":"opened","issue":{"url":"https://api.github.com/repos/kdmurray91/lpipy/issues/1","labels_url":"https://api.github.com/repos/kdmurray91/lpipy/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/kdmurray91/lpipy/issues/1/comments","events_url":"https://api.github.com/repos/kdmurray91/lpipy/issues/1/events","html_url":"https://github.com/kdmurray91/lpipy/issues/1","id":115984864,"number":1,"title":"Fail to extract names.dmp from taxdump","user":{"login":"Adamtaranto","id":2160099,"avatar_url":"https://avatars.githubusercontent.com/u/2160099?v=3","gravatar_id":"","url":"https://api.github.com/users/Adamtaranto","html_url":"https://github.com/Adamtaranto","followers_url":"https://api.github.com/users/Adamtaranto/followers","following_url":"https://api.github.com/users/Adamtaranto/following{/other_user}","gists_url":"https://api.github.com/users/Adamtaranto/gists{/gist_id}","starred_url":"https://api.github.com/users/Adamtaranto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Adamtaranto/subscriptions","organizations_url":"https://api.github.com/users/Adamtaranto/orgs","repos_url":"https://api.github.com/users/Adamtaranto/repos","events_url":"https://api.github.com/users/Adamtaranto/events{/privacy}","received_events_url":"https://api.github.com/users/Adamtaranto/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-11-09T22:45:49Z","updated_at":"2015-11-09T22:45:49Z","closed_at":null,"body":"Taxdump.tar.gz is downloaded to a user directory, it contains the names and nodes files. \r\n```\r\nDownloading http://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz to /home/adam/.local/var/lpi/taxdump.tar.gz\r\n```\r\nProgram exits after trying to find and un-tar 'names.dmp' (looking in local directory??) from line 231 of taxonomy.py\r\n\r\n```\r\nDownloaded http://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz\r\nWe have a valid Taxdump file\r\nGI to tax prot file found, calculating checksum\r\nWe have a valid gi_taxid_prot file\r\nGI to tax nucl file found, calculating checksum\r\nWe have a valid gi_taxid_nucl file\r\nTraceback (most recent call last):\r\n  File \"./lpipy/misc/demo.py\", line 8, in <module>\r\n    db = NCBITaxonomyDB()\r\n  File \"/usr/local/lib/python2.7/dist-packages/lpi-0_untagged.11.gd0f1d6a-py2.7.egg/lpi/taxonomy.py\", line 99, in __init__\r\n    self._connect()\r\n  File \"/usr/local/lib/python2.7/dist-packages/lpi-0_untagged.11.gd0f1d6a-py2.7.egg/lpi/taxonomy.py\", line 117, in _connect\r\n    self._create_db()\r\n  File \"/usr/local/lib/python2.7/dist-packages/lpi-0_untagged.11.gd0f1d6a-py2.7.egg/lpi/taxonomy.py\", line 164, in _create_db\r\n    self._load_db()\r\n  File \"/usr/local/lib/python2.7/dist-packages/lpi-0_untagged.11.gd0f1d6a-py2.7.egg/lpi/taxonomy.py\", line 231, in _load_db\r\n    for taxon in dmpfile('names.dmp'):\r\n  File \"/usr/local/lib/python2.7/dist-packages/lpi-0_untagged.11.gd0f1d6a-py2.7.egg/lpi/taxonomy.py\", line 220, in dmpfile\r\n    with tar.extractfile(filename) as fh:\r\nAttributeError: __exit__\r\n```"}}