{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/pyensembl/issues/82","labels_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/82/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/82/comments","events_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/82/events","html_url":"https://github.com/hammerlab/pyensembl/issues/82","id":65226113,"number":82,"title":"pyensembl index does not have the same effect as deleting all DB files and re-installing","user":{"login":"tavinathanson","id":322932,"avatar_url":"https://avatars.githubusercontent.com/u/322932?v=3","gravatar_id":"","url":"https://api.github.com/users/tavinathanson","html_url":"https://github.com/tavinathanson","followers_url":"https://api.github.com/users/tavinathanson/followers","following_url":"https://api.github.com/users/tavinathanson/following{/other_user}","gists_url":"https://api.github.com/users/tavinathanson/gists{/gist_id}","starred_url":"https://api.github.com/users/tavinathanson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tavinathanson/subscriptions","organizations_url":"https://api.github.com/users/tavinathanson/orgs","repos_url":"https://api.github.com/users/tavinathanson/repos","events_url":"https://api.github.com/users/tavinathanson/events{/privacy}","received_events_url":"https://api.github.com/users/tavinathanson/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/hammerlab/pyensembl/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-03-30T14:33:44Z","updated_at":"2015-04-29T03:33:39Z","closed_at":null,"body":"Namely, I got this when I tried to install release 75:\r\n\r\n```\r\n~/drive/work/repos/cancer/nejm $ pyensembl index --release 75\r\nINFO:root:Cached file Homo_sapiens.GRCh37.75.gtf from URL ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz\r\nCreating database: /Users/tavi/Library/Caches/ensembl/Homo_sapiens.GRCh37.75.db\r\nReading Dataframe from /Users/tavi/Library/Caches/ensembl/Homo_sapiens.GRCh37.75.gtf.expanded.csv\r\n/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/pandas/io/parsers.py:1159: DtypeWarning: Columns (0,18) have mixed types. Specify dtype option on import or set low_memory=False.\r\n  data = self._reader.read(nrows)\r\nWARNING:root:Failed to create tables [nan, 'start_codon', 'Selenocysteine', 'UTR', 'exon', 'stop_codon', 'CDS', 'gene', 'transcript'] in database /Users/tavi/Library/Caches/ensembl/Homo_sapiens.GRCh37.75.db\r\nTraceback (most recent call last):\r\n  File \"/Users/tavi/.virtualenvs/nejm/bin/pyensembl\", line 9, in <module>\r\n    load_entry_point('pyensembl==0.6.2', 'console_scripts', 'pyensembl')()\r\n  File \"/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/pyensembl/shell.py\", line 57, in run\r\n    ensembl.index()\r\n  File \"/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/pyensembl/ensembl_release.py\", line 207, in index\r\n    self.db.create(force=force)\r\n  File \"/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/pyensembl/database.py\", line 540, in create\r\n    self._create_database(force=force)\r\n  File \"/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/pyensembl/database.py\", line 186, in _create_database\r\n    version=DATABASE_SCHEMA_VERSION)\r\n  File \"/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/datacache/database_helpers.py\", line 200, in db_from_dataframes\r\n    version=version)\r\n  File \"/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/datacache/database_helpers.py\", line 104, in _create_cached_db\r\n    \", \".join(table_names))\r\nTypeError: sequence item 0: expected string, float found\r\n```\r\n\r\nBut when I deleted files and started over, it was fine.\r\n\r\n`index` should basically be the same as starting over with the DB."},"comment":{"url":"https://api.github.com/repos/hammerlab/pyensembl/issues/comments/97294601","html_url":"https://github.com/hammerlab/pyensembl/issues/82#issuecomment-97294601","issue_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/82","id":97294601,"user":{"login":"arahuja","id":455755,"avatar_url":"https://avatars.githubusercontent.com/u/455755?v=3","gravatar_id":"","url":"https://api.github.com/users/arahuja","html_url":"https://github.com/arahuja","followers_url":"https://api.github.com/users/arahuja/followers","following_url":"https://api.github.com/users/arahuja/following{/other_user}","gists_url":"https://api.github.com/users/arahuja/gists{/gist_id}","starred_url":"https://api.github.com/users/arahuja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arahuja/subscriptions","organizations_url":"https://api.github.com/users/arahuja/orgs","repos_url":"https://api.github.com/users/arahuja/repos","events_url":"https://api.github.com/users/arahuja/events{/privacy}","received_events_url":"https://api.github.com/users/arahuja/received_events","type":"User","site_admin":false},"created_at":"2015-04-29T03:33:39Z","updated_at":"2015-04-29T03:33:39Z","body":"@iskandr Yea I seem to have ended up in a very environment by trying to switch between Python 3 and 2. I found the files in `~/.cache` and removed them."}}