{"action":"created","issue":{"url":"https://api.github.com/repos/endrebak/snpflip/issues/10","labels_url":"https://api.github.com/repos/endrebak/snpflip/issues/10/labels{/name}","comments_url":"https://api.github.com/repos/endrebak/snpflip/issues/10/comments","events_url":"https://api.github.com/repos/endrebak/snpflip/issues/10/events","html_url":"https://github.com/endrebak/snpflip/issues/10","id":120987670,"number":10,"title":"'non-unique multi-index' error when calling pd.concat on bim_table and reference_genome_data","user":{"login":"mr664","id":4489463,"avatar_url":"https://avatars.githubusercontent.com/u/4489463?v=3","gravatar_id":"","url":"https://api.github.com/users/mr664","html_url":"https://github.com/mr664","followers_url":"https://api.github.com/users/mr664/followers","following_url":"https://api.github.com/users/mr664/following{/other_user}","gists_url":"https://api.github.com/users/mr664/gists{/gist_id}","starred_url":"https://api.github.com/users/mr664/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr664/subscriptions","organizations_url":"https://api.github.com/users/mr664/orgs","repos_url":"https://api.github.com/users/mr664/repos","events_url":"https://api.github.com/users/mr664/events{/privacy}","received_events_url":"https://api.github.com/users/mr664/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-12-08T11:26:33Z","updated_at":"2015-12-09T08:57:14Z","closed_at":null,"body":"I'm attempting to check for strand flips between my human dataset and the human reference fasta (human_g1k_v37.fa). For this I've changed the chromosome names in the reference to >chr<num> and removed non-autosomal chromosomes.\r\n\r\nThe error listed below appears to occur when attempting to concatenate the bim_table and reference_genome_data.\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/home/matt/anaconda3/bin/snpflip\", line 42, in <module>\r\n    snp_table = create_snp_table(args[\"--bim-file\"], args[\"--fasta-genome\"])\r\n  File \"/home/matt/anaconda3/lib/python3.4/site-packages/snp_flip/table.py\", line 13, in create_snp_table\r\n    snp_table = pd.concat([bim_table, reference_genome_data], axis=1)\r\n  File \"/home/matt/anaconda3/lib/python3.4/site-packages/pandas/tools/merge.py\", line 810, in concat\r\n    return op.get_result()\r\n  File \"/home/matt/anaconda3/lib/python3.4/site-packages/pandas/tools/merge.py\", line 987, in get_result\r\n    indexers[ax] = obj_labels.reindex(new_labels)[1]\r\n  File \"/home/matt/anaconda3/lib/python3.4/site-packages/pandas/core/index.py\", line 5159, in reindex\r\n    \"cannot handle a non-unique multi-index!\")\r\nException: cannot handle a non-unique multi-index!\r\n```"},"comment":{"url":"https://api.github.com/repos/endrebak/snpflip/issues/comments/163154093","html_url":"https://github.com/endrebak/snpflip/issues/10#issuecomment-163154093","issue_url":"https://api.github.com/repos/endrebak/snpflip/issues/10","id":163154093,"user":{"login":"mr664","id":4489463,"avatar_url":"https://avatars.githubusercontent.com/u/4489463?v=3","gravatar_id":"","url":"https://api.github.com/users/mr664","html_url":"https://github.com/mr664","followers_url":"https://api.github.com/users/mr664/followers","following_url":"https://api.github.com/users/mr664/following{/other_user}","gists_url":"https://api.github.com/users/mr664/gists{/gist_id}","starred_url":"https://api.github.com/users/mr664/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr664/subscriptions","organizations_url":"https://api.github.com/users/mr664/orgs","repos_url":"https://api.github.com/users/mr664/repos","events_url":"https://api.github.com/users/mr664/events{/privacy}","received_events_url":"https://api.github.com/users/mr664/received_events","type":"User","site_admin":false},"created_at":"2015-12-09T08:57:14Z","updated_at":"2015-12-09T08:57:14Z","body":"Yeah, that gz should contain the correct reference genome. Though keep in mine that I changed, with sed, the headers to '>chr1', '>chr2' etc. I also removed non-autosomes (so X, Y & psuedoautonomous).\r\n\r\nWhat's your preferred email address? I'll send the bim you to via that."}}