{"action":"created","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/549","labels_url":"https://api.github.com/repos/biopython/biopython/issues/549/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/549/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/549/events","html_url":"https://github.com/biopython/biopython/pull/549","id":82056864,"number":549,"title":"Allow parsing of TRANSFAC files that have only one space as separator…","user":{"login":"ghuls","id":1299177,"avatar_url":"https://avatars.githubusercontent.com/u/1299177?v=3","gravatar_id":"","url":"https://api.github.com/users/ghuls","html_url":"https://github.com/ghuls","followers_url":"https://api.github.com/users/ghuls/followers","following_url":"https://api.github.com/users/ghuls/following{/other_user}","gists_url":"https://api.github.com/users/ghuls/gists{/gist_id}","starred_url":"https://api.github.com/users/ghuls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ghuls/subscriptions","organizations_url":"https://api.github.com/users/ghuls/orgs","repos_url":"https://api.github.com/users/ghuls/repos","events_url":"https://api.github.com/users/ghuls/events{/privacy}","received_events_url":"https://api.github.com/users/ghuls/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-05-28T18:03:17Z","updated_at":"2015-05-30T06:39:37Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biopython/biopython/pulls/549","html_url":"https://github.com/biopython/biopython/pull/549","diff_url":"https://github.com/biopython/biopython/pull/549.diff","patch_url":"https://github.com/biopython/biopython/pull/549.patch"},"body":"… between field and value.\r\n\r\nSome TRANSFAC files use a TAB instead of 2 or more spaces as separator\r\nbetween field and value. The old code assumed that the value part\r\nof a line always starts at position 4.\r\n\r\nThis patch also allows to parse motif matrix lines which do not have\r\na leading \"0\" for numbers smaller or equal than 9.\r\n\r\nExample matrix:\r\n---------------\r\n\r\nNA\tALX1.p2\r\nPO\tA\tC\tG\tT\r\n1\t79.334802\t30.187075\t11.671023\t39.11148\r\n2\t75.758951\t39.804695\t33.95761\t10.783124\r\n3\t49.264106\t46.809618\t10.776781\t53.453875\r\n4\t1.624345\t0.749118\t0\t157.930917\r\n5\t136.373394\t4.4525\t5.369937\t14.108549\r\n6\t158.727167\t0\t0\t1.577213\r\n7\t1.508366\t7.678933\t0.690944\t150.426137\r\n8\t0.695534\t11.381705\t13.351513\t134.875628\r\n9\t88.004985\t21.998116\t16.720946\t33.580333\r\n10\t47.758261\t39.506319\t24.613038\t48.426762\r\n11\t31.136202\t60.868109\t7.840269\t60.4598\r\n12\t145.395351\t0.962932\t10.806892\t3.139205\r\n13\t0.692268\t10.059374\t1.564066\t147.988672\r\n14\t9.51174\t7.890105\t0\t142.902535\r\n15\t118.052898\t3.531078\t27.492738\t11.227666\r\n16\t14.304979\t27.682412\t31.513372\t86.803617\r\n17\t17.672332\t66.136874\t11.206336\t65.288838\r\n18\t58.639634\t21.05798\t18.928821\t61.677945\r\n//"},"comment":{"url":"https://api.github.com/repos/biopython/biopython/issues/comments/106996519","html_url":"https://github.com/biopython/biopython/pull/549#issuecomment-106996519","issue_url":"https://api.github.com/repos/biopython/biopython/issues/549","id":106996519,"user":{"login":"mdehoon","id":136062,"avatar_url":"https://avatars.githubusercontent.com/u/136062?v=3","gravatar_id":"","url":"https://api.github.com/users/mdehoon","html_url":"https://github.com/mdehoon","followers_url":"https://api.github.com/users/mdehoon/followers","following_url":"https://api.github.com/users/mdehoon/following{/other_user}","gists_url":"https://api.github.com/users/mdehoon/gists{/gist_id}","starred_url":"https://api.github.com/users/mdehoon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mdehoon/subscriptions","organizations_url":"https://api.github.com/users/mdehoon/orgs","repos_url":"https://api.github.com/users/mdehoon/repos","events_url":"https://api.github.com/users/mdehoon/events{/privacy}","received_events_url":"https://api.github.com/users/mdehoon/received_events","type":"User","site_admin":false},"created_at":"2015-05-30T06:39:37Z","updated_at":"2015-05-30T06:39:37Z","body":"I think it is too much of a corner case. Just email the SwissRegulon and Hocomoco maintainers and let them know their format is not quite consistent with the TRANSFAC format. Or send them a new file with the formatting issues fixed. Both of SwissRegulon and Hocomoco are made by our Fantom collaborators who in my experience are very helpful."}}