{"action":"created","issue":{"url":"https://api.github.com/repos/jeffdaily/parasail-python/issues/3","repository_url":"https://api.github.com/repos/jeffdaily/parasail-python","labels_url":"https://api.github.com/repos/jeffdaily/parasail-python/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/jeffdaily/parasail-python/issues/3/comments","events_url":"https://api.github.com/repos/jeffdaily/parasail-python/issues/3/events","html_url":"https://github.com/jeffdaily/parasail-python/issues/3","id":141999255,"number":3,"title":" Adding example for python","user":{"login":"jeffdaily","id":904248,"avatar_url":"https://avatars.githubusercontent.com/u/904248?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffdaily","html_url":"https://github.com/jeffdaily","followers_url":"https://api.github.com/users/jeffdaily/followers","following_url":"https://api.github.com/users/jeffdaily/following{/other_user}","gists_url":"https://api.github.com/users/jeffdaily/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffdaily/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffdaily/subscriptions","organizations_url":"https://api.github.com/users/jeffdaily/orgs","repos_url":"https://api.github.com/users/jeffdaily/repos","events_url":"https://api.github.com/users/jeffdaily/events{/privacy}","received_events_url":"https://api.github.com/users/jeffdaily/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-03-18T23:13:54Z","updated_at":"2016-06-18T14:55:13Z","closed_at":null,"body":"*Originally submitted by @ksahlin on parasail project. Now moved to this parasail-python project.*\r\n\r\nHi,\r\n\r\nThis library looks very interesting. I just installed it (together with the python binding). However, I would kindly request you to add some more information about the usage of the python wrapping library. For example, by walking through a more informative example (or pointing to where documentation about this could be found). For some reference to what the user might initially do (i.e. what I did)\r\n\r\n```\r\n>>> result = parasail.sw_scan_16(\"AAAAACGGGAGGGAGGAGAG\", \"AAAAAGGCGGGAGGGAGGGAGGAGA\", -11, -1, parasail.blosum62)\r\n>>> result\r\n<parasail.Result object at 0x106c0ceb8>\r\n>>> dir(result)\r\n['__class__', '__delattr__', '__doc__', '__format__', '__getattribute__', '__hash__', '__init__', '__int__', '__long__', '__new__', '__pyx_vtable__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', 'length', 'length_col', 'length_row', 'length_table', 'matches', 'matches_col', 'matches_row', 'matches_table', 'saturated', 'score', 'score_col', 'score_row', 'score_table', 'similar', 'similar_col', 'similar_row', 'similar_table']\r\n>>> result.length_table\r\n>>> result.matches\r\n0\r\n>>> result.length\r\n0\r\n>>> result.score\r\n1356\r\n>>> result.matches\r\n0\r\n```\r\nThis still leaves me clueless. \r\n\r\nAlso, I noticed that I had to run `python setup.py install`  (after build) to be able to import parasail, so that would be good to add to the installation instructions in the python section.\r\n\r\nFurthermore, I might add that I'm mainly interested in retrieving the CIGAR of the alignments, I noticed that you had opened an issue about it. That feature would be great.\r\n\r\nBest,\r\nKristoffer\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/jeffdaily/parasail-python/issues/comments/226946609","html_url":"https://github.com/jeffdaily/parasail-python/issues/3#issuecomment-226946609","issue_url":"https://api.github.com/repos/jeffdaily/parasail-python/issues/3","id":226946609,"user":{"login":"daveuu","id":2660660,"avatar_url":"https://avatars.githubusercontent.com/u/2660660?v=3","gravatar_id":"","url":"https://api.github.com/users/daveuu","html_url":"https://github.com/daveuu","followers_url":"https://api.github.com/users/daveuu/followers","following_url":"https://api.github.com/users/daveuu/following{/other_user}","gists_url":"https://api.github.com/users/daveuu/gists{/gist_id}","starred_url":"https://api.github.com/users/daveuu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daveuu/subscriptions","organizations_url":"https://api.github.com/users/daveuu/orgs","repos_url":"https://api.github.com/users/daveuu/repos","events_url":"https://api.github.com/users/daveuu/events{/privacy}","received_events_url":"https://api.github.com/users/daveuu/received_events","type":"User","site_admin":false},"created_at":"2016-06-18T14:55:13Z","updated_at":"2016-06-18T14:55:13Z","body":"If the parasail-python bindings module was to pander more in the direction of the casual python user but maintain performance, the CPython array class might be an option worth pursuing for returning aligned string representations of the input sequences: https://docs.python.org/3/library/array.html.\r\n\r\nIn supporting the buffer interface, my limited understanding of these sort of things makes me think these arrays allow C code generating the alignment strings to put them into Python-world in a performant way without the overhead of full-blown Python Lists or Strings."}}
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