{"action":"created","issue":{"url":"https://api.github.com/repos/ddofer/ProFET/issues/2","labels_url":"https://api.github.com/repos/ddofer/ProFET/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/ddofer/ProFET/issues/2/comments","events_url":"https://api.github.com/repos/ddofer/ProFET/issues/2/events","html_url":"https://github.com/ddofer/ProFET/issues/2","id":105592998,"number":2,"title":"trouble getting started","user":{"login":"cnjr2","id":1436363,"avatar_url":"https://avatars.githubusercontent.com/u/1436363?v=3","gravatar_id":"","url":"https://api.github.com/users/cnjr2","html_url":"https://github.com/cnjr2","followers_url":"https://api.github.com/users/cnjr2/followers","following_url":"https://api.github.com/users/cnjr2/following{/other_user}","gists_url":"https://api.github.com/users/cnjr2/gists{/gist_id}","starred_url":"https://api.github.com/users/cnjr2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cnjr2/subscriptions","organizations_url":"https://api.github.com/users/cnjr2/orgs","repos_url":"https://api.github.com/users/cnjr2/repos","events_url":"https://api.github.com/users/cnjr2/events{/privacy}","received_events_url":"https://api.github.com/users/cnjr2/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2015-09-09T13:08:26Z","updated_at":"2015-10-01T16:47:35Z","closed_at":null,"body":"Thank you for the development of ProFET!\r\n\r\nI wanted to try it out but I ran into some trouble. It would be great if you could point me towards where I am going wrong.\r\n\r\nI am using python 3.4 and I have have installed all the dependencies mentioned in the `README.md`. I have the following folder structure where `feat_extract` is my working directory:\r\n```\r\nfeat_extract/\r\n|_pipeline.py\r\n|_other ProFET files...\r\n|_test_seq/...\r\n|_train/\r\n| |_A/\r\n| | |_train_sequences_A.fasta\r\n| |_B/\r\n|   |_train_sequences_B.fasta\r\n|_test\r\n  |_A/\r\n  | |_test_sequences_A.fasta\r\n  |_B/\r\n    |_test_sequences_B.fasta\r\n```\r\nThe fasta files were created with the following set of commands:\r\n```\r\n    cd ./test_seq/Extracellular/\r\n    tail -n 1000 location-secreted_keyword-AKW-0964_reviewed_taxon-Tetrapoda_fragment-no_id-0.9.fasta > ../../train/A/train_sequences_A.fasta\r\n    tail -n 1000 NOT-secreted_NOT-extracellular_reviewed_taxon-Tetrapoda_fragment-no_id-0.5.fasta > ../../train/B/train_sequences_B.fasta\r\n    head -n 1000 location-secreted_keyword-AKW-0964_reviewed_taxon-Tetrapoda_fragment-no_id-0.9.fasta > ../../test/A/test_sequences_A.fasta\r\n    head -n 1000 NOT-secreted_NOT-extracellular_reviewed_taxon-Tetrapoda_fragment-no_id-0.5.fasta > ../../test/B/test_sequences_B.fasta\r\n    cd ../../\r\n```\r\nWhen running the command:\r\n```\r\npython pipeline.py --trainingSetDir ./train --testingSetDir ./test --trainFeatures True --testFeatures True --classType dir\r\n```\r\nI get the following error message:\r\n```\r\n<cProfile.Profile object at 0x107745db0>\r\nStarting to extract features from training set\r\ndirr change to: ./train\r\nMulticlass fasta_files list found: []\r\nFeatures generated\r\nRemoving any all zero features\r\ndf.shape:  (0, 0)\r\ndf_cleaned shape:  (0, 0)\r\nDone\r\nExtracted training data features\r\nTraining predictive model\r\nTraceback (most recent call last):\r\n  File \"pipeline.py\", line 171, in <module>\r\n    res = profiler.runcall(pipeline)\r\n  File \"/Users/charles/anaconda/envs/py34/lib/python3.4/cProfile.py\", line 109, in runcall\r\n    return func(*args, **kw)\r\n  File \"pipeline.py\", line 90, in pipeline\r\n    model, lb_encoder = trainClassifier(filename=trainingDir+'/trainingSetFeatures.csv',normFlag= False,classifierType= classifierType,kbest= 0,alpha= False,optimalFlag= False) #Win\r\n  File \"/Users/charles/Downloads/feat_extract/Model_trainer.py\", line 114, in trainClassifier\r\n    features, labels, lb_encoder,featureNames = load_data(filename, 'file')\r\n  File \"/Users/charles/Downloads/feat_extract/Model_trainer.py\", line 36, in load_data\r\n    df = pd.read_csv(dataFrame, index_col=[0,1]) # is index column 0 in multiindex as well?\r\n  File \"/Users/charles/anaconda/envs/py34/lib/python3.4/site-packages/pandas/io/parsers.py\", line 474, in parser_f\r\n    return _read(filepath_or_buffer, kwds)\r\n  File \"/Users/charles/anaconda/envs/py34/lib/python3.4/site-packages/pandas/io/parsers.py\", line 250, in _read\r\n    parser = TextFileReader(filepath_or_buffer, **kwds)\r\n  File \"/Users/charles/anaconda/envs/py34/lib/python3.4/site-packages/pandas/io/parsers.py\", line 566, in __init__\r\n    self._make_engine(self.engine)\r\n  File \"/Users/charles/anaconda/envs/py34/lib/python3.4/site-packages/pandas/io/parsers.py\", line 705, in _make_engine\r\n    self._engine = CParserWrapper(self.f, **self.options)\r\n  File \"/Users/charles/anaconda/envs/py34/lib/python3.4/site-packages/pandas/io/parsers.py\", line 1072, in __init__\r\n    self._reader = _parser.TextReader(src, **kwds)\r\n  File \"pandas/parser.pyx\", line 350, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:3173)\r\n  File \"pandas/parser.pyx\", line 594, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:5912)\r\nOSError: File b'./train/trainingSetFeatures.csv' does not exist\r\n```\r\nIt complains that `./train/trainingSetFeatures.csv' does not exist`. I see that a file with this name is being created in the `train` folder, however it is a table with only column names (no rows).\r\n\r\nThank you for your help."},"comment":{"url":"https://api.github.com/repos/ddofer/ProFET/issues/comments/144783894","html_url":"https://github.com/ddofer/ProFET/issues/2#issuecomment-144783894","issue_url":"https://api.github.com/repos/ddofer/ProFET/issues/2","id":144783894,"user":{"login":"ddofer","id":5120387,"avatar_url":"https://avatars.githubusercontent.com/u/5120387?v=3","gravatar_id":"","url":"https://api.github.com/users/ddofer","html_url":"https://github.com/ddofer","followers_url":"https://api.github.com/users/ddofer/followers","following_url":"https://api.github.com/users/ddofer/following{/other_user}","gists_url":"https://api.github.com/users/ddofer/gists{/gist_id}","starred_url":"https://api.github.com/users/ddofer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ddofer/subscriptions","organizations_url":"https://api.github.com/users/ddofer/orgs","repos_url":"https://api.github.com/users/ddofer/repos","events_url":"https://api.github.com/users/ddofer/events{/privacy}","received_events_url":"https://api.github.com/users/ddofer/received_events","type":"User","site_admin":false},"created_at":"2015-10-01T16:47:35Z","updated_at":"2015-10-01T16:47:35Z","body":"Worst case, just use the features generation methods/featureGen.py\n\nGood luck\nOn Oct 1, 2015 7:27 PM, \"cnjr2\" <notifications@github.com> wrote:\n\n> Thanks for the info. I will give it a shot!\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/ddofer/ProFET/issues/2#issuecomment-144779391>.\n>\n"}}