{"action":"created","issue":{"url":"https://api.github.com/repos/beiko-lab/timeclust/issues/1","repository_url":"https://api.github.com/repos/beiko-lab/timeclust","labels_url":"https://api.github.com/repos/beiko-lab/timeclust/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/beiko-lab/timeclust/issues/1/comments","events_url":"https://api.github.com/repos/beiko-lab/timeclust/issues/1/events","html_url":"https://github.com/beiko-lab/timeclust/issues/1","id":135774459,"number":1,"title":"error on timeclust filter","user":{"login":"fwhelan","id":3144468,"avatar_url":"https://avatars.githubusercontent.com/u/3144468?v=3","gravatar_id":"","url":"https://api.github.com/users/fwhelan","html_url":"https://github.com/fwhelan","followers_url":"https://api.github.com/users/fwhelan/followers","following_url":"https://api.github.com/users/fwhelan/following{/other_user}","gists_url":"https://api.github.com/users/fwhelan/gists{/gist_id}","starred_url":"https://api.github.com/users/fwhelan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fwhelan/subscriptions","organizations_url":"https://api.github.com/users/fwhelan/orgs","repos_url":"https://api.github.com/users/fwhelan/repos","events_url":"https://api.github.com/users/fwhelan/events{/privacy}","received_events_url":"https://api.github.com/users/fwhelan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-23T15:45:20Z","updated_at":"2016-02-23T15:52:42Z","closed_at":null,"body":"Hi Mike,\r\n\r\nThanks for such a detailed readme on a great resource! I'm working my way through and have encountered an issue with ``timeclust filter``:\r\n\r\n```\r\n$ timeclust filter -i timeclust_db.h5 -o timeclust_db_filtered.h5 -f abundance -t 100\r\nintializing empty arrays\r\nData array read!\r\nindices read!\r\narrays loaded from HDF5 file\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/timeclust\", line 9, in <module>\r\n    load_entry_point('timeclust==0.1.0', 'console_scripts', 'timeclust')()\r\n  File \"/usr/local/lib/python2.7/dist-packages/timeclust-0.1.0-py2.7.egg/timeclust/timeclust.py\", line 63, in main\r\n    timeseriesdb.filter_data(args.o, float(args.t), args.f)\r\n  File \"/usr/local/lib/python2.7/dist-packages/timeclust-0.1.0-py2.7.egg/timeclust/timeclust_database.py\", line 215, in filter_data\r\n    new_timeseriesdb.add_names(sample_name_array)\r\n  File \"/usr/local/lib/python2.7/dist-packages/timeclust-0.1.0-py2.7.egg/timeclust/timeclust_database.py\", line 73, in add_names\r\n    self.h5_table[\"samples/names\"][:] = names_list\r\n  File \"h5py/_objects.pyx\", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip_build_root/h5py/h5py/_objects.c:2467)\r\n  File \"h5py/_objects.pyx\", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip_build_root/h5py/h5py/_objects.c:2424)\r\n  File \"/usr/local/lib/python2.7/dist-packages/h5py/_hl/dataset.py\", line 585, in __setitem__\r\n    for fspace in selection.broadcast(mshape):\r\n  File \"/usr/local/lib/python2.7/dist-packages/h5py/_hl/selections.py\", line 304, in broadcast\r\n    raise TypeError(\"Can't broadcast %s -> %s\" % (target_shape, count))\r\nTypeError: Can't broadcast (50,) -> (46,)\r\nClosing file\r\nClosing file\r\n```\r\nI get a similar error when I try ``-t proportion`` or ``-t presence``. If I skip ``timeclust filter`` and try clustering on the unfiltered db, I also encounter an error.\r\n\r\nSome details: machine =  x86_64 x86_64 x86_64 GNU/Linux\r\n\r\n```\r\n$less seqs_J.fna\r\n>MPNH21_1572505 MISEQ:138:000000000-ABJYV:1:1101:13566:2229:ATCTCTT orig_bc=ATCTCTT new_bc=ATCTCTT bc_diffs=0\r\nCTGAGGAATATTGGTCAATGGACGGAAGTCTGAACCAGCCAAGTAGCGTGCAGGATGACGGCCCTATGGGTTGTAAACTGCTTTTGTATGGGGATAAAGTTAGGGACGTGTCCCTATTTGCAGGTACCATACGAATAAGGACCGGCTAATTCCGTG\r\n>MPNH21_1572506 MISEQ:138:000000000-ABJYV:1:1101:15965:2244:ATCTCTT orig_bc=ATCTCTT new_bc=ATCTCTT bc_diffs=0\r\nTGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGCAGGATGACGGCCCTCCGGGTTGTAAACTGCTTTTAGTTGGGAATAAAAAAAGGGACTTGTCCCTTCTTGTATGTACCTTCAGAGAAAGGACCGGCTAATTCCGTG\r\n>MPNH21_1572507 MISEQ:138:000000000-ABJYV:1:1101:18987:2248:ATCTCTT orig_bc=ATCTCTT new_bc=ATCTCTT bc_diffs=0\r\nTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTG\r\n$less map_J.txt\r\n#SampleID       BarcodeSequence LinkerPrimerSequence    Participant     SampleType      time_points         Description\r\nMPNH100 CCGTGCA CCTACGGGAGGCAGCAG       J       E  0       MPNH\r\nMPNH101 CGGCCTT CCTACGGGAGGCAGCAG       J       E  5       MPNH\r\n$ pip show h5py | grep Version\r\nVersion: 2.5.0\r\n$ pip show numpy | grep Version\r\nVersion: 1.10.4\r\n$ pip show scipy | grep Version\r\nVersion: 0.16.1\r\n$ pip show scikit-learn | grep Version\r\nVersion: 0.16.1\r\n$ pip show pandas | grep Version\r\nVersion: 0.17.1\r\n'```"},"comment":{"url":"https://api.github.com/repos/beiko-lab/timeclust/issues/comments/187760347","html_url":"https://github.com/beiko-lab/timeclust/issues/1#issuecomment-187760347","issue_url":"https://api.github.com/repos/beiko-lab/timeclust/issues/1","id":187760347,"user":{"login":"mwhall","id":1359810,"avatar_url":"https://avatars.githubusercontent.com/u/1359810?v=3","gravatar_id":"","url":"https://api.github.com/users/mwhall","html_url":"https://github.com/mwhall","followers_url":"https://api.github.com/users/mwhall/followers","following_url":"https://api.github.com/users/mwhall/following{/other_user}","gists_url":"https://api.github.com/users/mwhall/gists{/gist_id}","starred_url":"https://api.github.com/users/mwhall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mwhall/subscriptions","organizations_url":"https://api.github.com/users/mwhall/orgs","repos_url":"https://api.github.com/users/mwhall/repos","events_url":"https://api.github.com/users/mwhall/events{/privacy}","received_events_url":"https://api.github.com/users/mwhall/received_events","type":"User","site_admin":false},"created_at":"2016-02-23T15:52:42Z","updated_at":"2016-02-23T15:52:42Z","body":"Interesting. Looks like it is somehow trying to add more sample names than can actually exist. I'll have a look and see if I can reproduce this."}}