{"action":"created","issue":{"url":"https://api.github.com/repos/tlnagy/seq-analysis/issues/11","labels_url":"https://api.github.com/repos/tlnagy/seq-analysis/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/tlnagy/seq-analysis/issues/11/comments","events_url":"https://api.github.com/repos/tlnagy/seq-analysis/issues/11/events","html_url":"https://github.com/tlnagy/seq-analysis/issues/11","id":116607137,"number":11,"title":"bugs","user":{"login":"blueboytrl","id":14592557,"avatar_url":"https://avatars.githubusercontent.com/u/14592557?v=3","gravatar_id":"","url":"https://api.github.com/users/blueboytrl","html_url":"https://github.com/blueboytrl","followers_url":"https://api.github.com/users/blueboytrl/followers","following_url":"https://api.github.com/users/blueboytrl/following{/other_user}","gists_url":"https://api.github.com/users/blueboytrl/gists{/gist_id}","starred_url":"https://api.github.com/users/blueboytrl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/blueboytrl/subscriptions","organizations_url":"https://api.github.com/users/blueboytrl/orgs","repos_url":"https://api.github.com/users/blueboytrl/repos","events_url":"https://api.github.com/users/blueboytrl/events{/privacy}","received_events_url":"https://api.github.com/users/blueboytrl/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2015-11-12T18:10:20Z","updated_at":"2015-11-12T18:58:00Z","closed_at":null,"body":"@tlnagy I tried to run the new code.. There are several bugs:\r\n```python \r\ngroup_name = \"Et0H\"\r\nraw, mapped_barcode_data = seq.map_dataset(\"lanes_new_combined.fastq.h5\", group_name)\r\nprocessed = seq.process_data(mapped_barcode_data)\r\nregressed = seq.regress(processed, group_name, \"truseq_primers.csv\")\r\nfiltered = seq.groupby_filter(regressed)\r\nfiltered\r\n```\r\n1. ```ValueError: labels ['index'] not contained in axis```\r\n\r\nit seems because of this line \r\n```idx = pd.IndexSlice\r\nraw_barcode_data = raw_barcode_data.loc[idx[matched_group], :].reset_index().drop(\"index\", axis=1)```\r\n\r\n2  After I remove **drop(\"index\", axis=1)**, It shows\r\n'''KeyError: 'exp''''\r\n\r\nIt seems because in the h5 file, you already separated 'exp' to 'days' and 'timepoints' , so we do not need the following lines:\r\n```raw_barcode_data[[\"days\", \"timepoints\"]] = raw_barcode_data[\"exp\"].str.replace(r\"t\", \"_t\").str.split(\"_\", expand=True)```"},"comment":{"url":"https://api.github.com/repos/tlnagy/seq-analysis/issues/comments/156201506","html_url":"https://github.com/tlnagy/seq-analysis/issues/11#issuecomment-156201506","issue_url":"https://api.github.com/repos/tlnagy/seq-analysis/issues/11","id":156201506,"user":{"login":"blueboytrl","id":14592557,"avatar_url":"https://avatars.githubusercontent.com/u/14592557?v=3","gravatar_id":"","url":"https://api.github.com/users/blueboytrl","html_url":"https://github.com/blueboytrl","followers_url":"https://api.github.com/users/blueboytrl/followers","following_url":"https://api.github.com/users/blueboytrl/following{/other_user}","gists_url":"https://api.github.com/users/blueboytrl/gists{/gist_id}","starred_url":"https://api.github.com/users/blueboytrl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/blueboytrl/subscriptions","organizations_url":"https://api.github.com/users/blueboytrl/orgs","repos_url":"https://api.github.com/users/blueboytrl/repos","events_url":"https://api.github.com/users/blueboytrl/events{/privacy}","received_events_url":"https://api.github.com/users/blueboytrl/received_events","type":"User","site_admin":false},"created_at":"2015-11-12T18:58:00Z","updated_at":"2015-11-12T18:58:00Z","body":"did you already fix it?"}}