{"action":"closed","issue":{"url":"https://api.github.com/repos/katholt/srst2/issues/67","repository_url":"https://api.github.com/repos/katholt/srst2","labels_url":"https://api.github.com/repos/katholt/srst2/issues/67/labels{/name}","comments_url":"https://api.github.com/repos/katholt/srst2/issues/67/comments","events_url":"https://api.github.com/repos/katholt/srst2/issues/67/events","html_url":"https://github.com/katholt/srst2/issues/67","id":165660611,"number":67,"title":"VFDB clusterid naming convention problem, KeyError: '51__map__map_ATCC'","user":{"login":"toddknutson","id":7346750,"avatar_url":"https://avatars.githubusercontent.com/u/7346750?v=3","gravatar_id":"","url":"https://api.github.com/users/toddknutson","html_url":"https://github.com/toddknutson","followers_url":"https://api.github.com/users/toddknutson/followers","following_url":"https://api.github.com/users/toddknutson/following{/other_user}","gists_url":"https://api.github.com/users/toddknutson/gists{/gist_id}","starred_url":"https://api.github.com/users/toddknutson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/toddknutson/subscriptions","organizations_url":"https://api.github.com/users/toddknutson/orgs","repos_url":"https://api.github.com/users/toddknutson/repos","events_url":"https://api.github.com/users/toddknutson/events{/privacy}","received_events_url":"https://api.github.com/users/toddknutson/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-07-14T21:15:23Z","updated_at":"2016-07-20T05:33:04Z","closed_at":"2016-07-20T05:33:04Z","body":"Hi,\r\n\r\nI cloned your github code on 6/20/16, which contained the latest fixes for creating SRST2 compatible files using the updated VFDB downloads. However, when following the directions on your `database_clustering/readme.md` page, my final `VF_clustered.fasta` file contained an incorrectly formatted `[culster]__[gene]__[allele]__[VFDB]` name. If this file is used with SRST2, the program breaks with a python dictionary error: `KeyError: '51__map__map_ATCC'`, indicating this key does not exist.  \r\n\r\nI found that my final `VF_clustered.fasta` file contained a sequence with header: \r\n```\r\n>51__map__map_ATCC 25904__VFG001799 VFG001799(gi:8648965) (map) extracellular proteins Map [Eap/Map (VF0016)] [Staphylococcus aureus str. Newman D2C (ATCC 25904)]\r\n```\r\n      \r\nHowever, this is formatted wrong, and there should **not** be a space between ATCC and 25904. To fix the problem, I manually deleted the space and re-ran SRST2. This corrected the problem. However, I think one of the scripts used to parse the headers made an error in this case. I have not investigated which script or the code to find the bug. But I wanted to let you know. Thanks for a great tool!! The full error traceback is below:  \r\n\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/panfs/roc/groups/10/marthal4/knut0297/software/srst2/bin/srst2\", line 9, in <module>\r\n    load_entry_point('srst2==0.1.8', 'console_scripts', 'srst2')()\r\n  File \"/home/marthal4/knut0297/software/srst2/lib/python2.7/site-packages/srst2/srst2.py\", line 1711, in main\r\n    db_reports, db_results = run_srst2(args,fileSets,args.gene_db,\"genes\")\r\n  File \"/home/marthal4/knut0297/software/srst2/lib/python2.7/site-packages/srst2/srst2.py\", line 1248, in run_srst2\r\n    db_reports, db_results_list = process_fasta_db(args, fileSets, run_type, db_reports, db_results_list, fasta)\r\n  File \"/home/marthal4/knut0297/software/srst2/lib/python2.7/site-packages/srst2/srst2.py\", line 1310, in process_fasta_db\r\n    unique_gene_symbols, unique_allele_symbols,run_type,ST_db,results,gene_list,db_report,cluster_symbols,max_mismatch)\r\n  File \"/home/marthal4/knut0297/software/srst2/lib/python2.7/site-packages/srst2/srst2.py\", line 1471, in map_fileSet_to_db\r\n    column_header = cluster_symbols[cluster_id]\r\nKeyError: '51__map__map_ATCC'\r\n```\r\n    "}}
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