{"action":"opened","issue":{"url":"https://api.github.com/repos/katholt/srst2/issues/29","labels_url":"https://api.github.com/repos/katholt/srst2/issues/29/labels{/name}","comments_url":"https://api.github.com/repos/katholt/srst2/issues/29/comments","events_url":"https://api.github.com/repos/katholt/srst2/issues/29/events","html_url":"https://github.com/katholt/srst2/issues/29","id":55352745,"number":29,"title":"srst2.py throws error if allele has slash character","user":{"login":"ppcherng","id":4554005,"avatar_url":"https://avatars.githubusercontent.com/u/4554005?v=3","gravatar_id":"","url":"https://api.github.com/users/ppcherng","html_url":"https://github.com/ppcherng","followers_url":"https://api.github.com/users/ppcherng/followers","following_url":"https://api.github.com/users/ppcherng/following{/other_user}","gists_url":"https://api.github.com/users/ppcherng/gists{/gist_id}","starred_url":"https://api.github.com/users/ppcherng/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ppcherng/subscriptions","organizations_url":"https://api.github.com/users/ppcherng/orgs","repos_url":"https://api.github.com/users/ppcherng/repos","events_url":"https://api.github.com/users/ppcherng/events{/privacy}","received_events_url":"https://api.github.com/users/ppcherng/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-01-24T01:08:51Z","updated_at":"2015-01-24T01:08:51Z","closed_at":null,"body":"I ran srst2 against a gene database that happened to have some slash characters for some of the read names:\r\n\r\n70__aec27/clpV__aec27/clpV_EC042_0215__R033079 R033079 aec27/clpV (EC042_0215) - putative type VI secretion system protein [Escherichia coli str. 042 (EAEC O44:H18)]\r\n>ATGATCCAGATTGATTTAGCCACGCTGGTAAAGCGGCTTAACCCCTTTGCAAAACAGGCG\r\n...\r\n\r\nThis causes srst2.py to crash when generating pileups:\r\n\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/srst2\", line 9, in <module>\r\n    load_entry_point('srst2==0.1.5', 'console_scripts', 'srst2')()\r\n  File \"/usr/local/lib/python2.7/dist-packages/srst2/srst2.py\", line 1548, in main\r\n    db_reports, db_results = run_srst2(args,fileSets,args.gene_db,\"genes\")\r\n  File \"/usr/local/lib/python2.7/dist-packages/srst2/srst2.py\", line 1102, 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 \"/usr/local/lib/python2.7/dist-packages/srst2/srst2.py\", line 1164, 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 \"/usr/local/lib/python2.7/dist-packages/srst2/srst2.py\", line 1275, in map_fileSet_to_db\r\n    unique_gene_symbols, unique_allele_symbols, pileup_file)\r\n  File \"/usr/local/lib/python2.7/dist-packages/srst2/srst2.py\", line 859, in parse_scores\r\n    allele_pileup_file = create_allele_pileup(top_allele, pileup_file) # XXX Creates a new pileup file for that allele. Not currently cleaned up\r\n  File \"/usr/local/lib/python2.7/dist-packages/srst2/srst2.py\", line 765, in create_allele_pileup\r\n    with open(outpileup, 'w') as allele_pileup:\r\nIOError: [Errno 2] No such file or directory: '67__aec27/clpV__aec27/clpV_G2583_0230__R033067.ERR024627__ERR024627.Escherichia_VF_clustered.pileup'\r\n\r\nPossible solution is to just change the slashes to underscores\r\n"}}