{"action":"opened","issue":{"url":"https://api.github.com/repos/eldariont/svim/issues/1","repository_url":"https://api.github.com/repos/eldariont/svim","labels_url":"https://api.github.com/repos/eldariont/svim/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/eldariont/svim/issues/1/comments","events_url":"https://api.github.com/repos/eldariont/svim/issues/1/events","html_url":"https://github.com/eldariont/svim/issues/1","id":334029256,"node_id":"MDU6SXNzdWUzMzQwMjkyNTY=","number":1,"title":"error with gzipped fastq file and create working dir if it doesn't exist","user":{"login":"wdecoster","id":11660522,"node_id":"MDQ6VXNlcjExNjYwNTIy","avatar_url":"https://avatars2.githubusercontent.com/u/11660522?v=4","gravatar_id":"","url":"https://api.github.com/users/wdecoster","html_url":"https://github.com/wdecoster","followers_url":"https://api.github.com/users/wdecoster/followers","following_url":"https://api.github.com/users/wdecoster/following{/other_user}","gists_url":"https://api.github.com/users/wdecoster/gists{/gist_id}","starred_url":"https://api.github.com/users/wdecoster/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wdecoster/subscriptions","organizations_url":"https://api.github.com/users/wdecoster/orgs","repos_url":"https://api.github.com/users/wdecoster/repos","events_url":"https://api.github.com/users/wdecoster/events{/privacy}","received_events_url":"https://api.github.com/users/wdecoster/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-20T11:07:46Z","updated_at":"2018-06-20T11:07:46Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nThis looks like an interesting tool so I'm eager to give it a try.\r\n\r\nUsing a gzipped fastq file I get the following error:\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"svim/SVIM_COLLECT.py\", line 383, in <module>\r\n    sys.exit(main())\r\n  File \"svim/SVIM_COLLECT.py\", line 353, in main\r\n    full_reads_path = create_full_file(options.working_dir, options.reads, reads_type)\r\n  File \"svim/SVIM_COLLECT.py\", line 200, in create_full_file\r\n    if line.startswith('@'):\r\nTypeError: startswith first arg must be bytes or a tuple of bytes, not str\r\n```\r\n\r\nI could solve this by changing, in line 178 of SVIM_COLLECT.py the mode of `gzip.open()` from 'rb' to 'rt'.\r\n\r\nAdditionally, would it be possible that the script creates the working dir if it doesn't exist? Earlier I had the following error:\r\n\r\n```Traceback (most recent call last):\r\n  File \"svim/SVIM_COLLECT.py\", line 383, in <module>\r\n    sys.exit(main())\r\n  File \"svim/SVIM_COLLECT.py\", line 321, in main\r\n    fileHandler = logging.FileHandler(\"{0}/SVIM-COLLECT_{1}.log\".format(options.working_dir, strftime(\"%y%m%d_%H%M%S\", localtime())), mode=\"w\")\r\n  File \"/home/wdecoster/anaconda3/envs/svim/lib/python3.6/logging/__init__.py\", line 1030, in __init__\r\n    StreamHandler.__init__(self, self._open())\r\n  File \"/home/wdecoster/anaconda3/envs/svim/lib/python3.6/logging/__init__.py\", line 1059, in _open\r\n    return open(self.baseFilename, self.mode, encoding=self.encoding)\r\nFileNotFoundError: [Errno 2] No such file or directory: '/home/wdecoster/temp/test_svim/test/SVIM-COLLECT_180620_125723.log'\r\n```\r\nwhich was solved by creating the 'test' directory.\r\n\r\nCheers,\r\nWouter"}}
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