{"action":"created","issue":{"url":"https://api.github.com/repos/tanghaibao/jcvi/issues/75","repository_url":"https://api.github.com/repos/tanghaibao/jcvi","labels_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/75/labels{/name}","comments_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/75/comments","events_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/75/events","html_url":"https://github.com/tanghaibao/jcvi/issues/75","id":260095611,"number":75,"title":"Error:Pairwise synteny search","user":{"login":"ABDULLAHGUJJAR","id":31093427,"avatar_url":"https://avatars0.githubusercontent.com/u/31093427?v=4","gravatar_id":"","url":"https://api.github.com/users/ABDULLAHGUJJAR","html_url":"https://github.com/ABDULLAHGUJJAR","followers_url":"https://api.github.com/users/ABDULLAHGUJJAR/followers","following_url":"https://api.github.com/users/ABDULLAHGUJJAR/following{/other_user}","gists_url":"https://api.github.com/users/ABDULLAHGUJJAR/gists{/gist_id}","starred_url":"https://api.github.com/users/ABDULLAHGUJJAR/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ABDULLAHGUJJAR/subscriptions","organizations_url":"https://api.github.com/users/ABDULLAHGUJJAR/orgs","repos_url":"https://api.github.com/users/ABDULLAHGUJJAR/repos","events_url":"https://api.github.com/users/ABDULLAHGUJJAR/events{/privacy}","received_events_url":"https://api.github.com/users/ABDULLAHGUJJAR/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2017-09-24T16:08:57Z","updated_at":"2017-09-26T18:20:40Z","closed_at":null,"author_association":"NONE","body":"00:04:49 [synteny] A total of 0 BLAST imported from `hirsutum.raimondi.last.filtered`.\r\n00:04:49 [synteny] Chaining distance = 20\r\n00:04:49 [base] Load file `hirsutum.raimondi.anchors`\r\nTraceback (most recent call last):\r\n  File \"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py\", line 162, in _run_module_as_main\r\n    \"__main__\", fname, loader, pkg_name)\r\n  File \"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py\", line 72, in _run_code\r\n    exec code in run_globals\r\n  File \"/Users/Abdullah/Library/Python/2.7/lib/python/site-packages/jcvi/compara/catalog.py\", line 811, in <module>\r\n    main()\r\n  File \"/Users/Abdullah/Library/Python/2.7/lib/python/site-packages/jcvi/compara/catalog.py\", line 73, in main\r\n    p.dispatch(globals())\r\n  File \"/Users/Abdullah/Library/Python/2.7/lib/python/site-packages/jcvi/apps/base.py\", line 87, in dispatch\r\n    globals[action](sys.argv[2:])\r\n  File \"/Users/Abdullah/Library/Python/2.7/lib/python/site-packages/jcvi/compara/catalog.py\", line 646, in ortholog\r\n    \"--liftover={0}\".format(last)])\r\n  File \"/Users/Abdullah/Library/Python/2.7/lib/python/site-packages/jcvi/compara/synteny.py\", line 1464, in scan\r\n    summary([anchor_file])\r\n  File \"/Users/Abdullah/Library/Python/2.7/lib/python/site-packages/jcvi/compara/synteny.py\", line 1042, in summary\r\n    nranchors = [_score(c) for c in clusters]  # non-redundant anchors\r\n  File \"/Users/Abdullah/Library/Python/2.7/lib/python/site-packages/jcvi/compara/synteny.py\", line 260, in _score\r\n    x, y = zip(*cluster)[:2]\r\nValueError: need more than 0 values to unpack"},"comment":{"url":"https://api.github.com/repos/tanghaibao/jcvi/issues/comments/332289363","html_url":"https://github.com/tanghaibao/jcvi/issues/75#issuecomment-332289363","issue_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/75","id":332289363,"user":{"login":"vivekkrish","id":711637,"avatar_url":"https://avatars3.githubusercontent.com/u/711637?v=4","gravatar_id":"","url":"https://api.github.com/users/vivekkrish","html_url":"https://github.com/vivekkrish","followers_url":"https://api.github.com/users/vivekkrish/followers","following_url":"https://api.github.com/users/vivekkrish/following{/other_user}","gists_url":"https://api.github.com/users/vivekkrish/gists{/gist_id}","starred_url":"https://api.github.com/users/vivekkrish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vivekkrish/subscriptions","organizations_url":"https://api.github.com/users/vivekkrish/orgs","repos_url":"https://api.github.com/users/vivekkrish/repos","events_url":"https://api.github.com/users/vivekkrish/events{/privacy}","received_events_url":"https://api.github.com/users/vivekkrish/received_events","type":"User","site_admin":false},"created_at":"2017-09-26T18:20:40Z","updated_at":"2017-09-26T18:20:40Z","author_association":"COLLABORATOR","body":"@ABDULLAHGUJJAR @tanghaibao, it seems that in your GFF3 file, the `mRNA` features do not have a `Name` attribute\r\n```\r\nA01\tEVM\tmRNA\t15705\t19194\t.\t+\t.\tID=Gh_A01G0001.1;Parent=Gh_A01G0001\r\n```\r\n\r\nAs such, by executing the command `python -m jcvi.formats.gff bed --type=mRNA --key=Name` on the GFF3 file, the script is inventing a new `Name` for each **mRNA** (using the template `ftype_linenumber`), and in that process, also mangling the name.\r\n\r\nFor e.g. the first **mRNA** feature appears on the line 4953. So, the invented `Name` is **mrna_4953**, which when mangled with the `%2C` (which is the comma symbol), corresponds to `m%2Cr%2Cn%2Ca%2C_%2C4%2C9%2C5%2C3`.\r\n\r\nThe issue is in this section of the code: https://github.com/tanghaibao/jcvi/blob/master/formats/gff.py#L179-L188\r\n\r\nI have gone ahead and issued a fix which should correct the issue.\r\n\r\nHowever, you should reformat your command to extract the `ID` attribute instead of `Name`."}}
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