{"action":"created","issue":{"url":"https://api.github.com/repos/bioperl/bioperl-live/issues/268","repository_url":"https://api.github.com/repos/bioperl/bioperl-live","labels_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/268/labels{/name}","comments_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/268/comments","events_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/268/events","html_url":"https://github.com/bioperl/bioperl-live/issues/268","id":297146988,"number":268,"title":"Bio::DB::GenPept Failed to get sequence by id","user":{"login":"Endle","id":3221521,"avatar_url":"https://avatars3.githubusercontent.com/u/3221521?v=4","gravatar_id":"","url":"https://api.github.com/users/Endle","html_url":"https://github.com/Endle","followers_url":"https://api.github.com/users/Endle/followers","following_url":"https://api.github.com/users/Endle/following{/other_user}","gists_url":"https://api.github.com/users/Endle/gists{/gist_id}","starred_url":"https://api.github.com/users/Endle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Endle/subscriptions","organizations_url":"https://api.github.com/users/Endle/orgs","repos_url":"https://api.github.com/users/Endle/repos","events_url":"https://api.github.com/users/Endle/events{/privacy}","received_events_url":"https://api.github.com/users/Endle/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-02-14T15:54:31Z","updated_at":"2018-02-16T14:50:10Z","closed_at":null,"author_association":"NONE","body":"<http://search.cpan.org/dist/BioPerl/Bio/DB/GenPept.pm#get_Seq_by_id>\r\n\r\nIt says\r\n\r\n>  Title   : get_Seq_by_id\r\n>  Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')\r\n>  Function: Gets a Bio::Seq object by its name\r\n>  Returns : a Bio::Seq object\r\n>  Args    : the id (as a string) of a sequence\r\n>  Throws  : \"id does not exist\" exception\r\n\r\nHowever, I ran `$seq = $db->get_Seq_by_id('ROA1_HUMAN')` and it threw an error\r\n\r\n```------------- EXCEPTION: Bio::Root::Exception -------------\r\nMSG: WebDBSeqI Request Error:\r\nHTTP/1.1 400 Bad Request\r\nCache-Control: private\r\nConnection: close\r\nDate: Wed, 14 Feb 2018 15:53:52 GMT\r\nServer: Apache\r\nVary: Accept-Encoding\r\nContent-Type: text/plain; charset=UTF-8\r\nAccess-Control-Allow-Origin: *\r\nClient-Date: Wed, 14 Feb 2018 15:53:52 GMT\r\nClient-Peer: 130.14.29.110:443\r\nClient-Response-Num: 1\r\nClient-SSL-Cert-Issuer: /C=US/O=DigiCert Inc/OU=www.digicert.com/CN=DigiCert SHA2 High Assurance Server CA\r\nClient-SSL-Cert-Subject: /C=US/ST=Maryland/L=Bethesda/O=National Library of Medicine/CN=*.ncbi.nlm.nih.gov\r\nClient-SSL-Cipher: ECDHE-RSA-AES256-GCM-SHA384\r\nClient-SSL-Socket-Class: IO::Socket::SSL\r\nClient-Transfer-Encoding: chunked\r\nContent-Disposition: attachment; filename=\"sequence.gp\"\r\nContent-Security-Policy: upgrade-insecure-requests\r\nNCBI-PHID: 990CFB17A845AF510000000000FD00E1\r\nNCBI-SID: 990CFB17A845B901_0253SID\r\nSet-Cookie: ncbi_sid=990CFB17A845B901_0253SID; domain=.nih.gov; path=/; expires=Thu, 14 Feb 2019 15:53:52 GMT\r\nStrict-Transport-Security: max-age=31536000; includeSubDomains; preload\r\nX-UA-Compatible: IE=Edge\r\nX-XSS-Protection: 1; mode=block\r\n\r\n Error: CEFetchPApplication::proxy_stream(): Failed to understand id: ROA1_HUMAN\r\n\r\n\r\nSTACK: Error::throw\r\nSTACK: Bio::Root::Root::throw /home/lizhenbo/perl5/lib/perl5/Bio/Root/Root.pm:447\r\nSTACK: Bio::DB::WebDBSeqI::_stream_request /home/lizhenbo/perl5/lib/perl5/Bio/DB/WebDBSeqI.pm:779\r\nSTACK: Bio::DB::WebDBSeqI::get_seq_stream /home/lizhenbo/perl5/lib/perl5/Bio/DB/WebDBSeqI.pm:472\r\nSTACK: Bio::DB::WebDBSeqI::get_Stream_by_id /home/lizhenbo/perl5/lib/perl5/Bio/DB/WebDBSeqI.pm:293\r\nSTACK: Bio::DB::WebDBSeqI::get_Seq_by_id /home/lizhenbo/perl5/lib/perl5/Bio/DB/WebDBSeqI.pm:158\r\nSTACK: PartVI_fetchFASTA.pl:27\r\n-----------------------------------------------------------\r\n\r\n------------- EXCEPTION: Bio::Root::Exception -------------\r\nMSG: id 'ROA1_HUMAN' does not exist\r\nSTACK: Error::throw\r\nSTACK: Bio::Root::Root::throw /home/lizhenbo/perl5/lib/perl5/Bio/Root/Root.pm:447\r\nSTACK: Bio::DB::WebDBSeqI::get_Seq_by_id /home/lizhenbo/perl5/lib/perl5/Bio/DB/WebDBSeqI.pm:172\r\nSTACK: PartVI_fetchFASTA.pl:27\r\n-----------------------------------------------------------\r\n```"},"comment":{"url":"https://api.github.com/repos/bioperl/bioperl-live/issues/comments/366255697","html_url":"https://github.com/bioperl/bioperl-live/issues/268#issuecomment-366255697","issue_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/268","id":366255697,"user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars1.githubusercontent.com/u/49265?v=4","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"created_at":"2018-02-16T14:50:10Z","updated_at":"2018-02-16T14:50:10Z","author_association":"OWNER","body":"@Endle might be useful, yes.  It's there but not well-documented."}}
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