{"action":"closed","issue":{"url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/243","repository_url":"https://api.github.com/repos/sanger-pathogens/Roary","labels_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/243/labels{/name}","comments_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/243/comments","events_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/243/events","html_url":"https://github.com/sanger-pathogens/Roary/issues/243","id":147181835,"number":243,"title":"Use of Roary with Mycoplasma genomes (Genetic Code Table 4)","user":{"login":"dutchscientist","id":10428112,"avatar_url":"https://avatars.githubusercontent.com/u/10428112?v=3","gravatar_id":"","url":"https://api.github.com/users/dutchscientist","html_url":"https://github.com/dutchscientist","followers_url":"https://api.github.com/users/dutchscientist/followers","following_url":"https://api.github.com/users/dutchscientist/following{/other_user}","gists_url":"https://api.github.com/users/dutchscientist/gists{/gist_id}","starred_url":"https://api.github.com/users/dutchscientist/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dutchscientist/subscriptions","organizations_url":"https://api.github.com/users/dutchscientist/orgs","repos_url":"https://api.github.com/users/dutchscientist/repos","events_url":"https://api.github.com/users/dutchscientist/events{/privacy}","received_events_url":"https://api.github.com/users/dutchscientist/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/sanger-pathogens/Roary/labels/question","name":"question","color":"cc317c"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-04-10T01:24:51Z","updated_at":"2016-04-18T08:43:33Z","closed_at":"2016-04-18T08:43:33Z","body":"I am trying to use Roary with Mycoplasma genomes, which use Genetic Code Table 4, i.e. TGA is used for Trp (W). Unfortunately Roary seems to expect the standard translation table, and genes with a TGA are not included in the analysis, probably because of a mismatch between the predicted length in the annotation and the length found by Roary when translating the GFF, or by Roary not recognising the stopcodon signs?\r\n\r\nI don't see an option to specify an alternative Genetic Code Table in the command line of Roary. Can this be done? Is there an option of using the Prokka FAA files as input instead?"}}