{"action":"created","issue":{"url":"https://api.github.com/repos/LabTranslationalArchitectomics/riboWaltz/issues/7","repository_url":"https://api.github.com/repos/LabTranslationalArchitectomics/riboWaltz","labels_url":"https://api.github.com/repos/LabTranslationalArchitectomics/riboWaltz/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/LabTranslationalArchitectomics/riboWaltz/issues/7/comments","events_url":"https://api.github.com/repos/LabTranslationalArchitectomics/riboWaltz/issues/7/events","html_url":"https://github.com/LabTranslationalArchitectomics/riboWaltz/issues/7","id":322862324,"number":7,"title":"Quantification of overall p-site & a-site occupancy for each transcript","user":{"login":"bontus","id":7118547,"avatar_url":"https://avatars1.githubusercontent.com/u/7118547?v=4","gravatar_id":"","url":"https://api.github.com/users/bontus","html_url":"https://github.com/bontus","followers_url":"https://api.github.com/users/bontus/followers","following_url":"https://api.github.com/users/bontus/following{/other_user}","gists_url":"https://api.github.com/users/bontus/gists{/gist_id}","starred_url":"https://api.github.com/users/bontus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bontus/subscriptions","organizations_url":"https://api.github.com/users/bontus/orgs","repos_url":"https://api.github.com/users/bontus/repos","events_url":"https://api.github.com/users/bontus/events{/privacy}","received_events_url":"https://api.github.com/users/bontus/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-14T15:16:33Z","updated_at":"2018-05-22T09:56:32Z","closed_at":null,"author_association":"NONE","body":"Hi Fabio,\r\n\r\nI was wondering if you could implement a function to count the total number of reads covering each of the 64 codons for each transcript based on the p-site as well as the **a-site**. This would be very useful for calculating whether ribosome footprints are observed more often than expected for one codon (= possible ribosome stalling due to low tRNA concentration).\r\nConceptually you should be able to re-use most of the code from codon_usage_psite(), this is what I did previously.\r\nBTW, the new version works quite well, I have yet to test it with the problematic sample, but it seems that I can run another dataset in its entirety without swapping (clearly using > 16 GB RAM though).\r\n\r\nBest,\r\nRené\r\n"},"comment":{"url":"https://api.github.com/repos/LabTranslationalArchitectomics/riboWaltz/issues/comments/390933587","html_url":"https://github.com/LabTranslationalArchitectomics/riboWaltz/issues/7#issuecomment-390933587","issue_url":"https://api.github.com/repos/LabTranslationalArchitectomics/riboWaltz/issues/7","id":390933587,"user":{"login":"fabiolauria","id":10961255,"avatar_url":"https://avatars3.githubusercontent.com/u/10961255?v=4","gravatar_id":"","url":"https://api.github.com/users/fabiolauria","html_url":"https://github.com/fabiolauria","followers_url":"https://api.github.com/users/fabiolauria/followers","following_url":"https://api.github.com/users/fabiolauria/following{/other_user}","gists_url":"https://api.github.com/users/fabiolauria/gists{/gist_id}","starred_url":"https://api.github.com/users/fabiolauria/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fabiolauria/subscriptions","organizations_url":"https://api.github.com/users/fabiolauria/orgs","repos_url":"https://api.github.com/users/fabiolauria/repos","events_url":"https://api.github.com/users/fabiolauria/events{/privacy}","received_events_url":"https://api.github.com/users/fabiolauria/received_events","type":"User","site_admin":false},"created_at":"2018-05-22T09:56:32Z","updated_at":"2018-05-22T09:56:32Z","author_association":"COLLABORATOR","body":"Hi René,\r\nfollowing yuor suggestion I updated the codon_usage_psite function introducing the parameter \"site\". It allows to chose one of the three ribosome sites for computing the \"empirical codon usage indexes\" i.e. the normalized number of reads covering each of the 64 codons. On the same line I modified the psite_info function introducing the possibility to add one ore more columns reporting the nucleotide sequence covered not only by the P-site but also by the A-site or the E-site (again through the \"site\" parameter).\r\n\r\nBests,\r\nFabio"}}
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