{"action":"opened","issue":{"url":"https://api.github.com/repos/mattb112885/clusterDbAnalysis/issues/81","repository_url":"https://api.github.com/repos/mattb112885/clusterDbAnalysis","labels_url":"https://api.github.com/repos/mattb112885/clusterDbAnalysis/issues/81/labels{/name}","comments_url":"https://api.github.com/repos/mattb112885/clusterDbAnalysis/issues/81/comments","events_url":"https://api.github.com/repos/mattb112885/clusterDbAnalysis/issues/81/events","html_url":"https://github.com/mattb112885/clusterDbAnalysis/issues/81","id":194836549,"number":81,"title":"Error in convertGenbank2table.py in /pseudo in genbank","user":{"login":"michoug","id":12357985,"avatar_url":"https://avatars.githubusercontent.com/u/12357985?v=3","gravatar_id":"","url":"https://api.github.com/users/michoug","html_url":"https://github.com/michoug","followers_url":"https://api.github.com/users/michoug/followers","following_url":"https://api.github.com/users/michoug/following{/other_user}","gists_url":"https://api.github.com/users/michoug/gists{/gist_id}","starred_url":"https://api.github.com/users/michoug/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/michoug/subscriptions","organizations_url":"https://api.github.com/users/michoug/orgs","repos_url":"https://api.github.com/users/michoug/repos","events_url":"https://api.github.com/users/michoug/events{/privacy}","received_events_url":"https://api.github.com/users/michoug/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-11T15:04:20Z","updated_at":"2016-12-11T15:04:20Z","closed_at":null,"body":"Dear All,\r\n\r\nI was parsing a genbank file (more precisely a gbff file (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/365/GCF_000009365.1_ASM936v1/GCF_000009365.1_ASM936v1_genomic.gbff.gz)) and due to the fact that some genes are annotated as /pseudo there are several errors such as :\r\n\r\nWARNING: CDS found with no translation\r\nQualifiers:\r\nlocus_tag\t['ABO_RS05435']\r\ninference\t['EXISTENCE: similar to AA sequence:RefSeq:WP_011588335.1']\r\nold_locus_tag\t['ABO_1051']\r\ncodon_start\t['1']\r\npseudo\t['']\r\nexception\t['unextendable partial coding region']\r\ntransl_table\t['11']\r\nnote\t['Derived by automated computational analysis using gene prediction method: Protein Homology.']\r\n\r\nwith coordinates : complement(<1191967..1192467)\r\n\r\nand then \r\n\r\nBAD - the gene in the following location did not have a match in the table file!\r\n[<1191966:1192467](-)\r\nATGCCAAAACGGATATTCCGCAAATACCTGCCAACACCCGAACGTATTCGACAAACCAAGTCGTTGAGTTTTCTCGGGGAAGTGCTATCGGACCCAAACCTTTGGCACATTAACCGTCGTTCACTGGCCGGCGCAGCCTTTATCGGTATCTTCTCCGGTCTGTTACCTATCCCCCTGCAAATGGGGTTGGCCGCCCTGTTGGCGGTGCGCTTCCACTGCAACCTGCCGCTTTCGATTATGCTGGTATGGATTTCCAATCCAGTGACTTATGTGCCGATTTTCTATTTCACCTACCGCATTGGCGCCTGGCTGCTGGGAATGCCGCCCCACAGCGGTGAAGGCATCACCGTCGCCTGGTTTGTGGAACAGCTCATCCCATTATGGGTAGGTTCAATGCTATGCGCATTCGGGTTTGGCGGATTAGCGTACATGGCAGTAAAAGTCAGCTGGCGGCTAGCTGTAATTCGAAGTTGGAATCTACGCGCGCACCGGCGCGCACGG\r\n\r\nBest\r\nGreg"}}
{"actor":{"display_login":"michoug"}}