{"action":"opened","issue":{"url":"https://api.github.com/repos/wonjunetai/pulse/issues/1","labels_url":"https://api.github.com/repos/wonjunetai/pulse/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/wonjunetai/pulse/issues/1/comments","events_url":"https://api.github.com/repos/wonjunetai/pulse/issues/1/events","html_url":"https://github.com/wonjunetai/pulse/issues/1","id":128582622,"number":1,"title":"Automate preprocessing step","user":{"login":"wonjunetai","id":5567908,"avatar_url":"https://avatars.githubusercontent.com/u/5567908?v=3","gravatar_id":"","url":"https://api.github.com/users/wonjunetai","html_url":"https://github.com/wonjunetai","followers_url":"https://api.github.com/users/wonjunetai/followers","following_url":"https://api.github.com/users/wonjunetai/following{/other_user}","gists_url":"https://api.github.com/users/wonjunetai/gists{/gist_id}","starred_url":"https://api.github.com/users/wonjunetai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wonjunetai/subscriptions","organizations_url":"https://api.github.com/users/wonjunetai/orgs","repos_url":"https://api.github.com/users/wonjunetai/repos","events_url":"https://api.github.com/users/wonjunetai/events{/privacy}","received_events_url":"https://api.github.com/users/wonjunetai/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-01-25T16:43:38Z","updated_at":"2016-01-25T16:43:38Z","closed_at":null,"body":"This includes:\r\n\r\n* Find exon-skipping alternative splicing events from RNA-seq\r\n```\r\npython src_rnaseq/from_transcriptome_extract_AS_events.py > events.fa\r\n```\r\n\r\n* Identify Anchors in BLAST\r\n```\r\nblastall -p blastx -d /home/ccorbi/Work/ddbb_fasta/Uniprot/uniprot_sprot.fasta -i events.fa -o blastx_from_AS_events.out -v1 -b1 -m8\r\n```\r\n\r\n* Filter alternative splicing events without a good anchor\r\n```\r\npython src_preprocess/filtermap.py\r\n```\r\n\r\n* Generate Index File\r\n\r\n    * need to move uniprot_exon_indices_map.out to src_rnaseq\r\n```\r\npython src_rnaseq/generate_index_and_libs_rnaseq.py  ../src_preprocess/temp/rnaseq_huniprot_corrected_len_collapsed.txt \r\n```\r\n\r\n* Move files for feature extraction into a separate folder\r\n```\r\nmkdir ../features\r\ncp uniprot_exon_indices.txt ../features/\r\ncp cdna_transcripts.fasta ../features/\r\ncp pSeq_isoforms.fas ../features/\r\ncp ASlocation.out ../features/\r\n```"}}