{"action":"created","comment":{"url":"https://api.github.com/repos/hammerlab/vaxrank/pulls/comments/84821634","pull_request_review_id":5574098,"id":84821634,"diff_hunk":"@@ -63,85 +67,110 @@ def compute_template_data(\n         if len(vaccine_peptides) == 0:\n             logger.info(\"Skipping %s, no vaccine peptides\", variant_short_description)\n             continue\n-        gene_name = vaccine_peptides[0].mutant_protein_fragment.gene_name\n-        peptides = []\n-        variant_dict = {\n-            'num': i + 1,\n-            'short_description': variant_short_description,\n-            'gene_name': gene_name,\n-            'top_score': vaccine_peptides[0].combined_score,\n-            'predicted_effect': variants_to_top_coding_effect_dict.get(variant),\n-            'reads_supporting_variant_allele':\n-                vaccine_peptides[0].mutant_protein_fragment.n_alt_reads,\n-            'reads_supporting_reference_allele':\n-                vaccine_peptides[0].mutant_protein_fragment.n_ref_reads,\n-            'reads_supporting_other_alleles':\n-                vaccine_peptides[0].mutant_protein_fragment.n_other_reads,\n-            'peptides': peptides,\n-        }\n \n-        # compile peptide info\n-        for j, vaccine_peptide in enumerate(vaccine_peptides):\n-            epitopes = []\n-            # compile epitope info\n-            for epitope_prediction in vaccine_peptide.epitope_predictions:\n-                if epitope_prediction.overlaps_mutation:\n-                    score = epitope_prediction.logistic_score()\n-                    epitope_dict = {\n-                        'sequence': epitope_prediction.peptide_sequence,\n-                        'ic50': epitope_prediction.ic50,\n-                        'normalized_binding_score': score,\n-                        'allele': epitope_prediction.allele,\n-                    }\n-                    epitopes.append(epitope_dict)\n+        ############################### Variant info ###############################","path":"vaxrank/report.py","position":80,"original_position":80,"commit_id":"8143f93e2c2c83f52465084bbe6a5d4500ff8f46","original_commit_id":"8143f93e2c2c83f52465084bbe6a5d4500ff8f46","user":{"login":"ihodes","id":167803,"avatar_url":"https://avatars.githubusercontent.com/u/167803?v=3","gravatar_id":"","url":"https://api.github.com/users/ihodes","html_url":"https://github.com/ihodes","followers_url":"https://api.github.com/users/ihodes/followers","following_url":"https://api.github.com/users/ihodes/following{/other_user}","gists_url":"https://api.github.com/users/ihodes/gists{/gist_id}","starred_url":"https://api.github.com/users/ihodes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ihodes/subscriptions","organizations_url":"https://api.github.com/users/ihodes/orgs","repos_url":"https://api.github.com/users/ihodes/repos","events_url":"https://api.github.com/users/ihodes/events{/privacy}","received_events_url":"https://api.github.com/users/ihodes/received_events","type":"User","site_admin":false},"body":"What about factoring out all these Foo Infos into functions like `foo_info(...)`. Would be a bit easier to read and follow that way, I think?","created_at":"2016-10-25T02:32:22Z","updated_at":"2016-10-25T02:34:02Z","html_url":"https://github.com/hammerlab/vaxrank/pull/65#discussion_r84821634","pull_request_url":"https://api.github.com/repos/hammerlab/vaxrank/pulls/65","_links":{"self":{"href":"https://api.github.com/repos/hammerlab/vaxrank/pulls/comments/84821634"},"html":{"href":"https://github.com/hammerlab/vaxrank/pull/65#discussion_r84821634"},"pull_request":{"href":"https://api.github.com/repos/hammerlab/vaxrank/pulls/65"}}},"pull_request":{"url":"https://api.github.com/repos/hammerlab/vaxrank/pulls/65","id":90724999,"html_url":"https://github.com/hammerlab/vaxrank/pull/65","diff_url":"https://github.com/hammerlab/vaxrank/pull/65.diff","patch_url":"https://github.com/hammerlab/vaxrank/pull/65.patch","issue_url":"https://api.github.com/repos/hammerlab/vaxrank/issues/65","number":65,"state":"open","locked":false,"title":"Refactor report ordered dict","user":{"login":"julia326","id":3926242,"avatar_url":"https://avatars.githubusercontent.com/u/3926242?v=3","gravatar_id":"","url":"https://api.github.com/users/julia326","html_url":"https://github.com/julia326","followers_url":"https://api.github.com/users/julia326/followers","following_url":"https://api.github.com/users/julia326/following{/other_user}","gists_url":"https://api.github.com/users/julia326/gists{/gist_id}","starred_url":"https://api.github.com/users/julia326/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/julia326/subscriptions","organizations_url":"https://api.github.com/users/julia326/orgs","repos_url":"https://api.github.com/users/julia326/repos","events_url":"https://api.github.com/users/julia326/events{/privacy}","received_events_url":"https://api.github.com/users/julia326/received_events","type":"User","site_admin":false},"body":"A couple of report gen changes:\r\n    - Refactored report gen logic to use OrderedDicts. This brings all the work into the Python code, and avoids replication across templates, which now mostly just iterate over the OrderedDicts\r\n    - Prettied up the peptide table; now \"Manufacturability\" and \"Predicted mutant epitopes\" are both subsections.\r\n\r\nFixes #64 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