{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/oncotator/pulls/comments/34683194","id":34683194,"diff_hunk":"@@ -58,7 +58,7 @@\n \n It defines classes_and_methods\n \n-@author:     aramos, mgupta, and lichtens\n+@author:     aramos, lbergelson, mgupta, and lichtens","path":"oncotator/Oncotator.py","position":5,"original_position":5,"commit_id":"9611ade469cb9ab09e7d55220593f0b3f5c36c40","original_commit_id":"9611ade469cb9ab09e7d55220593f0b3f5c36c40","user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"body":":+1: ","created_at":"2015-07-15T14:25:50Z","updated_at":"2015-07-15T14:25:50Z","html_url":"https://github.com/broadinstitute/oncotator/pull/330#discussion_r34683194","pull_request_url":"https://api.github.com/repos/broadinstitute/oncotator/pulls/330","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/oncotator/pulls/comments/34683194"},"html":{"href":"https://github.com/broadinstitute/oncotator/pull/330#discussion_r34683194"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/oncotator/pulls/330"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/oncotator/pulls/330","id":39981945,"html_url":"https://github.com/broadinstitute/oncotator/pull/330","diff_url":"https://github.com/broadinstitute/oncotator/pull/330.diff","patch_url":"https://github.com/broadinstitute/oncotator/pull/330.patch","issue_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/330","number":330,"state":"open","locked":false,"title":"Issue 326 oxo g fix collapsing","user":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"body":"- ``--collapse-number-annotations`` added to CLI  This tells Oncotator to take a known set of numeric columns (listed below) and convert into a single value based on a rule (currently only ``min`` and ``mean`` are supported).  This will eliminate the possibility of a ``|`` appearing in the column as the values will be collapsed according to the rule.\r\n\r\nThe current columns and rules are found in ``column_collapse.config`` in the source code.  These are key:value of ``annotation_name:method_applied``\r\n\r\nNotes:\r\n- There is no easy way for users to modify the list and rules found in ``column_collapse.config``\r\n- Collapsing does not fail if blank or string values are found.  See examples below for behavior.\r\n- \"|\" is the only delimiter recognized.\r\n- The collapsing rules are driven off of annotation names, not column names in a TCGA MAF.  ``i_`` fields are included only to catch cases where these were specified in the input file.\r\n\r\nCollapsing rules as of this writing:\r\n```\r\n# This file is a config file for ColumnCollapser instances.\r\n#\r\n#  key:value is <name of the annotation to collapse>:<method of collapse>\r\n#\r\n#  Currently, the method of collapse can only be: \"min\" or \"mean\" (without quotes).  If left blank, mean will be selected.\r\n#\r\n[columns_to_collapse]\r\nALT_F2R1: min\r\ni_ALT_F2R1: min\r\nREF_F2R1: min\r\ni_REF_F2R1: min\r\nALT_F1R2: min\r\ni_ALT_F1R2: min\r\nREF_F1R2: min\r\ni_REF_F1R2: min\r\nt_Foxog: mean\r\ni_t_Foxog: mean\r\ni_tumor_f: mean\r\ntumor_f: mean\r\nt_ref_count: min\r\nt_alt_count: min\r\ni_t_ref_count: min\r\ni_t_alt_count: min\r\nn_ref_count: min\r\nn_alt_count: min\r\ni_n_ref_count: min\r\ni_n_alt_count: min\r\n\r\n# These columns are for testing\r\nhamilcar: mean\r\nbarca:\r\n```\r\n\r\nExamples (incl. bad inputs):\r\nmean:\r\n```\r\n0.1|0.2 --> 0.15\r\n4|10 --> 7\r\n```\r\nmin:\r\n```\r\n0.1|0.2 --> 0.1\r\n4|10 --> 4\r\n```\r\n\r\nother examples:\r\n```\r\n# For columns not in the config file\r\n4|6 --> 4|6\r\n\r\n# Other examples\r\n| --> <blank>\r\n|36 --> 36\r\n<blank> --> <blank>\r\n0|blah --> 0|blah\r\n```\r\n\r\n- A suffix is specified (``_full``) , which is used to create copies of the original, unaltered annotation.  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