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Revisions №60305

branch: master 「№60305」
Commited by: Steven Lewis
GitHub commit link: 「51cfd44147445970」 「№3297」
Difference from previous tested commit:  code diff
Commit date: 2018-07-17 16:06:47

Merge pull request #3297 from CyrusBiotechnology/indigo/argobody Code from @indigogo at Cyrus: Antibody grafting, option to define CDRs with an input JSON in exact same format as the preexisting output JSON (from Indigo:) Additions to antibody grafting public app. This adds a non-default option to define CDR loop begin/end positions with an input JSON configuration file. If this file is defined on cmdline input, then the RegEx-based CDR prediction is skipped and the CDR begin/end points are defined by the information in the input JSON. This PR adds the following: a new class to set the CDR sequence position information in AntibodySequence.sequence.cdr.* based on input json numbers. the input json is parsed using the json parsing tools in utility/json_utitlties.hh. JSON format is checked every time and exit with informative message is called if input JSON is misformatted. control logic in apps/public/antibody.cc to check if -json flag is defined on input, and if it is, skip the RegEx step and do the JSON reading step instead. I am not touching anything else in the antibody.cc code. The point of all this is to add functionality for connecting any CDR detection tool's output with antibody grafting protocol input.

Steven Lewis 1 year
I don't know what to make of the test failures - particularly as the tests were green in the PR pre-merge (http://benchmark.graylab.jhu.edu/revision?id=10139&branch=) and it's irrelevant code anyway. If someone knows what is up, and/or wants to revert, please do so! If we identify that this code is at fault I won't have time to fix it until the weekend.
Steven Lewis 1 year
I don't know what to make of the test failures - particularly as the tests were green in the PR pre-merge (http://benchmark.graylab.jhu.edu/revision?id=10139&branch=) and it's irrelevant code anyway. If someone knows what is up, and/or wants to revert, please do so! If we identify that this code is at fault I won't have time to fix it until the weekend. reposting with "notify list" [list]
Steven Lewis 1 year
I don't know what to make of the test failures - particularly as the tests were green in the PR pre-merge (http://benchmark.graylab.jhu.edu/revision?id=10139&branch=) and it's irrelevant code anyway. If someone knows what is up, and/or wants to revert, please do so! If we identify that this code is at fault I won't have time to fix it until the weekend. reposting with "notify list" [list]
Sergey Lyskov 1 year
Steven, this is not new: http://benchmark.graylab.jhu.edu/revision?branch=master&id=60301 - i think this is related to recent changes (http://benchmark.graylab.jhu.edu/revision?branch=master&id=60294 ?) and manifest itself as random failure of D110_DNA_interface T880_Other tests [list]
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