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.