This pull request has many updates that have been implemented over the past year of publication reviews. This branch builds on the #110 pull request from @FaizRizvi. There are still changes to be made and tests to be run, so this branch will be marked as a draft pull request.
Summary of Changes:
Updates to function docs
Error logging has been updated
logging.error has been changed to logging.info and set as default
logging.debug messages have been added in some places for detailed reporting
average function
Added timers
Added some logging information
benchmark function
Added a flag to skip plotting
data function
Support for hg19, hg38, and mm10 added
normalize function
Remove median-mad normalization
Updated code for output paths
peaks function
Added some logging
created a function for getting thresholds
predict function
Users can input 1,024 bp windows to use for prediction. The burden is on the user to make sure the windows have the same width and step across the whole chromosome. If the 32 bp output predictions do not line up, they will cause an error.
Users can input a bed file of ATAC-seq peaks (or any peaks) to use to refine prediction windows. If the user has provided windows, they will be filtered to those that overlap the input peak files. If the user does not provide peaks, all windows provided by the user or generated by default will be used.
Now has general parser argument for genome. Example: maxatac --genome mm10 predict ...
All functions should have uniform flags with multiple options. For example, user can now specify "-c", "--chroms", or "--chromosomes" with all functions to define chromosomes of interest.
Tests
Started writings tests for average, normalize, prepare, and predict
To Do:
[ ] Double check that all arguments are documented
[ ] Check that all arguments have the correct help information
[ ] Create tests for remaining functions
[ ] Create walkthroughs for prediction, benchmarking, and training
[ ] Add logging and debug information for all code
This pull request has many updates that have been implemented over the past year of publication reviews. This branch builds on the #110 pull request from @FaizRizvi. There are still changes to be made and tests to be run, so this branch will be marked as a draft pull request.
Summary of Changes:
logging.errorhas been changed tologging.infoand set as defaultlogging.debugmessages have been added in some places for detailed reportingaveragefunctionbenchmarkfunctiondatafunctionnormalizefunctionpeaksfunctionpredictfunctionmaxatac --genome mm10 predict ..."-c", "--chroms", or "--chromosomes"with all functions to define chromosomes of interest.To Do: