We want a single point of entry, with suboptions, rather than a fragmented code base, similar to how GATK is called for all of it's subfunctions:
gatk [ToolName] ToolArguments
I think most of the model creations could be changed to flags in the main gen_reads workflow. Rather than running gen_mut_model.py, then running gen_reads.py, we have one command, where if you need to create the mutation model you can either do it as part of the gen_reads run or as a standalone process.
The key component here is to move all the python code to Source, so that we don't have to mess around with importing from neigboring modules, as we currently do in genSeqErrorModel.py (importing the DiscreteDistribution class, though that can also probably be just replaced with standard modules). We would use a bash launcher or a python launcher in the main folder that would call the source code and perform the actual runs.
We want a single point of entry, with suboptions, rather than a fragmented code base, similar to how GATK is called for all of it's subfunctions:
gatk [ToolName] ToolArgumentsI think most of the model creations could be changed to flags in the main gen_reads workflow. Rather than running gen_mut_model.py, then running gen_reads.py, we have one command, where if you need to create the mutation model you can either do it as part of the gen_reads run or as a standalone process.
neat GenMutModel -i /path/to/fileneat GenReads -i /path/to/file --gmm /path/to/other_fileThe key component here is to move all the python code to Source, so that we don't have to mess around with importing from neigboring modules, as we currently do in genSeqErrorModel.py (importing the DiscreteDistribution class, though that can also probably be just replaced with standard modules). We would use a bash launcher or a python launcher in the main folder that would call the source code and perform the actual runs.