Organization of pipeline specific files about cbioportal_tools HOT 2 CLOSED

I;ve reorganized the directory structure, to include the folder analysis_pipelines under lib. This replaces the data_type folder. Under this are subfodlers for the genetic _alteration_types listed above. Each holds a python script that executes a pipeline for processing the data. Under data_type there were distinctly named files (eg. mutation_data.py) that contained shared support functions used by each of the pipelines. This was changed to support_functions.py. To implement these changes, the study config file was modified to include a separate analysis column, which specified the genetic_alteration_type. The file still contains a type column which is the datatype. The code contains an object of class CONFIG that was modified to handle this, and it is from this object that the path to the pipeline script is located. I've tested this for MUTATION_EXTENDED, using the Mutect pipeline. All the MUTATION_EXTENDED pipelines were modified, and should be working now. Other Genetic_alteration_types still need to be fixed. I'll set up some additional tests to ensure these are working okay

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I am setting up test datasets for each pipeline. As modifications to the code are made, I'll test each of the pipelines for successful creation of an import folder. If any failures, I'll open up an issue to address it in the code.

Closing this issue, will open as a separate issue to develop this further as I think some additional code reorganization would benefit being able to extend the tool with new pipelines.

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