Improving the API interface

improved_api_interface.py

class Pathway:
  def __init__(self, api):
    self.api = api      

  def datasets(self):
    """ Returns the list of all pathway datasets available"""
    pass

  def getPathways(self, datasets=[Dataset.KEGG]):
    """ Returns the list of all pathways available, optionally filtering by dataset"""
    pass

  def getPathwaysWithGenesInQuery(self, geneQuery=None, datasets=[Dataset.KEGG]):
    """ Returns the list of pathways that contains genes within geneQuery"""
    pass

  def getGenesInPathway(self, pathway):
    """ Returns the list of genes in the specified pathway """
    pass


class Variant:
  def __init__(self, api):
    self.api = api

  def datasets(self):
    """ Returns the list of all variant datasets available"""
    pass

  def tags(self, datasets=[Dataset.EXAC]):
    """ Returns the variant tags available, optionally filtered by datasets"""
    pass

  def gwasDatasets(self):
    """ Returns the GWAS datasets that are available"""
    pass

  def eqtlDatasets(self):
    """ Returns the eQTL datasets that are available"""
    pass

  def getEQTLs(self, biosample=None, genesQuery=None, datasets=[Dataset.GTEX]):
    """ Returns the eQTLs contained within datasets, filtered by optional biosamples and optionally affecting genes within geneQuery"""
    pass

  def getVariantsForGenesInQuery(self, geneQuery=None, variantTags=None, datasets=[Dataset.EXAC, Dataset.CLINVAR, Dataset.DBSNP]):
    """ Returns the variants contained within datasets, filtered by variantTags and affecting genes within geneQuery"""
    pass

  def getVariantsForAnnotationsInQuery(self, annotationQuery=None, variantTags=None, datasets=[Dataset.EXAC, Dataset.CLINVAR, Dataset.DBSNP]):
    """ Returns the variants contained within datasets, filtered by variantTags and affecting annotations within annotationQuery"""
    pass


class GenomicRegion:
  def __init__(self):
    pass

  def addInterval(self, contig, start, end):
    pass

  def removeInterval(self, contig, start, end):
    pass

  def getIntervals(self):
    pass

  def setIntervals(self, intervals):
    pass
  
  def createFromBED(self, path):
    pass
  
  def commit(self):
    pass
  
  def getQuery(self):
    pass

  

class Annotation:
  def __init__(self, api):
    self.api = api

  def datasets(self):
    """ Returns the list of annotation datasets available e.g ENCODE, ENSEMBL, ROADMAP """
    pass

  def biosamples(self, datasets=[Dataset.ENCODE]):
    """ Returns the list of biosamples available """
    pass

  def targets(self, biosamples=None, annotationTypes=None, datasets=[Dataset.ENCODE]):
    """ Returns the list of targets available """
    pass

  def annotationTypes(self, biosamples=None, datasets=[Dataset.ENCODE]):
    """ Returns the list of annotation types available """
    pass

  def getAnnotations(self, annotationTypes=None, biosamples=None, nnotationTargets=None, datasets=[Dataset.ENCODE]):
    """ Returns a query for the  specified annotation types"""
    pass

  def getGenes(self, names):
    """ helper method that fetches a single gene or list of genes"""
    pass