Source code for tmtk.toolbox.generate_chromosomal_regions_file

import os

[docs]def generate_chromosomal_regions_file(platform_id=None, reference_build='hg19', **kwargs): """ This creates a new chromosomal regions annotation file. :param platform_id: Give the new platform a name to fill first column :param reference_build: choose either hg18, hg19 or hg38 :return: a pandas dataframe with the new platform """ import rpy2.robjects as robjects import rpy2.robjects.pandas2ri as pandas2ri host_mapping = {'hg18': '', 'hg19': '', 'hg38': ''} mart_host = host_mapping[reference_build] only_y = kwargs.get('only_y', False) r_source = robjects.r['source'] module_location = os.path.dirname(__file__) r_source(os.path.join(module_location, 'query_biomart.R')) r_query_mart = robjects.globalenv['query_biomart'] r_check_install = robjects.globalenv['verify_biomart_install'] if pandas2ri.Vector(r_check_install())[0] != 'INSTALLED': raise Exception('Cannot find biomaRt in R environment.' 'To install biomaRt, open R console and run:' '\n\t>source("")' '\n\t>biocLite("biomaRt")' ) new_platform = pandas2ri.ri2py_dataframe(r_query_mart(mart_host, platform_id, only_y)) return new_platform