def load_individuals_into_database(): """launch the various scripts to insert data into the HGDP database.""" from schema.connection import session, metadata from schema.connection import Individual, Population, SNP, RefSeqGene # session.flush() print "now we are connected to the database:", metadata metadata.bind.echo = True samples_file = file('../../data/Annotations/samples_subset.csv', 'r') session.flush() parsers.samples_parser(samples_file) session.commit() print 'upload of tables finished'
def update_individuals(genotypesfile, ): """ upload individuals from the rosenberg files. """ from schema.connection import session, metadata # is session necessary? logging.basicConfig(level=logging.DEBUG) print metadata # metadata.bind = 'sqlite:///:memory:' metadata.bind.echo = True parsers.individuals_genotypesindex_parser(open(genotypesfile, 'r')) session.commit() # rosenberg_file = open(rosenberg_path, 'r') # parsers.rosenberg_parser(rosenberg_file) print 'fixed individuals.genotypes_index to database %s completed' % metadata
def upload_genotypes(genotypes_by_chr_dir, ): """ upload individuals from the rosenberg files. """ from schema.connection import session, metadata # is session necessary? logging.basicConfig(level=logging.DEBUG) print metadata # metadata.bind = 'sqlite:///:memory:' metadata.bind.echo = True genotypes_by_chr_dir = '/home/gioby/Data/HGDP/Genotypes_by_chr' for filename in glob.glob(genotypes_by_chr_dir + '/*.geno'): print filename parsers.genotypes_parser(open(filename, 'r')) session.commit() # rosenberg_file = open(rosenberg_path, 'r') # parsers.rosenberg_parser(rosenberg_file) print 'upload of Genotypes to database %s completed' % metadata