M01_covariances_correlations.py 文件源码

def buildCorrelationEntries(self, name, gene, weight_db_logic, snps_by_rsid):
        weights_in_gene = weight_db_logic.weights_by_gene[gene]
        rsids_from_genes = weights_in_gene.keys()

        #gather as much data as we can work on
        related_rsids, related_data = self.buildRelatedData(rsids_from_genes, snps_by_rsid, weights_in_gene)

        if len(related_rsids) == 0:
            return []

        self.updateFoundCorrelation(gene, name)

        #correlation matrix of related SNP's data
        array = numpy.array(related_data)
        cor = numpy.corrcoef(array)

        #translate into sql entries
        entries = self.buildMatrixOutputEntries(cor, rsids_from_genes, related_rsids, snps_by_rsid)
        if not len(entries):
            raise NameError("Couldn not build correlation entries for (%s,%s)" %(name,gene))
        return entries