コード例 #1
0
ファイル: test_worker.py プロジェクト: JohnCEarls/DataDirac
def test_gm(log_files, source_dataframe):
    print "Testing gene map and network map"
    ni = NetworkInfo( "net_info_table","c2.cp.biocarta.v4.0.symbols.gmt")
    genes = []
    for p in ni.get_pathways():
        genes.append(set(ni.get_genes(p)))
    for log in log_files:
        with open(log, 'r') as l:
            for run_json in l:
                run = json.loads( run_json )
                for allele in run['alleles']:
                    source_allele = "%s-%s" % ( run['file_id'], allele )
                    working_dir = find_working( 
                            run['data_matrices'][source_allele] )
                    gm_file = join( working_dir, 
                                run['data_matrices'][ source_allele ]['gm'])
                    nm_file = join( working_dir, 
                                run['data_matrices'][ source_allele ]['nm'])
                    gm = np.load(gm_file)
                    nm = np.load(nm_file)
                    for i in range(1, len(nm)):
                        start = nm[i-1]
                        end = nm[i]
                        if start < end:
                            base_set = genes[i-1]
                            my_net = gm[2*start:2*end]
                            my_net_genes = source_dataframe.index[my_net]
                            gene_set = set(my_net_genes)
                            assert gene_set.issubset(base_set), "Genes do not match network genes"

                            assert (end - start) == scipy.misc.comb(len(gene_set),2, exact=1), "Wrong number of genes"
    print "Gene map and network map tests ... PASSED"
コード例 #2
0
ファイル: accumulator.py プロジェクト: JohnCEarls/DataDirac
 def networks(self):
     if self._pathways is None:
         ni = NetworkInfo( *self.net_info )
         self._pathways = ni.get_pathways()
         self.logger.debug("Got Networks")
     return self._pathways
コード例 #3
0
ファイル: aggregate.py プロジェクト: JohnCEarls/DataDirac
 def deprecated_networks(self):
     if self._pathways is None:
         print self.net_info
         ni = NetworkInfo( *self.net_info )
         self._pathways = ni.get_pathways()
     return self._pathways