From be189d4edaf03d61c903663b24eb0dc9f07da7bd Mon Sep 17 00:00:00 2001 From: Sebastien-Raguideau Date: Tue, 3 Mar 2020 15:33:49 +0000 Subject: [PATCH] added 5th argument for vbgmm, using .values --- bin/concoct_refine | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/bin/concoct_refine b/bin/concoct_refine index 13e5fc2..4ec4968 100755 --- a/bin/concoct_refine +++ b/bin/concoct_refine @@ -16,15 +16,15 @@ def main(args): original_data = p.read_csv(args.original_data, header=0, index_col=0) - original_data_matrix = original_data.to_numpy() + original_data_matrix = original_data.values scg_freq = p.read_csv(args.scg_file, header=0, index_col=0) - scg_freq_matrix = scg_freq.to_numpy() + scg_freq_matrix = scg_freq.values med_scgs = np.median(scg_freq_matrix, axis=1) - clusters_matrix = clusters.to_numpy() + clusters_matrix = clusters.values cluster_freq = np.bincount(clusters_matrix[:,0]) @@ -45,7 +45,7 @@ def main(args): NK = med_scgs[k]*args.expansion_factor print("Run CONCOCT for " + str(k) + "with " + str(NK) + "clusters" + " using " + str(args.threads) + "threads") - assigns = vbgmm.fit(np.copy(transform_k,order='C'), int(NK), args.seed, args.threads) + assigns = vbgmm.fit(np.copy(transform_k,order='C'), int(NK), args.seed, args.threads, args.i) kK = np.max(assigns) + 1 @@ -76,6 +76,10 @@ if __name__ == "__main__": parser.add_argument('-t','--threads',default=1, type=int, help=("number of threads to use defaults to one")) + parser.add_argument('-i','--iterations',type=int, default=500, + help=('Specify maximum number of iterations for the VBGMM. ' + 'Default value is 500')) + args = parser.parse_args() main(args)