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added 5th argument for vbgmm, using .values #284

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added 5th argument for vbgmm, using .values #284

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12 changes: 8 additions & 4 deletions bin/concoct_refine
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Original file line number Diff line number Diff line change
Expand Up @@ -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])

Expand All @@ -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


Expand Down Expand Up @@ -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)
Expand Down