def main(): # First, retrieve the genes that are available in embedding. embedding_genes = file_operations.get_embedding_genes() # Mouse.embedding is an nxn matrix, where n is the number of genes in # Mouse.embedding.id. f = open('./Sheng/data/network/integrated_network/Mouse.embedding', 'r') out = open('./data/embedding_edges.txt', 'w') for i, line in enumerate(f): row_gene = embedding_genes[i] line = line.split() assert len(line) == len(embedding_genes) # Start at i+1, since we only want upper triangular matrix.. for j in range(i + 1, len(line)): column_gene = embedding_genes[j] weight = line[j] out.write('%s\t%s\t%s\n' % (row_gene, column_gene, weight)) out.close() f.close()