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()
