def generate_expressions(gene_ids, path):
"""Generate random expression data."""
genes = {}
with gzip.open(os.path.join(path, 'expressions.tab.gz'), 'wb') as f:
f.write('{}\t{}\n'.format('Gene', 'Expression').encode('utf-8'))
with gzopen(gene_ids) as gene_ids:
all_genes = [line.strip() for line in gene_ids]
for gene in all_genes:
expression = random.gammavariate(1, 100)
f.write('{}\t{}\n'.format(gene, expression).encode('utf-8'))
genes[escape_mongokey(gene)] = expression
with open(os.path.join(path, 'expressions.json'), 'w') as json_file:
js_out = '{{"exp_json":{}}}'.format(json.dumps({'genes': genes}, separators=(',', ':')))
json_file.write(js_out)
def create_etc(gene_ids, path, file_name):
"""Generate an expression time course."""
genes = {}
with open(os.path.join(path, file_name), 'w') as f:
csvwriter = csv.writer(f, delimiter=str('\t'))
times = [0, 4, 8, 12, 16, 20, 24]
csvwriter.writerow(['Gene'] + times)
with gzopen(gene_ids) as gene_ids:
all_genes = [line.strip() for line in gene_ids]
for gene in all_genes:
expression = [str(random.gammavariate(1, 100)) for _ in range(7)]
genes[gene] = expression
csvwriter.writerow([gene] + expression)
with open(os.path.join(path, 'etc.json'), 'w') as json_file:
js_out = '{{"etc":{}}}'.format(json.dumps({'genes': genes, 'timePoints': times}, separators=(',', ':')))
json_file.write(js_out)
gzip.open(os.path.join(path, 'etc.json.gz'), 'wb').write(js_out.encode('utf-8'))
