def process_file(path, options):
logging.info('Processing file "%s"' % path)
output_path = get_output_path(path, options)
reader = csv.reader(open(path,'rU'), delimiter='\t')
writer = csv.writer(open(output_path, 'wt'), delimiter='\t')
writer.writerow(['chrom', 'index', 'forward', 'reverse'])
manager = ChromosomeManager(reader)
while not manager.done:
cname = manager.chromosome_name()
logging.info('Processing chromosome %s' % cname)
data = manager.load_chromosome()
for read in data:
writer.writerow([cname] + read)
def process_file(fpath, options):
options.chromosome = ''
manager = ChromosomeManager(csv.reader(open(fpath, 'rU'), delimiter='\t'))
inputs = []
outputs = []
threads = []
genetrack_path = os.path.join(os.path.dirname(__file__), 'genetrack.py')
temp_dir = tempfile.mkdtemp()
logging.info('Preparing file "%s"' % fpath)
while not manager.done:
name = manager.chromosome_name()
logging.info('Preparing chromosome %s' % name)
data = manager.load_chromosome()
input_name = os.path.join(temp_dir, name + '.txt')
f = open(input_name, 'wt')
writer = csv.writer(f, delimiter='\t')
for read in data:
writer.writerow([name] + read)
f.close()
inputs.append(input_name)
# Process each chromosome
for input in inputs:
c = 'python %s %s -s %d -e %d -u %d -d %d -k %d -F %d -o %s' % (
genetrack_path, input, options.sigma, options.exclusion, options.up_width, options.down_width, options.chunk_size,
options.filter, options.format)
t = ProcessFileThread(c)
t.start()
threads.append(t)
output_path = get_output_path(input, options)
outputs.append(output_path)
# Wait for completion
for thread in threads:
thread.join()
# Merge together output files
logging.info('Merging output files')
options.chromosome = ''
real_output = open(get_output_path(fpath, options), 'wt')
for output in outputs:
shutil.copyfileobj(open(output, 'rt'), real_output)
os.unlink(output)
real_output.close()
shutil.rmtree(temp_dir)
