def info(args):
input_dirs = args.input_dirs
if input_dirs is None:
logging.error('Please specify SSEA directories using "-d" or "--dir"')
return 1
for path in find_paths(input_dirs):
sample_set_json_file = os.path.join(path, Config.SAMPLE_SET_JSON_FILE)
sample_set = SampleSet.parse_json(sample_set_json_file)[0]
compname = computerize_name(sample_set.name)
print '\t'.join([compname, path])
def info(args):
input_dirs = args.input_dirs
if input_dirs is None:
logging.error('Please specify SSEA directories using "-d" or "--dir"')
return 1
for path in find_paths(input_dirs):
sample_set_json_file = os.path.join(path, Config.SAMPLE_SET_JSON_FILE)
sample_set = SampleSet.parse_json(sample_set_json_file)[0]
compname = computerize_name(sample_set.name)
print '\t'.join([compname, path])
def to_smx(args):
filename = args.sample_set_file
sep = args.sep
prefix = args.prefix
if not os.path.exists(filename):
logging.error("Sample set file '%s' not found" % (filename))
return 1
for ss in _parse_sample_sets(filename, sep):
lines = []
lines.append('\t'.join(['name', ss.name]))
lines.append('\t'.join(['desc', ss.desc]))
for sample in sorted(ss.value_dict):
lines.append('\t'.join([sample, str(ss.value_dict[sample])]))
suffix = computerize_name(ss.name)
path = prefix + '.' + suffix + '.smx'
with open(path, 'w') as f:
for line in lines:
print >>f, line
def merge(args):
# get args
input_paths_file = args.input_paths_file
input_dirs = args.input_dirs
output_dir = args.output_dir
# check args
input_paths = set()
if input_paths_file is not None:
if not os.path.exists(input_paths_file):
logging.error('Input paths file "%s" not found' %
(input_paths_file))
else:
with open(input_paths_file) as fileh:
for line in fileh:
path = line.strip()
if check_path(path):
input_paths.add(path)
if input_dirs is not None:
input_paths.update(find_paths(input_dirs))
if len(input_paths) == 0:
logging.error('No valid SSEA results directories found.. Exiting.')
return 1
if not os.path.exists(output_dir):
logging.debug('Creating output directory "%s"' % (output_dir))
os.makedirs(output_dir)
# read paths already in output directory
existing_paths = set()
for path in glob.iglob(os.path.join(output_dir, "*")):
if os.path.exists(path) and os.path.isdir(path):
existing_paths.add(path)
# merge input paths
for src in input_paths:
sample_set_json_file = os.path.join(src, Config.SAMPLE_SET_JSON_FILE)
sample_set = SampleSet.parse_json(sample_set_json_file)[0]
dirname = computerize_name(sample_set.name)
dst = os.path.join(output_dir, dirname)
if os.path.exists(dst):
logging.error(
'Conflict when merging sample set name "%s" from path "%s"' %
(sample_set.name, src))
else:
logging.debug('Moving sample set "%s" from "%s" to "%s"' %
(sample_set.name, src, dst))
shutil.move(src, dst)
def merge(args):
# get args
input_paths_file = args.input_paths_file
input_dirs = args.input_dirs
output_dir = args.output_dir
# check args
input_paths = set()
if input_paths_file is not None:
if not os.path.exists(input_paths_file):
logging.error('Input paths file "%s" not found' % (input_paths_file))
else:
with open(input_paths_file) as fileh:
for line in fileh:
path = line.strip()
if check_path(path):
input_paths.add(path)
if input_dirs is not None:
input_paths.update(find_paths(input_dirs))
if len(input_paths) == 0:
logging.error('No valid SSEA results directories found.. Exiting.')
return 1
if not os.path.exists(output_dir):
logging.debug('Creating output directory "%s"' % (output_dir))
os.makedirs(output_dir)
# read paths already in output directory
existing_paths = set()
for path in glob.iglob(os.path.join(output_dir, "*")):
if os.path.exists(path) and os.path.isdir(path):
existing_paths.add(path)
# merge input paths
for src in input_paths:
sample_set_json_file = os.path.join(src, Config.SAMPLE_SET_JSON_FILE)
sample_set = SampleSet.parse_json(sample_set_json_file)[0]
dirname = computerize_name(sample_set.name)
dst = os.path.join(output_dir, dirname)
if os.path.exists(dst):
logging.error('Conflict when merging sample set name "%s" from path "%s"' % (sample_set.name, src))
else:
logging.debug('Moving sample set "%s" from "%s" to "%s"' % (sample_set.name, src, dst))
shutil.move(src, dst)
def info(args):
filename = args.sample_set_file
sep = args.sep
if not os.path.exists(filename):
logging.error("Sample set file '%s' not found" % (filename))
return 1
print '\t'.join(['compname', 'name', 'desc', 'total', 'hits',
'misses', 'nas'])
for ss in _parse_sample_sets(filename, sep):
hits = 0
misses = 0
nas = 0
tot = 0
for v in ss.value_dict.itervalues():
if v == 1:
hits += 1
elif v == 0:
misses += 1
else:
nas += 1
tot += 1
print '\t'.join(map(str, [computerize_name(ss.name), ss.name, ss.desc, tot, hits, misses, nas]))
def extract(args):
list_file = args.sample_set_list_file
sample_set_file = args.sample_set_file
sep = args.sep
if not os.path.exists(sample_set_file):
logging.error("Sample set file '%s' not found" % (sample_set_file))
return 1
compname_dict = {}
name_dict = {}
for ss in _parse_sample_sets(sample_set_file, sep):
compname_dict[computerize_name(ss.name)] = ss
name_dict[ss.name] = ss
with open(list_file) as fileh:
for line in fileh:
name = line.strip()
found = False
if name in compname_dict:
print compname_dict[name].to_json()
found = True
elif name in name_dict:
print name_dict[name].to_json()
found = True
if not found:
logging.error('Sample set "%s" not found' % (name))