class Project(Aggregate):
"""A project containing several samples. You can describe your
projects in the a JSON placed in the repository."""
all_paths = Aggregate.all_paths + """
/info.json
/samples/
"""
def __repr__(self): return '<%s object "%s" with %i samples>' % \
(self.__class__.__name__, self.name, len(self))
def __init__(self, json_path, project_dir):
# Parse the json file describing the project #
self.json_path = FilePath(json_path)
with open(json_path) as handle: self.info = json.load(handle)
# Required parameters #
self.num = self.info['project_num']
self.name = self.info['project_name']
self.long_name = self.info['project_long_name']
# Optional parameters #
self.abstract = self.info.get('abstract')
self.run_name = self.info.get('illumina_run_id')
self.account = self.info.get('uppmax_project_id')
# Base directory #
self.base_dir = project_dir + self.name + '/'
# Delayed init #
self.loaded = False
def load(self):
"""A delayed kind of __init__ that is not called right away to avoid
crowding the RAM of the python interpreter when you just import gefes"""
# Load #
self.loaded = True
# Automatic paths #
self.p = AutoPaths(self.base_dir, self.all_paths)
# Make an alias to the json #
self.json_path.link_to(self.p.info_json, safe=True)
# Make all the samples object that this project possesses #
if self.info.get('auto_parse_samples'):
search_dir = self.info['samples_base_dir']
search_dir = os.path.expanduser(search_dir)
paths = glob.glob(search_dir + '*.fastq*')
if not paths: paths = glob.glob(search_dir + '*.fasta*')
if not paths: raise Exception("Found no FASTA or FASTQ path in %s" % search_dir)
if all([re.search("_R[12]_", p) for p in paths]): pairs = join_paired_filepaths(paths)
else: pairs = sort_string_by_pairs(paths)
self.samples = [Sample(self, p[0], p[1], num=i) for i,p in enumerate(pairs)]
self.samples.sort(key=lambda x: natural_sort(x.name))
else:
self.samples = [Sample(self, info=info) for info in self.info['samples']]
# The samples of a project are it's children in a way #
self.children = self.samples
# Call the mother function #
return Aggregate.load(self)
