def has_trait(self, trait):
h5files = fsutils.get_h5files_in_dir(self.search_path, self.trait_dir)
for h5file in h5files:
service = trait_service.TraitService(h5file=h5file)
if service.has_trait(trait):
return True
raise NotFoundError("Trait " + trait)
def has_gene(self, gene):
service = trait_service.TraitService(self.trait_file)
#search = cr.search_all_assocs(gene=gene, start=0, size=0, properties=self.properties)
#if search[-1] > 0:
# return True
if service.has_gene(gene):
return True
raise NotFoundError("Gene " + gene)
def has_trait(self, trait):
service = trait_service.TraitService(self.trait_file)
#search = cr.search_all_assocs(trait=trait, start=0, size=0, properties=self.properties)
#if search[-1] > 0:
# return True
if service.has_trait(trait):
return True
raise NotFoundError("Trait " + trait)
def _get_traversed_size(self, retrieved_index, trait):
if retrieved_index == 0:
h5file = fsutils.create_h5file_path(self.search_path, dir_name=self.trait_dir, file_name=trait)
service = trait_service.TraitService(h5file)
trait_size = service.get_trait_size(trait)
service.close_file()
return trait_size
return retrieved_index
def get_list_of_traits(self):
traits = []
h5files = fsutils.get_h5files_in_dir(self.search_path, self.trait_dir)
for h5file in h5files:
service = trait_service.TraitService(h5file=h5file)
traits.extend(service.list_traits())
service.close_file()
return sorted(traits)
def chrom_for_trait(self):
#h5file = fsutils.create_h5file_path(self.search_path, self.trait_dir, self.trait_file)
trait_service = ts.TraitService(self.trait_file)
chroms = trait_service.chrom_from_trait(self.trait)
if len(chroms) == 1:
self.chromosome = chroms[0]
elif len(chroms) > 1:
logger.debug("more than one chrom for this trait?"
) # need to handle this error
else:
logger.debug(
"No chrom for this trait?") # need to handle this error
def __init__(self, trait, start, size, config_properties=None):
self.trait = trait
self.start = start
self.size = size
self.properties = properties_handler.get_properties(config_properties)
self.search_path = properties_handler.get_search_path(self.properties)
self.trait_dir = self.properties.trait_dir
self.datasets = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
# index marker will be returned along with the datasets
# it is the number that when added to the 'start' value that we started the query with
# will pinpoint where the next search needs to continue from
self.index_marker = 0
self.h5file = fsutils.create_h5file_path(self.search_path,
dir_name=self.trait_dir,
file_name=trait)
if not os.path.isfile(self.h5file):
raise NotFoundError("Trait " + trait)
self.service = trait_service.TraitService(self.h5file)
self.max_size_of_trait = self.service.get_trait_size(self.trait)
def get_list_of_genes(self):
service = trait_service.TraitService(self.trait_file)
genes = service.list_genes()
return genes
def get_list_of_traits(self):
service = trait_service.TraitService(self.trait_file)
traits = service.list_traits()
return traits