def _construct_links_of_interest(self):
"""Construct an iterator for all pairs of annotation terms to be
tested.
"""
if self.opts.selected_links:
links, num_links = self.parse_selected_links(self.opts.selected_links)
elif self.opts.selected_terms or self.opts.selected_terms_with_all:
if self.opts.selected_terms:
selected_terms_file_name = self.opts.selected_terms
else:
selected_terms_file_name = self.opts.selected_terms_with_all
logger.info("Parsing selected terms file %s." % selected_terms_file_name)
selected_terms_file = open(selected_terms_file_name, "rb")
num_selected_terms = convutils.count_lines(selected_terms_file)
selected_terms = parsers.parse_selected_terms_file(selected_terms_file)
if self.opts.selected_terms:
num_links = self._calc_num_links_selected_terms(num_selected_terms)
links = self.make_selected_terms_links(selected_terms)
else:
num_links = self._calc_num_links_selected_with_all(num_selected_terms)
links = self.make_selected_terms_links_with_all(selected_terms, self.annotations_dict)
else:
links, num_links = self.make_all_possible_links(self.annotations_dict)
self.links, self.num_links = links, num_links
def parse_selected_links(self, selected_links_file_name):
logger.info("Parsing selected links file %s." % selected_links_file_name)
selected_links_file = open(selected_links_file_name, "rb")
num_links = convutils.count_lines(selected_links_file)
# Reset the file to the beginning to parse it.
selected_links_file.seek(0)
links = parsers.parse_selected_links_file(selected_links_file)
return links, num_links