Source code for snakemake.output_index

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018-2019, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"

from itertools import chain


[docs]class OutputIndex: def __init__(self, rules): import datrie def prefixes(rule): return (str(o.constant_prefix()) for o in rule.products) def reverse_suffixes(rule): return (str(o.constant_suffix())[::-1] for o in rule.products) def calc_trie(subpatterns): t = datrie.Trie("".join(p for rule in rules for p in subpatterns(rule))) empty = list() for rule in rules: has_empty = False for p in subpatterns(rule): if not p: has_empty = True if p not in t: t[p] = [rule] else: t[p].append(rule) if has_empty: empty.append(rule) return t, empty self.prefix_trie, self.empty_prefix = calc_trie(prefixes) self.suffix_trie, self.empty_suffix = calc_trie(reverse_suffixes)
[docs] def match(self, targetfile): def match_pattern(pattern, trie, empty): return chain(chain.from_iterable(trie.iter_prefix_values(pattern)), empty) f = str(targetfile) hits = set(match_pattern(f, self.prefix_trie, self.empty_prefix)) return hits.intersection( match_pattern(f[::-1], self.suffix_trie, self.empty_suffix) )