How to use the prophyle.prophyle_assignment.KraklineParser function in prophyle

To help you get started, we’ve selected a few prophyle examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github prophyle / prophyle / prophyle / prophyle_assignment.py View on Github external
def __init__(
        self, output_fo, tree_index, kmer_lca=False, tie_lca=False, annotate=False, mask_unmatched_bases=False
    ):
        self.output_fo = output_fo
        self.tree_index = tree_index
        self.k = self.tree_index.k
        self.kmer_lca = kmer_lca
        self.annotate = annotate
        self.tie_lca = tie_lca
        self.mask_unmatched_bases = mask_unmatched_bases

        self.krakline_parser = KraklineParser()

        self.hitmasks_dict = {}
        self.covmasks_dict = {}
        self.ass_dict = {}

        self.max_nodenames = []
        self.max_val = 0
github prophyle / prophyle / prophyle / prophyle_assignment.py View on Github external
def __init__(self, output_fo, tree_index, kmer_lca=False, tie_lca=False, annotate=False):
        self.output_fo = output_fo
        self.tree_index = tree_index
        self.k = self.tree_index.k
        self.kmer_lca = kmer_lca
        self.annotate = annotate
        self.tie_lca = tie_lca

        self.krakline_parser = KraklineParser()

        self.hitmasks_dict = {}
        self.covmasks_dict = {}
        self.ass_dict = {}

        self.max_nodenames = []
        self.max_val = 0