cleaning stage 2
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@ -35,10 +35,10 @@ cdef extern from "kmer_similarity.h" nogil:
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OBIDMS_column_p qual_col1,
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OBIDMS_column_p qual_col2,
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uint8_t kmer_size,
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int32_t* kmer_pos_array,
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int32_t** kmer_pos_array,
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int32_t* kmer_pos_array_height_p,
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int32_t* shift_array,
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int32_t** shift_array,
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int32_t* shift_array_height_p,
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int32_t* shift_count_array,
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int32_t** shift_count_array,
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int32_t* shift_count_array_height_p,
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bint build_consensus)
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@ -113,7 +113,7 @@ cdef class Taxonomy(OBIWrapper) :
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raise NotImplementedError()
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cpdef Taxon get_taxon_by_taxid(self, int taxid): # TODO check deleted taxon behavior (403122)
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cpdef Taxon get_taxon_by_taxid(self, int taxid):
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cdef ecotx_t* taxon_p
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cdef object taxon_capsule
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taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer(), taxid)
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@ -256,13 +256,13 @@ cdef class Taxonomy(OBIWrapper) :
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cdef Taxon taxon
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try:
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taxon = self.get_taxon_by_taxid(taxid)
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except: # TODO error handling (related to deleted taxon thing)
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except:
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raise StopIteration
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if taxon is not None:
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while taxon.parent.taxid != 1: # TODO was 0 before?
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while taxon.taxid != 1:
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yield taxon
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taxon = taxon.parent
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yield self[1]
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yield taxon
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else:
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raise StopIteration
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