cleaning stage 2

This commit is contained in:
2019-03-29 16:46:17 +01:00
46 changed files with 240 additions and 2223 deletions

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@ -35,10 +35,10 @@ cdef extern from "kmer_similarity.h" nogil:
OBIDMS_column_p qual_col1,
OBIDMS_column_p qual_col2,
uint8_t kmer_size,
int32_t* kmer_pos_array,
int32_t** kmer_pos_array,
int32_t* kmer_pos_array_height_p,
int32_t* shift_array,
int32_t** shift_array,
int32_t* shift_array_height_p,
int32_t* shift_count_array,
int32_t** shift_count_array,
int32_t* shift_count_array_height_p,
bint build_consensus)

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@ -113,7 +113,7 @@ cdef class Taxonomy(OBIWrapper) :
raise NotImplementedError()
cpdef Taxon get_taxon_by_taxid(self, int taxid): # TODO check deleted taxon behavior (403122)
cpdef Taxon get_taxon_by_taxid(self, int taxid):
cdef ecotx_t* taxon_p
cdef object taxon_capsule
taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer(), taxid)
@ -256,13 +256,13 @@ cdef class Taxonomy(OBIWrapper) :
cdef Taxon taxon
try:
taxon = self.get_taxon_by_taxid(taxid)
except: # TODO error handling (related to deleted taxon thing)
except:
raise StopIteration
if taxon is not None:
while taxon.parent.taxid != 1: # TODO was 0 before?
while taxon.taxid != 1:
yield taxon
taxon = taxon.parent
yield self[1]
yield taxon
else:
raise StopIteration