From 123fb9d7ba36f0a087059367154a980ce38e3c76 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 21 Mar 2018 16:38:26 +0100
Subject: [PATCH] Cython API: in taxonomy, added get_taxon_at_rank() function
 for Taxonomy class and rank_idx property for Taxon class

---
 python/obitools3/dms/taxo/taxo.pxd |  3 ++-
 python/obitools3/dms/taxo/taxo.pyx | 23 +++++++++++++++++++----
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/python/obitools3/dms/taxo/taxo.pxd b/python/obitools3/dms/taxo/taxo.pxd
index 85c4420..0e4cbd0 100644
--- a/python/obitools3/dms/taxo/taxo.pxd
+++ b/python/obitools3/dms/taxo/taxo.pxd
@@ -23,8 +23,9 @@ cdef class Taxonomy(OBIWrapper) :
     cpdef object get_family(self, int taxid)
     cpdef bytes get_scientific_name(self, int taxid)
     cpdef bytes get_rank(self, int taxid)
+    cpdef object get_taxon_at_rank(self, int taxid, object rank)
+
 
-    
 cdef class Taxon :
     cdef ecotx_t*  _pointer
     cdef Taxonomy  _tax
\ No newline at end of file
diff --git a/python/obitools3/dms/taxo/taxo.pyx b/python/obitools3/dms/taxo/taxo.pyx
index 3724ea5..86ebcf4 100644
--- a/python/obitools3/dms/taxo/taxo.pyx
+++ b/python/obitools3/dms/taxo/taxo.pyx
@@ -46,7 +46,7 @@ cdef class Taxonomy(OBIWrapper) :
         taxo._ranks = []
         for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) :
             taxo._ranks.append(obi_taxo_rank_index_to_label(r, (<OBIDMS_taxonomy_p>pointer).ranks))
-        
+                
         return taxo
 
 
@@ -71,7 +71,7 @@ cdef class Taxonomy(OBIWrapper) :
         taxo._ranks = []
         for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) :
             taxo._ranks.append(obi_taxo_rank_index_to_label(r, (<OBIDMS_taxonomy_p>pointer).ranks))
-        
+                
         return taxo
 
     
@@ -157,7 +157,16 @@ cdef class Taxonomy(OBIWrapper) :
         if taxon_p == NULL:
             raise Exception("Error getting a taxon with given taxid", taxid)
         return self._ranks[taxon_p.rank]
-    
+
+
+    cpdef object get_taxon_at_rank(self, int taxid, object rank):
+        if isinstance(rank, str) or isinstance(rank, bytes):
+            rank = self._ranks.index(tobytes(rank))
+        try:
+            return [x.taxid for x in self.parental_tree_iterator(taxid) if x.rank_idx==rank][0]
+        except IndexError:
+            return None
+
     
     def __len__(self):
         return self.pointer().taxa.count
@@ -272,7 +281,7 @@ cdef class Taxon :    # TODO dict subclass?
     def __richcmp__(self, Taxon taxon2, int op):
         return (self.name == taxon2.name) and \
                (self.taxid == taxon2.taxid) and \
-               (self.rank == taxon2.rank) and \
+               (self.rank_idx == taxon2.rank_idx) and \
                (self.farest == taxon2.farest) and \
                (self.parent.taxid == taxon2.parent.taxid) and \
                (self.preferred_name == taxon2.preferred_name)
@@ -293,6 +302,11 @@ cdef class Taxon :    # TODO dict subclass?
     def rank(self):
         return ((self._tax)._ranks)[(self._pointer).rank]
 
+    # rank_idx property getter
+    @property
+    def rank_idx(self):
+        return (self._pointer).rank
+
     # farest property getter
     @property
     def farest(self):
@@ -321,6 +335,7 @@ cdef class Taxon :    # TODO dict subclass?
         d['taxid']          = self.taxid
         d['name']           = self.name
         d['rank']           = self.rank
+        d['rank_idx']       = self.rank_idx
         d['preferred name'] = self.preferred_name
         d['parent']         = self.parent.taxid
         d['farest']         = self.farest