Merge pull request #50 from Ecogenomics/pierre_dev

bug fixed when pplacer_leaf < 95% ANI
Ecogenomics · Sep 21, 2018 · 572aec8 · 572aec8
2 parents d5f1cdb + 7a5935e
commit 572aec8
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diff --git a/gtdbtk/VERSION b/gtdbtk/VERSION
@@ -1,3 +1,5 @@
+0.1.3
+- v0.1.3 resolves bug that would occur when a user genome has a FastANI >= 95% with reference genomes but not with the closest pplacer leaf node. 
 0.1.2
 - resolve bug that would occasionally cause genomes to not be correctly associated with a reference genome in the pplacer tree. FastANI was still identifying correct species assignments.
 0.1.1

diff --git a/gtdbtk/classify.py b/gtdbtk/classify.py
@@ -613,10 +613,10 @@ def _sort_fastani_results(self, fastani_verification, all_fastani_dict, summaryf
                     else:
                         taxa_str = taxa_str[0:taxa_str.rindex(';')]
                         summary_list[1] = self.standardise_taxonomy(taxa_str)
+                        summary_list[6] = pplacer_leafnode
+                        summary_list[7] = ";".join(self.gtdb_taxonomy.get(
+                            add_ncbi_prefix(pplacer_leafnode)))
                         if pplacer_leafnode in all_fastani_dict.get(userleaf.taxon.label):
-                            summary_list[6] = pplacer_leafnode
-                            summary_list[7] = ";".join(self.gtdb_taxonomy.get(
-                                add_ncbi_prefix(pplacer_leafnode)))
                             summary_list[8] = all_fastani_dict.get(
                                 userleaf.taxon.label).get(pplacer_leafnode).get('ani')
                             summary_list[9] = all_fastani_dict.get(