fix import of skani tool

broadinstitute · Mar 18, 2024 · 3c56bbb · 3c56bbb
1 parent 2294d78
commit 3c56bbb
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/assembly.py b/assembly.py
@@ -41,6 +41,7 @@
 import assemble.mummer
 import assemble.muscle
 import assemble.gap2seq
+import assemble.skani
 
 # third-party
 import numpy
@@ -381,7 +382,7 @@ def parser_gapfill_gap2seq(parser=argparse.ArgumentParser(description='Close gap
 def cluster_references_ani(inRefs, outClusters, threads=None):
     ''' This step uses the skani triangle tool to define clusters of highly-related genomes.
     '''
-    skani = tools.skani.SkaniTool()
+    skani = assemble.skani.SkaniTool()
     clusters = skani.find_reference_clusters(inRefs, threads=threads)
     with open(outClusters, 'w') as outf:
         for cluster in clusters:
@@ -399,7 +400,7 @@ def parser_cluster_references_ani(parser=argparse.ArgumentParser(description='Cl
 
 def skani_contigs_to_refs(inContigs, inRefs, out_skani_dist, out_skani_dist_filtered, out_clusters_filtered, threads=None):
 
-    skani = tools.skani.SkaniTool()
+    skani = assemble.skani.SkaniTool()
     clusters = skani.find_reference_clusters(inRefs, threads=threads)
     skani.find_closest_references(inContigs, inRefs, out_skani_dist, threads=threads)
     refs_hit = set()

diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py
@@ -17,6 +17,7 @@
 import itertools
 import pytest
 import assemble.mummer
+import assemble.skani
 import tools.minimap2
 import tools.novoalign
 import tools.picard