Handle sketchlib import error

bacpop · Feb 7, 2020 · ccaa02d · ccaa02d
1 parent 790c290
commit ccaa02d
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/PopPUNK/__main__.py b/PopPUNK/__main__.py
@@ -211,6 +211,8 @@ def main():
     kmers = np.arange(args.min_k, args.max_k + 1, args.k_step)
 
     # Dict of DB access functions for assign_query (which is out of scope)
+    if no_sketchlib:
+        args.use_mash = True
     dbFuncs = setupDBFuncs(args, kmers, args.min_kmer_count)
     createDatabaseDir = dbFuncs['createDatabaseDir']
     constructDatabase = dbFuncs['constructDatabase']

diff --git a/PopPUNK/sketchlib.py b/PopPUNK/sketchlib.py
@@ -21,9 +21,15 @@
 import sharedmem
 import networkx as nx
 from scipy import optimize
-import h5py
 
-import pp_sketchlib
+# Try to import sketchlib
+try:
+    no_sketchlib = False
+    import pp_sketchlib
+    import h5py
+except ImportError as e:
+    sys.stderr.write("Sketchlib backend not available")
+    no_sketchlib = True
 
 from .mash import fitKmerCurve
 from .utils import iterDistRows