From ccaa02de609571287f6b3e7684e6e70bf2bad237 Mon Sep 17 00:00:00 2001
From: John Lees <lees.john6@gmail.com>
Date: Fri, 7 Feb 2020 14:30:50 +0000
Subject: [PATCH] Handle sketchlib import error

---
 PopPUNK/__main__.py  |  2 ++
 PopPUNK/sketchlib.py | 10 ++++++++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/PopPUNK/__main__.py b/PopPUNK/__main__.py
index 2e9a292b..23f0c5c8 100644
--- 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
index 260b9e66..df40cd36 100644
--- 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