Merge branch 'dev'

.travis.yml

@@ -10,7 +10,8 @@ install:
   - pip install -U cython
   - pip install -U numpy
   - pip install -U pandas $(if [[ "$TRAVIS_PYTHON_VERSION" == "3.4" ]]; then echo "--no-build-isolation"; fi)
-  - pip install -U biopython pyplink pybgen cyvcf2
+  - pip install -U biopython pyplink pybgen
+  - pip install 'cyvcf2<0.10'
   - pip list
 
 script: python setup.py test

geneparse/__init__.py

@@ -61,6 +61,7 @@ def __call__(self, pattern, *args, **kwargs):
 
         # Explode the path for every possible chromosome.
         chrom_to_reader = {}
+        last_exception = None
         for chrom in list(range(1, 23)) + ["X", "Y", "XY", "MT"]:
             chrom = str(chrom)
             cur = re.sub("{chrom}", chrom, pattern)
@@ -69,8 +70,15 @@ def __call__(self, pattern, *args, **kwargs):
                 chrom_to_reader[chrom] = self.reader_class(
                     cur, *args, **kwargs
                 )
-            except:
-                pass
+            except Exception as e:
+                last_exception = e
+
+        if len(chrom_to_reader) == 0:
+            raise ValueError(
+                "Could not initialize any genotype reader for chromosomes 1 "
+                "to 22 or X, Y, XY, MT.\nLast exception was: {}."
+                "".format(last_exception)
+            )
 
         return SplitChromosomeReader(chrom_to_reader)
 

geneparse/readers/vcf.py

@@ -27,12 +27,23 @@
 
 from ..core import Variant, ImputedVariant, Genotypes, GenotypesReader
 
-from cyvcf2 import VCF
 import numpy as np
 
+try:
+    from cyvcf2 import VCF
+    CYVCF2_AVAILABLE = True
+except ImportError:
+    CYVCF2_AVAILABLE = False
+
 
 class VCFReader(GenotypesReader):
     def __init__(self, filename, quality_field=None):
+        if not CYVCF2_AVAILABLE:
+            raise RuntimeError(
+                "cyvcf2 is not installed. Install cyvcf2 (from source or "
+                "using `pip install cyvcf2`) to use the VCF reader."
+            )
+
         self.get_vcf = lambda: VCF(filename)
         self.quality_field = quality_field
 

geneparse/tests/test_vcf.py

@@ -50,6 +50,7 @@
 }
 
 
+@unittest.skipIf(not vcf.CYVCF2_AVAILABLE, "cyvcf2 is not installed")
 class TestVCF(TestContainer, unittest.TestCase):
     @classmethod
     def setUpClass(cls):

setup.py

@@ -15,7 +15,7 @@
 
 MAJOR = 0
 MINOR = 7
-MICRO = 4
+MICRO = 5
 VERSION = "{0}.{1}.{2}".format(MAJOR, MINOR, MICRO)
 
 
@@ -63,8 +63,7 @@ def setup_package():
         zip_safe=False,
         install_requires=["numpy >= 1.11.0", "pandas >= 0.19.0",
                           "pyplink >= 1.3.4", "setuptools >= 26.1.0",
-                          "cyvcf2 >= 0.7.4", "biopython >= 1.68",
-                          "pybgen >= 0.5.0"],
+                          "biopython >= 1.68", "pybgen >= 0.5.0"],
         packages=find_packages(),
         package_data={"geneparse.tests": ["data/*", "data/*/*"]},
         classifiers=["Development Status :: 4 - Beta",