Minor changes in dependencies + minor cleanup

kage/command_line_interface.py

@@ -1,7 +1,6 @@
 import logging
 import sys
 from .util import log_memory_usage_now
-#logging.basicConfig(level=logging.INFO, format='%(module)s %(asctime)s %(levelname)s: %(message)s')
 logging.basicConfig(stream=sys.stdout, level=logging.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
 import itertools
 from itertools import repeat
@@ -40,14 +39,11 @@
 np.random.seed(1)
 np.seterr(all="ignore")
 
-logging.info("Using Python version " + platform.python_version())
-
 
 def main():
     run_argument_parser(sys.argv[1:])
 
 
-
 def analyse_variants(args):
     from .node_count_model import NodeCountModel
     from obgraph.genotype_matrix import MostSimilarVariantLookup
@@ -474,12 +470,9 @@ def analyse_kmer_index(args):
         reverse_kmers = ReverseKmerIndex.from_file(args.reverse_kmer_index)
         index = KmerIndex.from_file(args.kmer_index)
         variant_to_nodes = VariantToNodes.from_file(args.variant_to_nodes)
-
         from .variant_kmer_analyser import VariantKmerAnalyser
         analyser = VariantKmerAnalyser(reverse_kmers, index, variant_to_nodes, args.write_good_variants_to_file)
         analyser.analyse()
-
-
         logging.info("Done")
 
     # Analyse variant kmers
@@ -609,8 +602,6 @@ def create_helper_model(args):
             to_shared_memory(model, "model"+args.shared_memory_unique_id)
             logging.info("Put data in shared memory")
 
-            # genotyped_variants = VcfVariants(header_lines=variants.get_header())
-
             for from_variant, to_variant, subhelpers, subcombo in pool.imap(create_helper_model_single_thread,
                                                                               zip(variant_intervals, repeat(args))):
                 logging.info("Done with one chunk")

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, Extension
 
 setup(name='kage-genotyper',
-      version='0.0.16',
+      version='0.0.18',
       description='KAGE',
       long_description_content_type="text/markdown",
       url='http://github.com/ivargr/kage',
@@ -12,9 +12,10 @@
       zip_safe=False,
       install_requires=['numpy', 'tqdm', 'pyfaidx', 'pathos', 'cython', 'scipy',
                         'obgraph>=0.0.8',
-                        'graph_kmer_index>=0.0.12',
-                        'kmer_mapper',
-                        'graph_read_simulator', 'shared_memory_wrapper'
+                        'graph_kmer_index>=0.0.14',
+                        'kmer_mapper>=0.0.15',
+                        'graph_read_simulator',
+                        'shared_memory_wrapper>=0.0.4'
                         ],
       include_dirs=["."],
       classifiers=[

tests/test_genotyping.py

@@ -10,7 +10,7 @@
 from kage.combination_model_genotyper import CombinationModelGenotyper
 from kage.helper_index import make_helper_model_from_genotype_matrix,make_helper_model_from_genotype_matrix_and_node_counts
 
-class Tester:
+class Helper:
     def __init__(self):
 
         self.n_nodes = 8
@@ -24,7 +24,7 @@ def prepare(self):
 
         self.variant_to_nodes = VariantToNodes(np.array([1, 2, 3, 4]), np.array([5, 6, 7, 8]))
         self.most_simliar_variant_lookup = MostSimilarVariantLookup(np.arange(self.n_variants)-1, np.ones(self.n_variants))
-        self.node_count_model = NodeCountModelAdvanced(np.zeros(self.max_node_id), np.zeros(self.max_node_id), np.zeros(self.max_node_id), np.zeros((self.max_node_id, 5)), np.zeros(self.max_node_id, dtype=np.bool))
+        self.node_count_model = NodeCountModelAdvanced(np.zeros(self.max_node_id), np.zeros(self.max_node_id), np.zeros(self.max_node_id), np.zeros((self.max_node_id, 5)), np.zeros(self.max_node_id, dtype=bool))
        # self.helper_variants, self.genotype_combo_matrix = make_helper_model_from_genotype_matrix(self.genotype_matrix, self.most_simliar_variant_lookup)
         self.helper_variants, self.genotype_combo_matrix = \
             make_helper_model_from_genotype_matrix_and_node_counts(self.genotype_matrix, self.node_count_model, self.variant_to_nodes)
@@ -106,7 +106,7 @@ def testcase2(self):
         for variant in input_variants:
             assert variant.genotype == "0/0"
 
-tester = Tester()
+tester = Helper()
 
 def test1():
     tester.testcase_all_homo_alt()