removed six imports, __future__ imports, added Apache license headers…

… where missing

setup.py

@@ -11,7 +11,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function
 import os
 import re
 

tests/__init__.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/benchmark_vcf_load.py

@@ -1,3 +1,15 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """
 Time how long it takes to open a VCF.
 

tests/common.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/data.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_cli_effects.py

@@ -1,3 +1,15 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from tempfile import NamedTemporaryFile
 import pandas as pd
 

tests/test_cli_genes.py

@@ -1,3 +1,15 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from varcode.cli.genes_script import main as run_script
 from .data import ov_wustle_variants, db_snp_variants
 

tests/test_collection_filtering.py

@@ -10,9 +10,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from nose.tools import eq_
-from varcode import VariantCollection
 
+from varcode import VariantCollection
+from .common import eq_
 from .data import (
     snp_rs4244285,
     snp_rs1537415

tests/test_common.py

@@ -10,8 +10,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from nose.tools import eq_
 import varcode
+from .common import eq_
 
 def test_memoize():
     class State(object):

tests/test_effect_collection.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_effect_collection_serialization.py

@@ -1,4 +1,16 @@
 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import pickle
 
 from varcode import EffectCollection

tests/test_exonic_splice_site.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2018. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_frameshift_helpers.py

@@ -1,3 +1,15 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from varcode.effects.effect_prediction_coding_frameshift import (
     cdna_codon_sequence_after_insertion_frameshift,
     cdna_codon_sequence_after_deletion_or_substitution_frameshift,

tests/test_mm10_klf6_frameshift.py

@@ -1,3 +1,15 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from varcode import Variant
 from varcode.effects import FrameShift
 from varcode.effects.effect_prediction_coding_frameshift import (

tests/test_mouse.py

@@ -1,4 +1,14 @@
-from __future__ import absolute_import
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 from .common import eq_
 

tests/test_mutate.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_no_duplicate_variants.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_string_helpers.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_timings.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_variant.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

tests/test_variant_collection.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

varcode/cli/__init__.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from .variant_args import (
     add_variant_args,
     make_variants_parser,

varcode/cli/effects_script.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import division, absolute_import
-
 import logging.config
 import pkg_resources
 import sys

varcode/cli/genes_script.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import division, absolute_import
 import logging
 import logging.config
 import pkg_resources

varcode/cli/variant_args.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 from argparse import ArgumentParser
 
 from ..vcf import load_vcf

varcode/cli/version_info.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2018. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from collections import OrderedDict
 from os.path import dirname
 from .. import __file__ as package_init_file_path

varcode/common.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 from collections import defaultdict
 
 from functools import wraps

varcode/effects/__init__.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

varcode/effects/common.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,15 +10,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from Bio.Seq import Seq
-from six import string_types, text_type
+
 
 
 def bio_seq_to_str(seq):
-    if isinstance(seq, Seq):
-        return str(seq)
-    elif isinstance(seq, string_types):
-        return text_type(seq)
-    return seq
+    if type(seq) is str:
+        return seq
+    else:
+        return str(seq) 
+

varcode/effects/effect_classes.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2018. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 
 from memoized_property import memoized_property
 from serializable import Serializable

varcode/effects/effect_collection.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 from collections import OrderedDict
 
 import pandas as pd

varcode/effects/effect_helpers.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -16,7 +14,6 @@
 Helper functions for determine effect annotation for a variant
 """
 
-from __future__ import print_function, division, absolute_import
 
 from ..nucleotides import PURINE_NUCLEOTIDES, AMINO_NUCLEOTIDES
 

varcode/effects/effect_ordering.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from .effect_classes import (
     Failure,
     IncompleteTranscript,