diff --git a/setup.py b/setup.py index 7a22020..ccaf017 100644 --- a/setup.py +++ b/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 diff --git a/tests/__init__.py b/tests/__init__.py index 63a267b..1ae7f0c 100644 --- a/tests/__init__.py +++ b/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 diff --git a/tests/benchmark_vcf_load.py b/tests/benchmark_vcf_load.py index af1476d..0210b46 100644 --- a/tests/benchmark_vcf_load.py +++ b/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. diff --git a/tests/common.py b/tests/common.py index 999c76f..908dbfc 100644 --- a/tests/common.py +++ b/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 diff --git a/tests/data.py b/tests/data.py index 0335921..79ac90a 100644 --- a/tests/data.py +++ b/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 diff --git a/tests/test_cli_effects.py b/tests/test_cli_effects.py index 3f8c54f..657d907 100644 --- a/tests/test_cli_effects.py +++ b/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 diff --git a/tests/test_cli_genes.py b/tests/test_cli_genes.py index 79c347a..06c9a60 100644 --- a/tests/test_cli_genes.py +++ b/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 diff --git a/tests/test_collection_filtering.py b/tests/test_collection_filtering.py index c68cc25..964d242 100644 --- a/tests/test_collection_filtering.py +++ b/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 diff --git a/tests/test_common.py b/tests/test_common.py index a2cdad0..dee73af 100644 --- a/tests/test_common.py +++ b/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): diff --git a/tests/test_effect_collection.py b/tests/test_effect_collection.py index 859784b..e0d6c7a 100644 --- a/tests/test_effect_collection.py +++ b/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 diff --git a/tests/test_effect_collection_serialization.py b/tests/test_effect_collection_serialization.py index c172f73..514a559 100644 --- a/tests/test_effect_collection_serialization.py +++ b/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 diff --git a/tests/test_exonic_splice_site.py b/tests/test_exonic_splice_site.py index e756561..63b53dd 100644 --- a/tests/test_exonic_splice_site.py +++ b/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 diff --git a/tests/test_frameshift_helpers.py b/tests/test_frameshift_helpers.py index 9b1dea7..6f7c725 100644 --- a/tests/test_frameshift_helpers.py +++ b/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, diff --git a/tests/test_mm10_klf6_frameshift.py b/tests/test_mm10_klf6_frameshift.py index 4aade48..3012bea 100644 --- a/tests/test_mm10_klf6_frameshift.py +++ b/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 ( diff --git a/tests/test_mouse.py b/tests/test_mouse.py index d3cd588..319e916 100644 --- a/tests/test_mouse.py +++ b/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_ diff --git a/tests/test_mutate.py b/tests/test_mutate.py index 64c4b0a..258758d 100644 --- a/tests/test_mutate.py +++ b/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 diff --git a/tests/test_no_duplicate_variants.py b/tests/test_no_duplicate_variants.py index 11a061e..6c88f61 100644 --- a/tests/test_no_duplicate_variants.py +++ b/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 diff --git a/tests/test_string_helpers.py b/tests/test_string_helpers.py index ae5592e..0fbc8a5 100644 --- a/tests/test_string_helpers.py +++ b/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 diff --git a/tests/test_timings.py b/tests/test_timings.py index 92c3cb9..3666889 100644 --- a/tests/test_timings.py +++ b/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 diff --git a/tests/test_variant.py b/tests/test_variant.py index 0a4acf2..894ab65 100644 --- a/tests/test_variant.py +++ b/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 diff --git a/tests/test_variant_collection.py b/tests/test_variant_collection.py index 1b628dd..5efa15f 100644 --- a/tests/test_variant_collection.py +++ b/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 diff --git a/varcode/cli/__init__.py b/varcode/cli/__init__.py index f21d5b4..693cc44 100644 --- a/varcode/cli/__init__.py +++ b/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, diff --git a/varcode/cli/effects_script.py b/varcode/cli/effects_script.py index 22094a4..475671b 100644 --- a/varcode/cli/effects_script.py +++ b/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 diff --git a/varcode/cli/genes_script.py b/varcode/cli/genes_script.py index 16f8441..146d454 100644 --- a/varcode/cli/genes_script.py +++ b/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 diff --git a/varcode/cli/variant_args.py b/varcode/cli/variant_args.py index 810c089..756415a 100644 --- a/varcode/cli/variant_args.py +++ b/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 diff --git a/varcode/cli/version_info.py b/varcode/cli/version_info.py index 11b0e6f..e083dc6 100644 --- a/varcode/cli/version_info.py +++ b/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 diff --git a/varcode/common.py b/varcode/common.py index 799a264..5c5020d 100644 --- a/varcode/common.py +++ b/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 diff --git a/varcode/effects/__init__.py b/varcode/effects/__init__.py index 21f2e51..c98462b 100644 --- a/varcode/effects/__init__.py +++ b/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 diff --git a/varcode/effects/common.py b/varcode/effects/common.py index c14256d..d39358f 100644 --- a/varcode/effects/common.py +++ b/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) + \ No newline at end of file diff --git a/varcode/effects/effect_classes.py b/varcode/effects/effect_classes.py index 978cfef..5bb544a 100644 --- a/varcode/effects/effect_classes.py +++ b/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 diff --git a/varcode/effects/effect_collection.py b/varcode/effects/effect_collection.py index b8d88a0..de1f381 100644 --- a/varcode/effects/effect_collection.py +++ b/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 diff --git a/varcode/effects/effect_helpers.py b/varcode/effects/effect_helpers.py index 4eb840f..0f6aff8 100644 --- a/varcode/effects/effect_helpers.py +++ b/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 diff --git a/varcode/effects/effect_ordering.py b/varcode/effects/effect_ordering.py index f13c07d..38f6112 100644 --- a/varcode/effects/effect_ordering.py +++ b/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, diff --git a/varcode/effects/effect_prediction.py b/varcode/effects/effect_prediction.py index b45fb7a..f38b80a 100644 --- a/varcode/effects/effect_prediction.py +++ b/varcode/effects/effect_prediction.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 import logging from Bio.Seq import reverse_complement diff --git a/varcode/effects/effect_prediction_coding.py b/varcode/effects/effect_prediction_coding.py index 768ab7e..7069a9b 100644 --- a/varcode/effects/effect_prediction_coding.py +++ b/varcode/effects/effect_prediction_coding.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 .effect_prediction_coding_frameshift import predict_frameshift_coding_effect from .effect_prediction_coding_in_frame import predict_in_frame_coding_effect diff --git a/varcode/effects/effect_prediction_coding_frameshift.py b/varcode/effects/effect_prediction_coding_frameshift.py index cd3a9c9..7a17261 100644 --- a/varcode/effects/effect_prediction_coding_frameshift.py +++ b/varcode/effects/effect_prediction_coding_frameshift.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 @@ -17,8 +15,6 @@ reading frame. """ -from __future__ import print_function, division, absolute_import - from ..string_helpers import trim_shared_prefix from .effect_classes import ( diff --git a/varcode/effects/effect_prediction_coding_in_frame.py b/varcode/effects/effect_prediction_coding_in_frame.py index af0d329..58e1c38 100644 --- a/varcode/effects/effect_prediction_coding_in_frame.py +++ b/varcode/effects/effect_prediction_coding_in_frame.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 @@ -16,7 +14,6 @@ Effect annotation for variants which modify the coding sequence without changing the reading frame. """ -from __future__ import division, absolute_import, print_function from ..string_helpers import trim_shared_flanking_strings from .effect_classes import ( diff --git a/varcode/effects/mutate.py b/varcode/effects/mutate.py index 76c53d2..77f3be7 100644 --- a/varcode/effects/mutate.py +++ b/varcode/effects/mutate.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 - def insert_before(sequence, offset, new_residues): """Mutate the given sequence by inserting the string `new_residues` before diff --git a/varcode/effects/transcript_helpers.py b/varcode/effects/transcript_helpers.py index 3483183..186e944 100644 --- a/varcode/effects/transcript_helpers.py +++ b/varcode/effects/transcript_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 @@ -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 - def interval_offset_on_transcript(start, end, transcript): """ diff --git a/varcode/effects/translate.py b/varcode/effects/translate.py index 174280d..016015d 100644 --- a/varcode/effects/translate.py +++ b/varcode/effects/translate.py @@ -1,4 +1,3 @@ -# # 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 @@ -16,8 +15,6 @@ TODO: generalize this to work with the mitochondrial codon table. """ -from __future__ import division, absolute_import, print_function - from Bio.Data import CodonTable from Bio.Seq import Seq diff --git a/varcode/maf.py b/varcode/maf.py index 556d7fe..fba4220 100644 --- a/varcode/maf.py +++ b/varcode/maf.py @@ -1,5 +1,3 @@ -# Copyright (c) 2016-2017. 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 import logging import pandas diff --git a/varcode/nucleotides.py b/varcode/nucleotides.py index d20c71e..28ba029 100644 --- a/varcode/nucleotides.py +++ b/varcode/nucleotides.py @@ -1,4 +1,3 @@ -# # 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 diff --git a/varcode/reference.py b/varcode/reference.py index 34177e0..8b8be26 100644 --- a/varcode/reference.py +++ b/varcode/reference.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 diff --git a/varcode/string_helpers.py b/varcode/string_helpers.py index d792bb7..efeed07 100644 --- a/varcode/string_helpers.py +++ b/varcode/string_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 diff --git a/varcode/ucsc_reference_names.py b/varcode/ucsc_reference_names.py index 07adf8d..3649965 100644 --- a/varcode/ucsc_reference_names.py +++ b/varcode/ucsc_reference_names.py @@ -1,5 +1,3 @@ -# Copyright (c) 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 diff --git a/varcode/util.py b/varcode/util.py index e1fc750..61fc698 100644 --- a/varcode/util.py +++ b/varcode/util.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 @@ -12,11 +10,9 @@ # See the License for the specific language governing permissions and # limitations under the License. -from __future__ import print_function, division, absolute_import import random from Bio.Seq import reverse_complement -from pyensembl import EnsemblRelease from pyensembl import genome_for_reference_name from .nucleotides import STANDARD_NUCLEOTIDES diff --git a/varcode/variant.py b/varcode/variant.py index ef9f474..56acc2c 100644 --- a/varcode/variant.py +++ b/varcode/variant.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 print_function, division, absolute_import - from pyensembl.locus import normalize_chromosome from serializable import Serializable from typechecks import require_instance diff --git a/varcode/variant_collection.py b/varcode/variant_collection.py index a57ac94..9faea44 100644 --- a/varcode/variant_collection.py +++ b/varcode/variant_collection.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 print_function, division, absolute_import - from collections import OrderedDict import pandas as pd diff --git a/varcode/vcf.py b/varcode/vcf.py index 5f248ea..f4ca45d 100644 --- a/varcode/vcf.py +++ b/varcode/vcf.py @@ -1,4 +1,3 @@ -# # 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 +11,6 @@ # limitations under the License. -from __future__ import absolute_import, print_function, division import os import requests import zlib diff --git a/varcode/vcf_output.py b/varcode/vcf_output.py index 2f2c4fb..ec5d89f 100644 --- a/varcode/vcf_output.py +++ b/varcode/vcf_output.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 @@ -13,7 +11,6 @@ # limitations under the License. -from __future__ import absolute_import, print_function, division from collections import defaultdict import sys