updated tests

tests/test_allele_reads.py

@@ -15,7 +15,7 @@
 from isovar.read_collector import ReadCollector
 from varcode import Variant
 
-from mock_objects import MockAlignmentFile, make_pysam_read
+from .mock_objects import MockAlignmentFile, make_pysam_read
 from .testing_helpers import assert_equal_fields
 from .common import eq_
 

tests/test_assembly.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 time import time
 
 from isovar.read_collector import ReadCollector

tests/test_gather_variant_reads_wgs.py

@@ -13,12 +13,12 @@
 from pyensembl import ensembl_grch38
 
 from varcode import Variant
-from .common import eq_
 
-from .testing_helpers import load_bam
 
 from isovar import ReadCollector
 
+from .common import eq_
+from .testing_helpers import load_bam
 
 def test_partition_variant_reads_snv():
     alignment_file = load_bam("data/cancer-wgs-primary.chr12.bam")

tests/test_isovar_result.py

@@ -13,8 +13,8 @@
 from isovar import run_isovar
 from isovar import ProteinSequence
 from varcode import Variant
-from .testing_helpers import data_path
 
+from .testing_helpers import data_path
 from .common import eq_
 
 

tests/test_locus_reads.py

@@ -11,13 +11,13 @@
 # limitations under the License.
 
 from varcode import Variant
+
 from isovar.locus_read import LocusRead
 from isovar.dataframe_helpers import locus_reads_dataframe
 from isovar.read_collector import ReadCollector
 
-from mock_objects import MockAlignmentFile, make_pysam_read
+from .mock_objects import MockAlignmentFile, make_pysam_read
 from .testing_helpers import assert_equal_fields, load_bam, data_path
-
 from .common import eq_
 
 def test_locus_reads_snv():

tests/test_protein_sequences.py

@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from mock_objects import make_dummy_protein_sequence
-
 from varcode import VariantCollection
 
 from isovar.read_collector import ReadCollector
@@ -23,8 +21,10 @@
 from isovar.main import ProteinSequenceCreator
 from isovar.protein_sequence import ProteinSequence
 from isovar.protein_sequence_helpers import sort_protein_sequences
+
 from .common import eq_
 from .testing_helpers import load_bam, load_vcf, data_path
+from .mock_objects import make_dummy_protein_sequence
 
 
 def test_protein_sequence_substitution():

tests/test_somatic_variant_with_0_supporting_rna_reads.py

@@ -1,4 +1,14 @@
-from __future__ import print_function, division, 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 varcode import Variant
 

tests/test_somatic_variant_with_2_supporting_rna_reads.py

@@ -1,9 +1,19 @@
-from __future__ import print_function, division, 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 varcode import Variant
 
-
 from isovar.read_collector import ReadCollector
+
 from .genomes_for_testing import grch38
 from .testing_helpers import load_bam
 from .common import eq_ 

tests/test_translation.py

@@ -1,6 +1,17 @@
-
+# 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 isovar import ProteinSequenceCreator, ReadCollector
+
 from .common import eq_ 
 from .testing_helpers import load_bam, load_vcf
 

tests/test_value_object.py

@@ -1,3 +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.
+
+
 from isovar.value_object import ValueObject
 from .common import eq_ 
 

tests/test_variant_helpers.py

@@ -1,14 +1,26 @@
+# 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 isovar.variant_helpers import (
     trim_variant_fields,
     trim_variant,
     base0_interval_for_variant,
     interbase_range_affected_by_variant_on_transcript
 )
-from .common import eq_ 
+
 from varcode import Variant
 
 from .genomes_for_testing import grch38
+from .common import eq_ 
 
 def test_trim_variant_substitution():
     loc, ref, alt = trim_variant(Variant("chr1", 10, "C", "G", grch38))

tests/test_variant_orf.py

@@ -1,4 +1,15 @@
-from .common import eq_ 
+# 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 isovar.variant_orf import (
@@ -12,6 +23,8 @@
 from isovar.allele_read import AlleleRead
 from isovar.dna import reverse_complement_dna
 
+from .common import eq_ 
+
 def test_compute_offset_to_first_complete_codon_no_trimming():
     # if nothing gets trimmed from the reference sequence, then
     # the offset to the first codon shouldn't change

tests/test_variant_reads_with_dummy_samfile.py

@@ -1,11 +1,22 @@
+# 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_ 
 from varcode import Variant
 
 from isovar.allele_read import AlleleRead
 from isovar.read_collector import ReadCollector
 
-from mock_objects import MockAlignmentFile, make_pysam_read
+from .mock_objects import MockAlignmentFile, make_pysam_read
 from .genomes_for_testing import grch38
 
 

tests/test_variant_sequences.py

@@ -1,4 +1,15 @@
-from .common import eq_ 
+# 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
 
@@ -11,7 +22,7 @@
 
 from .testing_helpers import load_bam
 from .genomes_for_testing import grch38
-
+from .common import eq_ 
 
 def test_sequence_counts_snv():
     samfile = load_bam("data/cancer-wgs-primary.chr12.bam")