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import unittest
import base
class Test(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/maf_extract_ranges_indexed.py ./test_data/maf_tests/mm8_chr7_tiny.maf -c -m 5 -p mm8."
input_stdin = base.TestFile(filename="./test_data/maf_tests/dcking_ghp074.bed")
output_stdout = base.TestFile(filename="./test_data/maf_tests/dcking_ghp074.maf")
class TestAccessNotRef(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/maf_extract_ranges_indexed.py ./test_data/maf_tests/mm8_chr7_tiny.maf -c -m 5 -p hg18."
input_stdin = base.TestFile(filename="./test_data/maf_tests/hg18.bed")
output_stdout = base.TestFile(filename="./test_data/maf_tests/test_hg18.maf")
class TestAccessRef(base.BaseScriptTest, unittest.TestCase):
command_line = (
"./scripts/maf_extract_ranges_indexed.py ./test_data/maf_tests/mm8_chr7_tiny_mm8_ind.maf -c -m 5 -p mm8."
)
input_stdin = base.TestFile(filename="./test_data/maf_tests/dcking_ghp074.bed")
output_stdout = base.TestFile(filename="./test_data/maf_tests/dcking_ghp074.maf")
class TestAccessNotRefNotIndexed(base.BaseScriptTest, unittest.TestCase):
command_line = (
"./scripts/maf_extract_ranges_indexed.py ./test_data/maf_tests/mm8_chr7_tiny_mm8_ind.maf -c -m 5 -p hg18."
)
input_stdin = base.TestFile(filename="./test_data/maf_tests/hg18.bed")
output_stdout = base.TestFile(filename="./test_data/maf_tests/empty.maf")
class TestELines(base.BaseScriptTest, unittest.TestCase):
command_line = (
"./scripts/maf_extract_ranges_indexed.py ./test_data/maf_tests/mm10_chr12_lessspe.maf -c -m 5 -p mm10."
)
input_stdin = base.TestFile(filename="./test_data/maf_tests/mm10_chr12.bed")
output_stdout = base.TestFile(filename="./test_data/maf_tests/mm10_chr12_slice.maf")
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