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import unittest
import base
class Test1(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/out_to_chain.py ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.out --chrsizes ./test_data/epo_tests/hg19.chrom.sizes ./test_data/epo_tests/mm9.chrom.sizes"
command_line = "./scripts/bnMapper.py ./test_data/epo_tests/hpeaks.bed ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.chain"
output_stdout = base.TestFile(filename="./test_data/epo_tests/hpeaks.mapped.bed4")
class Test2(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/bnMapper.py -fBED12 ./test_data/epo_tests/hpeaks.bed ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.chain"
output_stdout = base.TestFile(filename="./test_data/epo_tests/hpeaks.mapped.bed12")
class Test3(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/bnMapper.py -g9 ./test_data/epo_tests/hpeaks.bed ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.chain"
output_stdout = base.TestFile(filename="./test_data/epo_tests/hpeaks.mapped.bed4")
class Test4(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/bnMapper.py -g3 ./test_data/epo_tests/hpeaks.bed ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.chain"
output_stdout = base.TestFile(filename="./test_data/epo_tests/hpeaks.mapped.nopeak2.bed4")
class Test5(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/bnMapper.py -g9 -t0.67 ./test_data/epo_tests/hpeaks.bed ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.chain"
output_stdout = base.TestFile(filename="./test_data/epo_tests/hpeaks.mapped.bed4")
class Test6(base.BaseScriptTest, unittest.TestCase):
command_line = "./scripts/bnMapper.py -g9 -t0.7 ./test_data/epo_tests/hpeaks.bed ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.chain"
output_stdout = base.TestFile(filename="./test_data/epo_tests/hpeaks.mapped.nopeak2.bed4")
class Test7(base.BaseScriptTest, unittest.TestCase):
command_line = (
"./scripts/bnMapper.py ./test_data/epo_tests/hg19_one_peak.bed ./test_data/epo_tests/hg19.mm9.rBest.chain.gz"
)
output_stdout = base.TestFile(filename="./test_data/epo_tests/hg19_one_peak.mapped.bed")
if __name__ == "__main__":
unittest.main()
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