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()
