class Test(base.BaseScriptTest, unittest.TestCase): command_line = "./scripts/line_select.py ${features}" input_features = base.TestFile("""0 1 1 0 1 0""") input_stdin = base.TestFile("""a b d e f""") output_stdout = base.TestFile("""b e""")
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 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")
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 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. < ${bed}" input_bed = base.TestFile( filename="./test_data/maf_tests/dcking_ghp074.bed") output_stdout = base.TestFile( filename="./test_data/maf_tests/dcking_ghp074.maf")
class Test1(base.BaseScriptTest, unittest.TestCase): command_line = "./scripts/maf_build_index.py ${maf} ${maf_index}" input_maf = base.TestFile( filename="./test_data/maf_tests/mm8_chr7_tiny.maf") output_maf_index = base.TestFile( filename="./test_data/maf_tests/mm8_chr7_tiny.maf.index")
class Test(base.BaseScriptTest, unittest.TestCase): command_line = "./scripts/lzop_build_offset_table.py" input_stdin = base.TestFile( filename="./test_data/maf_tests/mm8_chr7_tiny.maf.lzo") output_stdout = base.TestFile( filename="./test_data/maf_tests/mm8_chr7_tiny.maf.lzot")