Index

A

annotation (class in parsing_routines.gff_gtf_tools)

C

convert_BigWig2Wig() (in module parsing_routines.wig_tools)

G

generic_set_region() (in module parsing_routines.general_classes_and_functions)

I

input_file() (in module script_options.custom_callables)

input_path() (in module script_options.custom_callables)

N

ngseq.renameChromosomes (module) ngseq.summarizeWigPerFeature (module)

ngseq.switchStrand (module)

O

openfile() (in module parsing_routines.general_classes_and_functions) output_file() (in module script_options.custom_callables)

output_path() (in module script_options.custom_callables)

P

parse_gff_v3() (in module parsing_routines.gff_gtf_tools) parsing_routines.general_classes_and_functions (module)

parsing_routines.gff_gtf_tools (module) parsing_routines.wig_tools (module)

R

region (class in parsing_routines.general_classes_and_functions)

S

script_logging.standard_logging (module) script_options.custom_callables (module) script_options.standard_parsers (module)

setUp() (tests.custom_callables.TestParsingRoutines method) (tests.general_classes_and_functions.TestGeneralClasses method) (tests.gff_gtf_tools.TestGFFGTFTools method) (tests.standard_logging.TestStandardLogging method) (tests.standard_parsers.TestStandardArgparse method) (tests.wig_tools.TestWigTools method) standard_logger() (in module script_logging.standard_logging) standard_parser() (in module script_options.standard_parsers)

T

tearDown() (tests.custom_callables.TestParsingRoutines method) (tests.standard_logging.TestStandardLogging method) (tests.standard_parsers.TestStandardArgparse method) test_annotation() (tests.gff_gtf_tools.TestGFFGTFTools method) test_generic_set_region() (tests.general_classes_and_functions.TestGeneralClasses method) test_input_file() (tests.custom_callables.TestParsingRoutines method) test_input_path() (tests.custom_callables.TestParsingRoutines method) test_openfile() (tests.general_classes_and_functions.TestGeneralClasses method) test_output_file() (tests.custom_callables.TestParsingRoutines method) test_output_path() (tests.custom_callables.TestParsingRoutines method) test_parse_gff_v3() (tests.gff_gtf_tools.TestGFFGTFTools method) test_region() (tests.general_classes_and_functions.TestGeneralClasses method) test_standard_logger_attributes() (tests.standard_logging.TestStandardLogging method) test_standard_logger_basic_logging() (tests.standard_logging.TestStandardLogging method) test_standard_logger_parsed_arguments() (tests.standard_logging.TestStandardLogging method) test_standard_parser_infile() (tests.standard_parsers.TestStandardArgparse method) test_standard_parser_log() (tests.standard_parsers.TestStandardArgparse method) test_standard_parser_outfile() (tests.standard_parsers.TestStandardArgparse method) test_standard_parser_returns() (tests.standard_parsers.TestStandardArgparse method) test_standard_parser_tmpdir() (tests.standard_parsers.TestStandardArgparse method) test_standard_parser_verbosity() (tests.standard_parsers.TestStandardArgparse method)

test_wigData_and_wigTrack_set_region() (tests.wig_tools.TestWigTools method) test_wigData_BigWig() (tests.wig_tools.TestWigTools method) test_wigData_multi_chromosome() (tests.wig_tools.TestWigTools method) test_wigTrack_fixedStep() (tests.wig_tools.TestWigTools method) test_wigTrack_region_functions() (tests.wig_tools.TestWigTools method) test_wigTrack_variableStep() (tests.wig_tools.TestWigTools method) TestGeneralClasses (class in tests.general_classes_and_functions) TestGFFGTFTools (class in tests.gff_gtf_tools) TestParsingRoutines (class in tests.custom_callables) tests.custom_callables (module) tests.general_classes_and_functions (module) tests.gff_gtf_tools (module) tests.standard_logging (module) tests.standard_parsers (module) tests.wig_tools (module) TestStandardArgparse (class in tests.standard_parsers) TestStandardLogging (class in tests.standard_logging) TestWigTools (class in tests.wig_tools)

W

wigData (class in parsing_routines.wig_tools)

wigTrack (class in parsing_routines.wig_tools)