Index

_

__init__ (module)

_Arguments (class in ArgumentParserValidator)

A

abstractmethod() (in module decorators) add_cell() (in module excel) add_error() (ArgumentParserValidator._Arguments method) all_are_true() (in module misc) alter_arg() (TestSupport.TestSupport static method) AMPERSAND (in module const) APPEND (in module const)

arglist() (ArgumentParserValidator._Arguments method) ArgumentParserValidator (class in ArgumentParserValidator) (module) arm() (genomics.genome_data method) arm_length() (genomics.genome_data method) assert_re() (TestSupport.TestSupport method) AT (in module const)

B

BACKSLASH (in module const) BACKTICK (in module const) BatchMailer (class in email_handler) boolean_group_profile() (in module pandas_tools)

boolean_profile() (in module pandas_tools) build_column() (in module excel) build_row() (in module excel)

C

CARET (in module const) cell_name() (in module excel) chromosome_chunks() (in module genomics) chromosome_length() (genomics.genome_data method) clean_environment() (in module gittools) collect_mapped_items() (in module pandas_tools) COLON (in module const) column_cells() (in module excel) column_headers() (in module excel) column_index() (in module excel) column_names() (in module excel)

column_values() (in module excel) columns_showing_value() (in module pandas_tools) combinations() (in module set_operations) COMMA (in module const) condense_dataframe() (in module pandas_tools) const (module) constant_dict() (in module reflection) constant_iterator() (in module reflection) convert_chrpos_to_locus() (in module pandas_tools) convert_delta() (in module timeutil) convert_locus_to_chrpos() (in module pandas_tools)

D

DASH (in module const) DASHES (in module const) DAYS_PER_WEEK (in module timeutil) decorators (module) delete_arg() (TestSupport.TestSupport static method) delete_rows() (in module excel)

DOLLAR (in module const) DOMAIN (in module email_handler) DOT (in module const) dotted_list() (in module misc) draw_tree() (in module phylogenetics)

E

elide_list() (in module misc) email_handler (module) EMPTY (in module const) EQUALS (in module const)

error() (ArgumentParserValidator.ArgumentParserValidator method) excel (module) excelfile_rows() (in module excel) expand_env_vars() (in module misc)

F

fai_dict() (in module genomics) fai_locus() (genomics.genome_data method) find_files() (in module misc)

first_line() (in module misc) frame_label() (in module misc)

G

genome_data (class in genomics) genomics (module) get_property() (in module misc) git_commit() (in module gittools) git_fileadd() (in module gittools) git_filecommit() (in module gittools) git_filestatus() (in module gittools)

git_init() (in module gittools) git_lastlog() (in module gittools) git_reset() (in module gittools) git_version_ok() (in module gittools) gittools (module) GT (in module const)

H

HASH (in module const) headerdict() (in module misc) help_desired() (ArgumentParserValidator.ArgumentParserValidator method) hide_column() (in module excel) hide_row() (in module excel)

host_and_path() (in module misc) host_class() (in module misc) hostname() (in module misc) HOURS_PER_DAY (in module timeutil) hundredK_roundup() (in module genomics)

I

idx_merge() (in module pandas_tools) import_vtools_dataframe() (in module pandas_tools) is_MacOSX() (in module misc) is_valid_dir() (ArgumentParserValidator._Arguments method) is_valid_exclusive() (ArgumentParserValidator._Arguments method)

is_valid_file() (ArgumentParserValidator._Arguments method) is_valid_filelist() (ArgumentParserValidator._Arguments method) is_valid_filepath() (in module misc) is_valid_range() (ArgumentParserValidator._Arguments method) item_selector() (in module misc)

L

labexceptions (module) LabtoolsWarning LANGLET (in module const) last_cell_coordinate() (in module excel) last_column() (in module excel) last_row() (in module excel) LBRACE (in module const) LBRACKET (in module const)

line_to_dict() (in module misc) list_namespace() (TestSupport.TestSupport static method) localfile() (TestSupport.TestSupport method) localpath() (in module misc) log_test() (TestSupport.TestSupport method) LPAREN (in module const) LT (in module const)

M

MAILHOST (in module email_handler) make_version_list() (in module version_tool) maximal_subsets() (in module set_operations) MICROSECONDS_PER_MILLISECOND (in module timeutil) MICROSECONDS_PER_SECOND (in module timeutil)

MILLISECONDS_PER_SECOND (in module timeutil) misc (module) my_callername() (in module reflection) my_methodname() (in module reflection)

N

nameroot() (in module misc) Namespace (class in reflection) namesuffix() (in module misc)

new_test_filename() (TestSupport.TestSupport method) NEWLINE (in module const) normalize_chr_name() (in module genomics)

O

obsolete_sort_setsize_and_keylength() (in module set_operations) OK (in module const)

one_is_true() (in module misc) one_row_per_locus() (in module pandas_tools)

P

pandas_tools (module) parse_args() (ArgumentParserValidator.ArgumentParserValidator method) parse_colon_delta() (in module timeutil) parse_comparable_delta() (in module timeutil) pct() (in module misc) PERCENT (in module const) phylogenetics (module) plural() (in module misc) PLUS (in module const)

pretty_delta() (in module timeutil) print_errors() (ArgumentParserValidator._Arguments method) print_namespace() (in module TestSupport) printable_elapsed_stamp() (in module timeutil) progdir() (in module misc) program_path() (in module misc) ProgrammingFlawWarning progress_bar_runner() (in module decorators)

Q

QMARK (in module const)

QUOTE (in module const)

R

range_overlap() (in module excel) RANGLET (in module const) RBRACE (in module const) RBRACKET (in module const) READ (in module const) read_genome_bed() (in module genomics) read_genome_fai() (in module genomics) rearrange_column() (in module pandas_tools) reflection (module) removeDir() (TestSupport.TestSupport static method)

rename_column() (in module pandas_tools) report_timed_loop() (in module timeutil) report_timer() (in module timeutil) rounded_seconds_in_delta() (in module timeutil) row_cells() (in module excel) row_values() (in module excel) rows_showing_value() (in module pandas_tools) RPAREN (in module const) run_test() (in module TestSupport)

S

save_trace() (in module reflection) SECONDS_PER_HOUR (in module timeutil) SECONDS_PER_MINUTE (in module timeutil) select_keyset_of_largest_intersection() (in module set_operations) SEMICOLON (in module const) send_simple_mail() (email_handler.BatchMailer method) set_column_widths() (in module excel) set_combinations() (in module set_operations) set_operations (module) sheet_names() (in module excel) shell_glob_filenames() (in module misc) SHOUT (in module const) silent_zero() (in module misc) SLASH (in module const)

sort_by_setsize_and_keylength() (in module set_operations) sortable_coord() (in module genomics) sortable_coord_to_bedfile_coord() (in module genomics) sortable_coord_to_vcf_coord() (in module genomics) sortable_line_to_bedline() (in module genomics) sortable_line_to_vcfline() (in module genomics) SPACE (in module const) spaced_list() (in module misc) spaced_row() (in module misc) stable_sort_dataframe() (in module pandas_tools) stampit() (in module timeutil) STAR (in module const) start_timer() (in module timeutil) suffixed_name() (in module misc)

T

TAB (in module const) targetfile() (TestSupport.TestSupport method) test_block() (in module TestSupport) test_file_diff() (TestSupport.TestSupport method) testname() (TestSupport.TestSupport method) TestSupport (class in TestSupport) (module) TICK (in module const)

TILDE (in module const) time_method() (in module timeutil) timestamp() (in module timeutil) timeutil (module) transversion_to_apply() (in module pandas_tools) trim_chrom() (in module genomics) typecheck() (in module reflection)

U

UNDERBAR (in module const)

username() (in module misc)

V

valid_range() (ArgumentParserValidator.ArgumentParserValidator static method) validate_columns() (in module misc) validation_errors() (ArgumentParserValidator._Arguments method)

valueof_arg() (TestSupport.TestSupport static method) VBAR (in module const) version_tool (module)

W

walltime() (in module timeutil) WRITE (in module const)

write_annotation() (in module phylogenetics) write_distance_matrix() (in module set_operations)

Z

zero_div() (in module misc)