spliced package

Subpackages

• spliced.client package
  • Submodules
  • spliced.client.command module
  • spliced.client.splice module
  • spliced.client.validate module
  • Module contents
• spliced.experiment package
  • Submodules
  • spliced.experiment.base module
  • spliced.experiment.spack module
  • Module contents
• spliced.predict package
  • Subpackages
    • spliced.predict.smeagle package
      • Submodules
      • spliced.predict.smeagle.asp module
      • spliced.predict.smeagle.smeagle module
      • spliced.predict.smeagle.solver module
      • Module contents
  • Submodules
  • spliced.predict.abi_laboratory module
  • spliced.predict.base module
  • spliced.predict.libabigail module
  • spliced.predict.spack module
  • spliced.predict.symbols module
  • Module contents
• spliced.utils package
  • Submodules
  • spliced.utils.fileio module
  • spliced.utils.terminal module
  • Module contents

Submodules

spliced.logger module

class spliced.logger.ColorizingStreamHandler(nocolor=False, stream=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>, use_threads=False)

Bases: StreamHandler

BLACK = 0

BLUE = 4

BOLD_SEQ = '\x1b[1m'

COLOR_SEQ = '\x1b[%dm'

CYAN = 6

GREEN = 2

MAGENTA = 5

RED = 1

RESET_SEQ = '\x1b[0m'

WHITE = 7

YELLOW = 3

can_color_tty()

colors = {'CRITICAL': 1, 'DEBUG': 4, 'ERROR': 1, 'INFO': 2, 'WARNING': 3}

decorate(record)

emit(record)

Emit a record.

If a formatter is specified, it is used to format the record. The record is then written to the stream with a trailing newline. If exception information is present, it is formatted using traceback.print_exception and appended to the stream. If the stream has an ‘encoding’ attribute, it is used to determine how to do the output to the stream.

property is_tty

class spliced.logger.Logger

Bases: object

cleanup()

debug(msg)

error(msg)

exit(msg, return_code=1)

handler(msg)

info(msg)

location(msg)

progress(done=None, total=None)

set_level(level)

set_stream_handler(stream_handler)

shellcmd(msg)

text_handler(msg)

The default snakemake log handler. Prints the output to the console. :param msg: the log message dictionary :type msg: dict

warning(msg)

spliced.logger.setup_logger(quiet=False, printshellcmds=False, nocolor=False, stdout=False, debug=False, use_threads=False, wms_monitor=None)

spliced.schemas module

spliced.version module

Module contents