pygustus.augustus

A python wrapper for the gene prediction program AUGUSTUS.

predict

def predict(*args, options=None, **kwargs)

Executes the binary of AUGUSTUS.

For the execution the given parameters are passed as command line arguments.

Arguments:

  • *args tuple - Exactly one argument should be passed here. Either the queryfilename or one of the help calls of AUGUSTUS (--help, --pramlist).
  • options AugustusOptions - Optional; If an instance of AugustusOptions is passed, it will be used for the call. Otherwise, a new instance is created based on the passed arguments (the default is None).
  • **kwargs dict - Arguments for AUGUSTUS or Pygustus as dict: lists with possible parameters can be obtained from the help methods or the Pygustus README (only Pygustus parameters).

config_get_bin

def config_get_bin()

Returns currently configured path to the executable of AUGUSTUS.

Returns:

  • string - The currently configured path to the executable of AUGUSTUS.

config_set_bin

def config_set_bin(value)

Updates the configured path to the executable of AUGUSTUS.

Arguments:

  • value string - The path to the execuatble of AUGUSTUS as string.

Raises:

  • RuntimeError - If the given path does not exist or the file is not executable.

config_set_default_bin

def config_set_default_bin()

Sets the configured path to the AUGUSTUS executable to 'augustus'.

This should exist if AUGUSTUS is properly installed on the system.

show_fasta_info

def show_fasta_info(inputfile)

Outputs information about a fasta file.

This method outputs information about the contents of the passed file in fasta format. It is based on the Pearl script summarizeACGTcontent.pl.

Arguments:

  • inputfile string - Path to the file in fasta format as string.

show_aug_help

def show_aug_help()

Shows the help output of AUGUSTUS.

show_aug_paramlist

def show_aug_paramlist()

Shows possible parameter names of AUGUSTUS.

show_species_info

def show_species_info()

Shows species information of AUGUSTUS.

help

def help()

Shows usage information.

pygustus.etraining

A python wrapper for the training of AUGUSTUS.

train

def train(*args, options=None, **kwargs)

Executes etraining and passes the given parameters as command line arguments.

Arguments:

  • *args tuple - Only the the queryfilename should be passed here.
  • options AugustusOptions - Optional; If an instance of AugustusOptions is passed, it will be used for the call. Otherwise, a new instance is created based on the passed arguments (the default is None).
  • **kwargs dict - Arguments for Etraining or Pygustus: lists with possible parameters can be obtained from the help methods or the Pygustus README (only Pygustus parameters).

config_get_bin

def config_get_bin()

Outputs currently configured path to the executable of etraining.

Returns:

  • string - The currently configured path to the executable of etraining.

config_set_bin

def config_set_bin(value)

Updates the configured path to the executable of etraining.

Arguments:

  • value string - The path to the execuatble of etraining.

Raises:

  • RuntimeError - If the given path does not exist or the file is not executable.

config_set_default_bin

def config_set_default_bin()

Sets the configured path to the etraining executable to 'etraining'.

This executable should exist if AUGUSTUS is properly installed on the system.