Auto Generated Documentation

This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. Program test arguments: hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html

hubArchiveCreator.configure_logger_dev(log_stdout=None)

Dev Logger is defined as following:

• Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout
• Still access to full, brute and traceback in stderr for errors
• And further access to debug if needed

hubArchiveCreator.configure_logger_stderr()

Configure what should be logged in stderr

hubArchiveCreator.configure_logger_user(log_stdout=None)

User Logger is defined as following:

• User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback

  in STDOUT

• Still access to full, brute and traceback for errors

  in STDERR

• And further access to debug if needed

  in .log

hubArchiveCreator.create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data)

Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub and update the dictionary of datatype

Parameters:

• ExtensionClass (Datatype) –
• array_inputs (list[string]) –
• inputs_data (dict) –

Return type:

dict

hubArchiveCreator.sanitize_name_input(string_to_sanitize)

Sanitize the string passed in parameter by replacing ‘/’ and ‘ ‘ by ‘_’

Parameters:string_to_sanitize –

:return :

Example:

>>> sanitize_name_input('this/is an//example')
this_is_an__example

hubArchiveCreator.sanitize_name_inputs(inputs_data)

Sanitize value of the keys “name” of the dictionary passed in parameter.

Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces. Also, it can contain ‘/’ character and could break the use of os.path function.

Parameters:inputs_data – dict[string, dict[string, string]]