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
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hubArchiveCreator.
configure_logger_dev
(log_stdout=None)[source]¶ - 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
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hubArchiveCreator.
configure_logger_user
(log_stdout=None)[source]¶ - 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
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hubArchiveCreator.
create_ordered_datatype_objects
(ExtensionClass, array_inputs, inputs_data)[source]¶ 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:
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hubArchiveCreator.
sanitize_name_input
(string_to_sanitize)[source]¶ 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
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hubArchiveCreator.
sanitize_name_inputs
(inputs_data)[source]¶ 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]]