MSMetaEnhancer package
The Application class serves as a top-level interface to use the tool.
The main method is (asynchronous) annotate_spectra, which runs the annotation process using given conversions. It is possible to specify particular conversion jobs, which will be executed in respecting the given order. If no jobs are given, all jobs supported by given services are used.
Additionally, it allows to load and save spectra files in supported formats, and curate given spectra.
- class MSMetaEnhancer.app.Application(log_level='info', log_file=None)
Bases:
object- async annotate_spectra(converters, jobs=None, repeat: bool = False, monitor: ~MSMetaEnhancer.libs.utils.Monitor.Monitor = <Monitor(Thread-2, initial)>, annotator: ~MSMetaEnhancer.libs.Annotator.Annotator = <MSMetaEnhancer.libs.Annotator.Annotator object>)
Annotates current Spectra data by specified jobs.
Used converters must be specified. Jobs do not have to be given, all available jobs will be executed instead.
- Parameters:
converters – given list of converters names
jobs – list specifying jobs to be executed
repeat – if some metadata was added, all jobs are executed again
monitor – given Monitor object to observe status of services
annotator – given Annotator object to run the actual annotation
- curate_metadata()
Updates metadata by curation process.
This includes e.g. normalisation of CAS numbers.
- load_data(filename, file_format)
High level method to load Spectra data from given file.
- Parameters:
filename – path to source spectra file
file_format – format of spectra
- save_data(filename, file_format)
High level method to save Spectra data to given file.
- Parameters:
filename – path to target file
file_format – desired format of spectra