Welcome to pymzTab-m’s documentation!¶
This is the mzTab-M reference implementation and validation API service for Python 3.
Note
This is an early development version, please use at your own risk and report issues to help improve it!
mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches. This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information.
mzTab-M has been developed with a view to support the following general tasks:
Facilitate the sharing of final experimental results, especially with researchers outside the field of metabolomics.
Export of results to external software, including programs such as Microsoft Excel® and Open Office Spreadsheet and statistical software / coding languages such as R and Python.
Act as an output format of (web-) services that report MS-based results and thus can produce standardized result pages.
Be able to link to the external experimental evidence e.g. by referencing back to mzML files.
Getting Started¶
The following example shows how to validate an MzTab object using the REST API for the jmzTab-M webapplication REST service
Note
In this example, the MzTab object will not validate! Please check the test API test for a more realistic example.
from __future__ import print_function
import time
import swagger_client
from swagger_client.rest import ApiException
from pprint import pprint
# create an instance of the API class
api_instance = swagger_client.ValidateApi(swagger_client.ApiClient(configuration))
mztabfile = swagger_client.MzTab() # MzTab | mzTab file that should be validated. This still needs to be populated!!!
level = 'info' # str | The level of errors that should be reported, one of ERROR, WARN, INFO. (optional) (default to info)
max_errors = 100 # int | The maximum number of errors to return. (optional) (default to 100)
semantic_validation = false # bool | Whether a semantic validation against the default rule set should be performed. (optional) (default to false)
try:
api_response = api_instance.validate_mz_tab_file(mztabfile, level=level, max_errors=max_errors, semantic_validation=semantic_validation)
pprint(api_response)
except ApiException as e:
print("Exception when calling ValidateApi->validate_mz_tab_file: %s\n" % e)