prims_metabolomics2: test/test_query_mass

initial commit

comparison

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--1:000000000000
+:dffc38727496
+'''Integration tests for the GCMS project'''
+from pkg_resources import resource_filename  # @UnresolvedImport # pylint: disable=E0611
+from MS import query_mass_repos
+import os.path
+import sys
+import unittest
+class IntegrationTest(unittest.TestCase):
+def test_simple(self):
+'''
+Simple initial test
+'''
+# Create out folder
+outdir = "output/query_mass_repos/"
+if not os.path.exists(outdir):
+os.makedirs(outdir)
+#Build up arguments and run
+#     input_file = sys.argv[1]
+#     molecular_mass_col = sys.argv[2]
+#     repository_file = sys.argv[3]
+#     mass_tolerance = float(sys.argv[4])
+#     output_result = sys.argv[5]
+input_file = resource_filename(__name__, "data/service_query_tabular.txt")
+molecular_mass_col = "mass (Da)"
+dblink_file = resource_filename(__name__, "data/MFSearcher ExactMassDB service.txt")
+output_result = resource_filename(__name__, outdir + "metexp_query_results_added.txt")
+sys.argv = ['test',
+input_file,
+molecular_mass_col,
+dblink_file,
+'0.001',
+'ms',
+output_result]
+# Execute main function with arguments provided through sys.argv
+query_mass_repos.main()
+def _read_file(filename):
+'''
+Helper method to quickly read a file
+@param filename:
+'''
+with open(filename) as handle:
+return handle.read()

Mercurial > repos > pieterlukasse > prims_metabolomics2