Mercurial > repos > pieterlukasse > prims_metabolomics

comparison test/test_export_to_metexp_tabular.py @ 0:9d5f4f5f764b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial commit to toolshed
author pieter.lukasse@wur.nl
date Thu, 16 Jan 2014 13:10:00 +0100
parents
children 19d8fd10248e
comparison
equal deleted inserted replaced
-1:000000000000 0:9d5f4f5f764b
1 '''Integration tests for the GCMS project'''
2
3 from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611
4 from GCMS import export_to_metexp_tabular
5 import os.path
6 import sys
7 import unittest
8
9
10 class IntegrationTest(unittest.TestCase):
11
12
13 def test_combine_output_simple(self):
14 '''
15 comment me
16 '''
17 # Create out folder
18 outdir = "output/metexp/"
19 if not os.path.exists(outdir):
20 os.makedirs(outdir)
21
22 #Build up arguments and run
23
24 rankfilter_and_caslookup_combined_file = resource_filename(__name__, "data/dummy1_produced_combine_output_single.txt")
25 msclust_quantification_and_spectra_file = resource_filename(__name__, "data/dummy1_sim.txt")
26 output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt")
27
28 sys.argv = ['test',
29 rankfilter_and_caslookup_combined_file,
30 msclust_quantification_and_spectra_file,
31 output_csv]
32 # Execute main function with arguments provided through sys.argv
33 export_to_metexp_tabular.main()
34
35 '''
36 # Asserts are based on reading in with process_data and comparing values of
37 # certain columns
38
39 # Check 3: library_lookup RI column, centrotype column, ri_svr column are correct:
40 caslookup_items = combine_output._process_data(input_caslookup)
41 rankfilter_items = combine_output._process_data(input_rankfilter)
42
43 # check that the caslookup RI column is correctly maintained in its original order in
44 # the combined file:
45 ri_caslookup = caslookup_items['RI']
46 ri_combine_single = combine_result_single_items['RI']
47 self.assertListEqual(ri_caslookup, ri_combine_single)
48
49 # check the centrotype column's integrity:
50 centrotype_caslookup = caslookup_items['Centrotype']
51 centrotype_combine_single = combine_result_single_items['Centrotype']
52 centrotype_rankfilter = _get_centrotype_rankfilter(rankfilter_items['ID'])
53 self.assertListEqual(centrotype_caslookup, centrotype_combine_single)
54 self.assertListEqual(centrotype_caslookup, centrotype_rankfilter)
55
56 # integration and integrity checks:
57 file_NIST = resource_filename(__name__, "data/integration/NIST_identification_results_tabular.txt")
58 file_NIST_items = combine_output._process_data(file_NIST)
59 # check that rank filter output has exactly the same ID items as the original NIST input file:
60 self.assertListEqual(file_NIST_items['ID'], rankfilter_items['ID'])
61 # check the same for the CAS column:
62 self.assertListEqual(_get_strippedcas(file_NIST_items['CAS']), rankfilter_items['CAS'])
63 # now check the NIST CAS column against the cas lookup results:
64 cas_NIST = _get_processedcas(file_NIST_items['CAS'])
65 self.assertListEqual(cas_NIST, caslookup_items['CAS'])
66 # now check the CAS of the combined result. If all checks are OK, it means the CAS column's order
67 # and values remained stable throughout all steps:
68 self.assertListEqual(rankfilter_items['CAS'], combine_result_single_items['CAS'])
69
70 # check that the rankfilter RIsvr column is correctly maintained in its original order in
71 # the combined file:
72 risvr_rankfilter = rankfilter_items['RIsvr']
73 risvr_combine_single = combine_result_single_items['RIsvr']
74 self.assertListEqual(risvr_rankfilter, risvr_combine_single)
75 '''
76
77
78
79 def _read_file(filename):
80 '''
81 Helper method to quickly read a file
82 @param filename:
83 '''
84 with open(filename) as handle:
85 return handle.read()