Mercurial > repos > pieterlukasse > prims_metabolomics
annotate test/test_export_to_metexp_tabular.py @ 61:d685210eef3e
fix in pdftotabular tool
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 19 Dec 2014 15:30:13 +0100 |
| parents | 19d8fd10248e |
| children |
| rev | line source |
|---|---|
| 0 | 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 | |
|
21
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
13 def test_MM_calculations(self): |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
14 ''' |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
15 test the implemented method for MM calculations for |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
16 given chemical formulas |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
17 ''' |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
18 export_to_metexp_tabular.init_elements_and_masses_map() |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
19 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
20 formula = "C8H18O3" |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
21 # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
22 result = export_to_metexp_tabular.get_molecular_mass(formula) |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
23 self.assertEqual(162.26, result) |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
24 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
25 formula = "CH2O3Fe2Ni" |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
26 # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
27 result = export_to_metexp_tabular.get_molecular_mass(formula) |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
28 self.assertAlmostEqual(232.44, result, 2) |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
29 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
30 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
31 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
32 |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
33 |
| 0 | 34 def test_combine_output_simple(self): |
| 35 ''' | |
| 36 comment me | |
| 37 ''' | |
| 38 # Create out folder | |
| 39 outdir = "output/metexp/" | |
| 40 if not os.path.exists(outdir): | |
| 41 os.makedirs(outdir) | |
| 42 | |
| 43 #Build up arguments and run | |
| 44 | |
| 45 rankfilter_and_caslookup_combined_file = resource_filename(__name__, "data/dummy1_produced_combine_output_single.txt") | |
| 46 msclust_quantification_and_spectra_file = resource_filename(__name__, "data/dummy1_sim.txt") | |
| 47 output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt") | |
| 48 | |
| 49 sys.argv = ['test', | |
| 50 rankfilter_and_caslookup_combined_file, | |
| 51 msclust_quantification_and_spectra_file, | |
|
21
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
52 output_csv, |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
53 'tomato', |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
54 'leafs', |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
55 'test experiment', |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
56 'pieter', |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
57 'DB5 column'] |
|
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
58 |
| 0 | 59 # Execute main function with arguments provided through sys.argv |
| 60 export_to_metexp_tabular.main() | |
| 61 | |
| 62 ''' | |
| 63 # Asserts are based on reading in with process_data and comparing values of | |
| 64 # certain columns | |
| 65 | |
| 66 # Check 3: library_lookup RI column, centrotype column, ri_svr column are correct: | |
| 67 caslookup_items = combine_output._process_data(input_caslookup) | |
| 68 rankfilter_items = combine_output._process_data(input_rankfilter) | |
| 69 | |
| 70 # check that the caslookup RI column is correctly maintained in its original order in | |
| 71 # the combined file: | |
| 72 ri_caslookup = caslookup_items['RI'] | |
| 73 ri_combine_single = combine_result_single_items['RI'] | |
| 74 self.assertListEqual(ri_caslookup, ri_combine_single) | |
| 75 | |
| 76 # check the centrotype column's integrity: | |
| 77 centrotype_caslookup = caslookup_items['Centrotype'] | |
| 78 centrotype_combine_single = combine_result_single_items['Centrotype'] | |
| 79 centrotype_rankfilter = _get_centrotype_rankfilter(rankfilter_items['ID']) | |
| 80 self.assertListEqual(centrotype_caslookup, centrotype_combine_single) | |
| 81 self.assertListEqual(centrotype_caslookup, centrotype_rankfilter) | |
| 82 | |
| 83 # integration and integrity checks: | |
| 84 file_NIST = resource_filename(__name__, "data/integration/NIST_identification_results_tabular.txt") | |
| 85 file_NIST_items = combine_output._process_data(file_NIST) | |
| 86 # check that rank filter output has exactly the same ID items as the original NIST input file: | |
| 87 self.assertListEqual(file_NIST_items['ID'], rankfilter_items['ID']) | |
| 88 # check the same for the CAS column: | |
| 89 self.assertListEqual(_get_strippedcas(file_NIST_items['CAS']), rankfilter_items['CAS']) | |
| 90 # now check the NIST CAS column against the cas lookup results: | |
| 91 cas_NIST = _get_processedcas(file_NIST_items['CAS']) | |
| 92 self.assertListEqual(cas_NIST, caslookup_items['CAS']) | |
| 93 # now check the CAS of the combined result. If all checks are OK, it means the CAS column's order | |
| 94 # and values remained stable throughout all steps: | |
| 95 self.assertListEqual(rankfilter_items['CAS'], combine_result_single_items['CAS']) | |
| 96 | |
| 97 # check that the rankfilter RIsvr column is correctly maintained in its original order in | |
| 98 # the combined file: | |
| 99 risvr_rankfilter = rankfilter_items['RIsvr'] | |
| 100 risvr_combine_single = combine_result_single_items['RIsvr'] | |
| 101 self.assertListEqual(risvr_rankfilter, risvr_combine_single) | |
| 102 ''' | |
| 103 | |
| 104 | |
| 105 | |
| 106 def _read_file(filename): | |
| 107 ''' | |
| 108 Helper method to quickly read a file | |
| 109 @param filename: | |
| 110 ''' | |
| 111 with open(filename) as handle: | |
| 112 return handle.read() |