Difference between revisions of "Unit tests for SanXoT"

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We present here a unit test for windows that can be performed using the following programs in the '''[[SanXoT software package]]''':
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We present here three unit tests for windows that can be performed using the following programs in the '''[[SanXoT software package]]''':
  
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* '''[[Aljamia]]'''
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* '''[[Aljamia]]''' (data parser)
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* '''[[Klibrate]]'''
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* '''[[Klibrate]]''' (weight calibrator)
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* '''[[SanXoT]]'''
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* '''[[SanXoT]]''' (integration and variance calculation)
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* '''[[SanXoTSieve]]'''
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* '''[[SanXoTSieve]]''' (removal of outliers)
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* '''[[Cardenio]]'''
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* '''[[Cardenio]]''' (merger of experiments)
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* '''[[SanXoTSqueezer]]'''
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* '''[[SanXoTSqueezer]]''' (category filter)
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* '''[[Sanson]]'''
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* '''[[SanXoTGauss]]''' (category cumulative gaussian graphs)
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* '''[[Coordinometer]]'''
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* '''[[Sanson]]''' (category clustering)
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* '''[[Coordinometer]]''' (calculator of the degree of coordination)
  
 
For detailed explanations, check '''[[notes about the Unit test for SanXoT]]'''.
 
For detailed explanations, check '''[[notes about the Unit test for SanXoT]]'''.
  
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To run the unit test, you need to download:
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==Test 1: The fundamental workflow==
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The fundamental workflow consists in the steps to quantify proteins using PSMs and quantitative information, following the steps:
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1) calibration of spectra
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2) integrating from spectra to peptides
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3) integrating from peptides to proteins
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4) quantifying proteins
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This test makes use of four programs: '''[[Aljamia]]''', '''[[Klibrate]]''', '''[[SanXoT]]''', and '''[[SanXoTSieve]]'''.
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To run this unit test, follow these steps:
  
 
1) download the windows executables, '''[[SanXoT.zip]]'''. Unzip them in a folder specific for the program.
 
1) download the windows executables, '''[[SanXoT.zip]]'''. Unzip them in a folder specific for the program.
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2) download the files for the unit test, '''[[SanXoT_test1.zip]]'''. Unzip to a working folder. You should have four text files:
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::* commands_test1.bat, a windows batch file with command lines to run this sample analysis.
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::* startingFile.xls, a tab-separated-values text file with identifications and quantitative data from a proteomics experiment.
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3) Get a) the path of your working folder (where you have unzipped the startingFile.xls), b) the path of the folder where you have unzipped the windows executables, and c) the unit of the latter (C:, D:, etc); modify the following lines in the command_test1.bat file accordingly:
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set unit=D:
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set programFolder="D:\SSP"
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set workingFolder="D:\SanXoT_test1"
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4) execute the bat file, copy and paste the whole commands_test1.bat text into a [https://en.wikipedia.org/wiki/Cmd.exe command prompt window] (you can also just double click the bat file; however, if an error arises, the CMD window created will close immediately, so the text of the error will not be available).
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5) wait until it finishes. It should take 30-60 seconds (for a regular PC with 64-bit Windows 10, 3.4 GHz, 32 GB RAM).
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6) compare your results with the data in the results folder of SanXoT_test1_results.zip (for example using a comparison software such as [https://en.wikipedia.org/wiki/Beyond_Compare Beyond Compare]). Only the files ending in *_log.txt and *_infoFile.txt should have differences (and only due to the different path for files, and the timestamp, all other features being identical, such as variances, Levenberg-Marquardt steps, and options).
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==Test 2: Experiment merging==
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Protein quantifications from different technical or biological replicates can be merged into experiment-independent quantifications, giving the biological and technical variance. In this test we
  
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2) download the files for the unit test, '''[[unitTestSanXoT.zip]]'''. Unzip to a working folder. You should have four text files:
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1) use the data from Test 1
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::* commands.bat, a windows batch file with command lines to run this sample analysis.
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2) perform the fundamental workflow for another parallel experiment
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::* startingFile.xls, a tab-separated-values text file with identifications and quantitative data from a proteomics experiment.
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3) we merge both experiments
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::* dbcats_rels.xls, a tab-separated-values with data downloaded from DAVID and modified using '''[[Camacho]]'''.
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::* tagFile.txt, a tab-separated-values with the tags to merge the experiments.
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This test makes use of four programs: '''[[Klibrate]]''', '''[[SanXoT]]''', '''[[SanXoTSieve]]''', and '''[[Cardenio]]'''.
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To run this unit test, follow these steps:
  
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3) Get the path of your working folder and modify the following lines in the command.bat text file accordingly:
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1) use the windows executables unzipped in step 1 of Test 1.
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2) download the files for the unit test, '''[[SanXoT_test2.zip]]'''. This contains all the files generated in Test 1, with the addition of the tag file (for '''[[Cardenio]]''').
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3) remember to change the following lines in the command_test2.bat file, as in step 3 for Test 1:
  
 
  set unit=D:
 
  set unit=D:
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  set programFolder="D:\programs\sanxot\standalone exes"
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  set programFolder="D:\SSP"
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  set workingFolder="D:\sanxot_unit_test\data"
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  set workingFolder="D:\unitTest"
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4) Execute the bat file, copy and paste the whole commands.bat text into a [https://en.wikipedia.org/wiki/Cmd.exe command prompt window] (you can also just double click the bat file; however, if an error arises, the CMD window created will close, so the text of the error will not be available).
 
  
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5) Wait until it finishes, in about 1-2 minutes (for a regular PC)
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4) execute the bat file (same as step 4 in Test 1).
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5) wait until it finishes. As in Test 1, this test should take 30-60 seconds (for a regular PC with 64-bit Windows 10, 3.4 GHz, 32 GB RAM).
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6) As in Test 1, the only files that are not identical should be the merge_logFile.txt from Cardenio, and the *_infoFiles.txt from SanXoT, SanXoTSieve and Klibrate.
  
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6) Compare your results with the data in the results folder of unitTestSanXoT.zip (for example using a comparison software such as [https://en.wikipedia.org/wiki/Beyond_Compare Beyond Compare]).
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==Test 3: Systems biology==

Revision as of 11:51, 14 February 2018

We present here three unit tests for windows that can be performed using the following programs in the SanXoT software package:

For detailed explanations, check notes about the Unit test for SanXoT.

Test 1: The fundamental workflow

The fundamental workflow consists in the steps to quantify proteins using PSMs and quantitative information, following the steps:

1) calibration of spectra 2) integrating from spectra to peptides 3) integrating from peptides to proteins 4) quantifying proteins

This test makes use of four programs: Aljamia, Klibrate, SanXoT, and SanXoTSieve.

To run this unit test, follow these steps:

1) download the windows executables, SanXoT.zip. Unzip them in a folder specific for the program. 2) download the files for the unit test, SanXoT_test1.zip. Unzip to a working folder. You should have four text files:

  • commands_test1.bat, a windows batch file with command lines to run this sample analysis.
  • startingFile.xls, a tab-separated-values text file with identifications and quantitative data from a proteomics experiment.

3) Get a) the path of your working folder (where you have unzipped the startingFile.xls), b) the path of the folder where you have unzipped the windows executables, and c) the unit of the latter (C:, D:, etc); modify the following lines in the command_test1.bat file accordingly: 

set unit=D:
set programFolder="D:\SSP"
set workingFolder="D:\SanXoT_test1"

4) execute the bat file, copy and paste the whole commands_test1.bat text into a command prompt window (you can also just double click the bat file; however, if an error arises, the CMD window created will close immediately, so the text of the error will not be available). 5) wait until it finishes. It should take 30-60 seconds (for a regular PC with 64-bit Windows 10, 3.4 GHz, 32 GB RAM). 6) compare your results with the data in the results folder of SanXoT_test1_results.zip (for example using a comparison software such as Beyond Compare). Only the files ending in *_log.txt and *_infoFile.txt should have differences (and only due to the different path for files, and the timestamp, all other features being identical, such as variances, Levenberg-Marquardt steps, and options).

Test 2: Experiment merging

Protein quantifications from different technical or biological replicates can be merged into experiment-independent quantifications, giving the biological and technical variance. In this test we

1) use the data from Test 1 2) perform the fundamental workflow for another parallel experiment 3) we merge both experiments

This test makes use of four programs: Klibrate, SanXoT, SanXoTSieve, and Cardenio.

To run this unit test, follow these steps:

1) use the windows executables unzipped in step 1 of Test 1. 2) download the files for the unit test, SanXoT_test2.zip. This contains all the files generated in Test 1, with the addition of the tag file (for Cardenio). 3) remember to change the following lines in the command_test2.bat file, as in step 3 for Test 1: 

set unit=D:
set programFolder="D:\SSP"
set workingFolder="D:\unitTest"

4) execute the bat file (same as step 4 in Test 1). 5) wait until it finishes. As in Test 1, this test should take 30-60 seconds (for a regular PC with 64-bit Windows 10, 3.4 GHz, 32 GB RAM). 6) As in Test 1, the only files that are not identical should be the merge_logFile.txt from Cardenio, and the *_infoFiles.txt from SanXoT, SanXoTSieve and Klibrate.

Test 3: Systems biology

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