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ScoringModule  
Updated Aug 23, 2011 by ramdo...@gmail.com

Scoring Module v1.0

Introduction

Scoring Module is an interface that allows users to sort a list of experiments, select the ones they need and provides them with the tools to create a file with the experiment IDs and the Treatment/Control (T/C) flag file that is then fed to the script export_saint.pl. The interface also allows the user to pass in the output files directly to SAINT/Compass.

Interface

The interface can be run from: http://tin.emililab.edu/Prohits/analyst/scoring_module/scoring_module.cgi

Scoring module allows the user to select their username and to select whether they want to display only their data or all of the data by checking on/off the checkbox on the welcome page.

After running the interface and creating the T/C flag file, that file will be available for download via htp in the next window that appears.

Example: Your input file (data_1314086188.txt) has been processed. Click here to download data_1314086188.txt It will be in the /smfiles/ folder.

10 Steps

Step1: Run export_saint.pl by running this shell command below (copy and paste in shell command window): (The link below will be autogenerated, but if you would like to run it on a different file, please replace

<your_text_file_name_here>
with your data file)

./export_saint.pl --experiments --experiments /var/www/html/Prohits/analyst/scoring_module/smfiles/

<your_text_file_name_here>
--fasta FINV_uniprot_sprot_human_BSA_TRY_BCN_GFP_TEV_JO041210.fasta --host tin.emililab.edu --database Prohits --password prohits -user prohits --keep none ls

Step2: After the command is successfully run, you can download the inter.dat, pre.dat and bait.dat files here below:

To download the output files, please click on these links after the process has completed:

Download: http://tin.emililab.edu/Prohits/analyst/scoring_module/bait.dat \n

Download: http://tin.emililab.edu/Prohits/analyst/scoring_module/prey.dat

Download: http://tin.emililab.edu/Prohits/analyst/scoring_module/inter.dat

Running SAINT

Step3: You can run saint by running the shell command below (copy and paste in shell command window):

./saint-spc-ctrl inter.dat prey.dat bait.dat 2000 10000

Step4: After running saint successfully, you can download the result files from the links below

To download the SAINT computed files, please click on these links after the process has completed:

http://tin.emililab.edu/Prohits/analyst/scoring_module/RESULT/

Running COMPASS

Step5: After downloading the inter.dat file from the link above, please run COMPASS using the inter.dat file and the script found on:

http://code.google.com/p/prohits/source/browse/trunk/Prohits/script/export_saint.pl

After running COMPASS, that will create 2 files. Please save the one called 'inter_compassscores_cytoscape.txt' as we will need this in Step 7

Step6: You need to fix the SAINT and COMPASS files. SAINT output file 'unique_interactions' has a bug that needs to be corrected To fix the bug, you will have to run the python script 'fix_saint_1.01.py' on the file 'unique_interactions' The python script found on:

http://code.google.com/p/prohits/source/browse/trunk/Prohits/analyst/scoring_module/Scripts/fix_saint/fix_saint_1.01.py fixes this issue

Step7: Your COMPASS file generated has duplicate entries in it with different scores. This needs to be collasped and an average must be calculated. To do this, you will have to run the python script 'collapse_compass.py' on the file 'inter_compassscores_cytoscape.txt' The python script found on:

http://code.google.com/p/prohits/source/browse/trunk/Prohits/analyst/scoring_module/Scripts/collapse_compass/collapse_compass.py

Normalizing results

Step8: After running Steps 6 and 7, you will have 2 new files 'unique_interactions_fixed' and 'collapsed_compass.txt' Your final task before uploading the results is to normalize the COMPASS scores and merge both SAINT and COMPASS scores into one file and upload it

To do this, you will have to run the python script 'combine_saint_comp.py' on the files 'unique_interactions_fixed' and 'collapsed_compass.txt' The python script can be found on:

http://code.google.com/p/prohits/source/browse/trunk/Prohits/analyst/scoring_module/Scripts/normalize/combine_saint_comp.py

Uploading results to database

Step9: After running Step 8, you now have the final file with the results: combined_saint_compass.txt

Use the interface on:

http://tin.emililab.edu/Prohits/analyst/scoring_module/upload_results.cgi

to upload your results to the database

Analysis Interface

Step 10: Click on this page to view the data and analyse

http://tin.emililab.edu/Prohits/analyst/scoring_module/analysis.cgi

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