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ScoringModule
Scoring Module v1.0IntroductionScoring 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. InterfaceThe 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 StepsStep1: 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 SAINTStep3: 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 COMPASSStep5: 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: Normalizing resultsStep8: 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: Uploading results to databaseStep9: 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 InterfaceStep 10: Click on this page to view the data and analyse http://tin.emililab.edu/Prohits/analyst/scoring_module/analysis.cgi |