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Instructions for installing the Ascore on a local linux machine


Requirements

1) A computer with linux installed

2) php CLI version must be installed. Go here for more information


Installation

Step 1: Submit your request to download the Ascore here

Step 2: Uncompress the zip file

I made a directory in my home directory called Ascore, then I unzipped the compressed file ascore.zip. You should see a directory structure as shown above. ascore.php is the main executable file, Out2XML is the program used to create a pepxml from your dta/out files.

Step 3: Create a pepxml file using Out2XML. If the precompiled version doesn't work, for more info on Out2XML go here to download and complile your own version go here

Out2XML is called by giving it the path to your dta/out/sequest.params files, followed by a 1 which means we are only making a pepxml file with the #1 hit from Sequest. Note, you must have a sequest.params file with your dta/outs. You can ignore the mzxml warning. In this example my dta/outs/params is in a directory called test. Each outfile must have a corresponding dta file.

Step 4: Analyze your data with ascore.php.

Out2XML creates a .xml file where the file name will be the name of the directory containing your dta/outs/params files. In this example, the directory is test. Out2XML is run as shown above (step 4), and creates a pepxml file named test.xml. DO NOT MOVE THE XML FILE. ascore.php is called with the '-f <path to xml file>'. The ascore output is shown where score is the peptide score and delta is the Ascore for each site from left to right.

Step 5: Review your data

The output should look like what you see above. When complete you will see a file ending with ASCORE.csv. This is a csv file which you can open with a spreadsheet program with outputed data. In this example the output file is named 'testASCORE.csv' because the xml file used was test.xml. Column 1 is the peptide score, 2 is the ascore sequence, 3 is the first ascore from left right followed by up to 6 more. The last column is the name of the out/dta file. That's it, email me if you have any questions.


Sample Data
Dta/Out/sequest.params file click here (right click to save as).
The resultant pepxml file from the above data click here (right click to save as).