Command Line Tools

This is a set of Perl scripts that allow you to submit Mascot jobs and download the results from the command line.

It is only of interest to developers who wish to create their own workflows/tools that involve Mascot searches.

There are three main scripts:

• daemon2MIME.pl This script creates a MIME format file from a Mascot Daemon Parameter file (which contains the Mascot search parameters) and a MS peaklisted specturm file (i.e. a mgf file). daemon2MIME.pl -p <Mascot Daemon parameter file> -f <input sepctrum file> This creates and saves the MIME file as "<input sepctrum file>.MIME". This file can be used by the next tool, or submitted directly to the Mascot executable if you have access to a Mascot headnode. 
• submitMIMEToMascot.pl This script sends a MIME file to the Mascot Server hardcoded inside the script. submitMIMEToMascot.pl -f <mimefileupload> -u <mascot username> -p <mascot password> This program waits until the job is finished before exiting. It does not retry if the server is busy. It writes to stdout the output of the Mascot executable in real time, just as if you had submitted a job inside a web browser.  
• downloadMascotResult.pl is similar to mascotDownload! Except it is in Perl and you can not register your username. downloadMascotResult.pl -f <file path on server given in URIs> -u <mascot username> -p <mascot password> [ -d local_dir_to_download_to]  e.g. downloadMascotResult.pl -f E:/data/20111101/F162934.dat -u username -p password -d C:temp
• exportMascotResult.pl is similar to mascotDownload. It performs a Mascot 'Export' function, according to hard-coded parameters in the Perl file. You will need to edit the file to change the paramters or modify the export type. 
• exportMascotResult.pl -f <file path on server given in URIs> -u <mascot username> -p <mascot password> [ -d local_dir_to_download_to] 
• e.g. to put it in Mascot Daemon, perl exportMascotResult.pl -f <resultfilepath> -u username -p password -d C:temp

Download

Download Perl scripts

There is only limited error-checking in any of the Perl scripts.

Tools

• APLToMGFConverter
• mascotResultDownload