Liston:Computer Scripts

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This page contains the source code for some of the bioinformatics scripts used by the Liston Lab. Most of the scripts are writen in Python 2.6.4 and are designed for Unix systems. The scripts must be compiled useing a Python compilier in the following format:  
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This page contains the source code for some of the bioinformatics scripts used by the Liston Lab. Most of the scripts are written in Python 2.6.4 and are designed for Unix systems. The scripts must be compiled using a Python compiler in the following format:  
     python theScript.py [modifiers] <Arguments>.  
     python theScript.py [modifiers] <Arguments>.  
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For example, in order to run the script sumqual.py one could enter the following into an unix shell:
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For example, in order to run the script sumqual.py one could enter the following into an Unix shell:
     python sumqual.py -c -v ../myQualFile.qual ../myMumFile
     python sumqual.py -c -v ../myQualFile.qual ../myMumFile
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This would complile and run the script sumqual.py with the modifiers -c and -v, useing myQualFile.qual  and myMumFile as arguments. All of the scripts save their output in a file in the current working directory, with a name usually composed of some combination of the arguments and the name of the script. However, one can save the output anywhere, under any name, useing the following technique:
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This would compile and run the script sumqual.py with the modifiers -c and -v, using myQualFile.qual  and myMumFile as arguments. All of the scripts save their output in a file in the current working directory, with a name usually composed of some combination of the arguments and the name of the script. However, one can save the output anywhere, under any name, using the following technique:
     python sumqual.py -c -v ../myQualFile.qual ../myMumFile > ../myOutput.ext
     python sumqual.py -c -v ../myQualFile.qual ../myMumFile > ../myOutput.ext
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The order in which the modifiers are given is not important, however, the order of the required arguments is important. For Example the above modifiers could be entered in the oppisite order (-v -c), but the two file paths need to be in a predetermined order. Every Script has a discription of what it does and how/when to use it in its source code. The list all the modifiers that the script supports and hat they do is also included. A similiar help menu can be viewed by calling the script with no arguments. For example, typing the following,
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The order in which the modifiers are given is not important, however, the order of the required arguments is important. For Example the above modifiers could be entered in the opposite order (-v -c), but the two file paths need to be in a predetermined order. Every Script has a description of what it does and how/when to use it in its source code. The list all the modifiers that the script supports and what they do is also included. A similar help menu can be viewed by calling the script with no arguments. For example, typing the following,
     python sumqual.py
     python sumqual.py
would cause a help menu to be printed to the screen.
would cause a help menu to be printed to the screen.

Revision as of 21:15, 30 December 2009

This page contains the source code for some of the bioinformatics scripts used by the Liston Lab. Most of the scripts are written in Python 2.6.4 and are designed for Unix systems. The scripts must be compiled using a Python compiler in the following format:

   python theScript.py [modifiers] <Arguments>. 

For example, in order to run the script sumqual.py one could enter the following into an Unix shell:

   python sumqual.py -c -v ../myQualFile.qual ../myMumFile

This would compile and run the script sumqual.py with the modifiers -c and -v, using myQualFile.qual and myMumFile as arguments. All of the scripts save their output in a file in the current working directory, with a name usually composed of some combination of the arguments and the name of the script. However, one can save the output anywhere, under any name, using the following technique:

   python sumqual.py -c -v ../myQualFile.qual ../myMumFile > ../myOutput.ext

The order in which the modifiers are given is not important, however, the order of the required arguments is important. For Example the above modifiers could be entered in the opposite order (-v -c), but the two file paths need to be in a predetermined order. Every Script has a description of what it does and how/when to use it in its source code. The list all the modifiers that the script supports and what they do is also included. A similar help menu can be viewed by calling the script with no arguments. For example, typing the following,

   python sumqual.py

would cause a help menu to be printed to the screen.

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