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== Python Scripts ==
== Python Scripts ==
Revision as of 03:41, 7 January 2010
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. A few are written as a list of unix commands designed to be executables.
Python Script Conventions
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. Some scripts have modifiers that require arguments of their own. These modifier arguments should be written directly after their respective modifier. For example, if the above modifier, -c, had a argument, one would type,
python sumqual.py -c theArgument -v ../myQualFile.qual ../myMumFile
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,
would cause a help menu to be printed to the screen.
Turn a list of annotations, that contians the start and stop indices, into a list of base indices, each followed by all the annotations that apply to it. baseanno.py