oddsandends.md

#Other things

Permissions

chmod +x filename

This makes files executeable. Reading on permissions.

##Python Path

Many computer scientists advise creating a single directory for all your scripts, and putting that in what is called your PythonPath.

I keep most of my scripts in a directory called scripts. In my .bashrc file, I include a line that says:

export PATH="/home/april/scripts:$PATH"

This allows me to execute my scripts from the scripts folder from anywhere on my computer.

##Scripts as modules

if __name__ == '__main__':
    get_files()

This line looks kind of weird. What it enables is a script to be loaded as a module. If, now I got to ipython, or include an import statement in a script, I can access the functionality of my get_files function. See the script file_load.py for an example.

##Interesting Modules for Biologists

###Sci-Kit Bio

Methods for parsing and formatting sequence data, playing with trees and automating testing.

http://scikit-bio.org/

###Sci-Kit Learn

Tools for data mining and analysis. PCA, regression, model selection and other mathematical operations.

http://scikit-learn.org/stable/index.html

Dendropy

Tools for manipulating phylogenetic trees and associated data matrices. Also has nice integration with various phylogenetic software.

http://pythonhosted.org/DendroPy/

Biopython

Biopython has tools mostly aimed at molecular biologists. DNA sequence parsing, format conversion

http://biopython.org/wiki/Main_Page