This project is for analysis of conotoxins. This project mainly used the following external modules (and all their dependencies):
- wxPython
- BioPython
- matplotlib
- scikit-learn
The current build is hosted on Dropbox, mainly due to being too large for Github in its zipped form (105 MB), and being over 300 MB in its uncompressed form. The current build is here: https://www.dropbox.com/s/lcriv3gxwsrynos/build.zip
The project right now is extremely unorganized, but this is the general ordering of things:
- The database of conotoxins was downloaded from ConoServer.
- Various sequences for different things were pulled from the database using the xml*Parse scripts in the consensus folder, and slightly modified depending on the data I wanted.
- xmlMachParse script in the consensus folder was used for generating the files in the nested MachineParse folder. These csv files were used to try to find well defined clusters for the Pharmacological Groups.
- The graphResults script takes the csv files in the MachineParse directory and graphs them using the matplotlib package. This is a poorly written script, various elements have to be altered in the code, rather than provided at the command line to change what is graphed.
- The alignFam folders in the consensus directory contain various groups of sequences that were pulled using the xmlParse scripts, then aligned using Clustal Omega (not ClustalW2!).
- The *_tree.txt files are phylogenetic trees in the Newick format, generated from ClustalW2 Phylogeny. These can be redrawn using any tool that can interpret the common Newick tree format.
- The submodules directory is meant to contain scripts that the ConoGUI calls to get stuff done.
- The __conotoxin __ script was the original attempt at a CLI tool, but has since been scrapped.