README

Welcome to our TCGA code repository! With this code you can parse and analyze 
the output of the VEP (Variant Effect Predictor by ENSEMBL). The scripts included
here are:

vep_parser.py : parses the output of the VEP
vep_results.py : analyzes the parsed output
figures.vep.py : plots the output of vep_results.py
params.py : a parameter file not meant to be run


The parameter file goes as follows:


params.py

## chrom = chromosome
## datafile = input file name prefix
## ignore_consequence = consequence to ignore. Currently takes only one value
## sift = maximum sift score allowed, this also blocks out all mutations that do not
##			have sift scores
## catalogue = catalogue which gene names are taken from
## n_runs = number of times the unique pairs of individuals are run

chrom = '1'
datafile = 'VEP_output_'
ignore_consequence = 'downstream_gene_variant'
sift = 0.05
catalogue = 'HGNC'
n_runs = 100




vep_parser.py

input: from params.py
output : mutation_array_cCHROMOSOME_sSIFT*100.dat
		 individuals_cCHROMOSOME.txt
		 genes_cCHROMOSOME.txt

This script is designed to take output from the VEP and put it into a readable
array of n_individuals x n_genes. It reads in the file line by line, saving the
human IDs and gene names. Then it creates the array in the correct size. It then
re-reads the file, populating the array. It then prints the array to file.


vep_results.py

input :  mutation_array_cCHROMOSOME_sSIFT*100.dat
		 individuals_cCHROMOSOME.txt
		 genes_cCHROMOSOME.txt

output : individual_pairs_overlap_cCHROMOSOME_sSIFT*100.txt
		 gene_pairs_overlap_cCHROMOSOME_sSIFT*100.txt
		 
This script reads in the output from vep_parser.py and runs it through two analysis
functions to output recurring genes in pairs of individuals and recurring pairs 
of genes. The input files individuals_c* and genes_c* are not necessary at this
moment, but might be used to limit the scope of future analysis, such as by 
population or to another smaller set of people.


vep_figures.py

input : individual_pairs_overlap_cCHROMOSOME_sSIFT*100.txt
		gene_pairs_overlap_cCHROMOSOME_sSIFT*100.txt
		genes_cCHROMOSOME.txt

output : plots/pair_distribution_cCHROMOSOME_sSIFT*100.png
		 plots/gene_pairs_cCHROMOSOME_sSIFT*100.png


This script plots the output of vep_results.py. It plots the overlapping genes
in unique pairs of individuals as a set of n_runs histograms. The colours are
the automatic python colours, but are not important on their own. The second
plot is a temperature map of how frequently pairs of genes occur in the sample set.
A gray square indicates that the pair of genes does not occur in the sample, 
whereas a black square shows that all of the people have these two genes mutated.