HIGHEST VALUE
(Author: Elena Kochetkova)
PROGRAM DESCRIPTION
This python-based program is useful for determining the 5% highest chi-squared values among the 500 analyses. This program finds the highest chi-square value for each permutation in a permutation analysis using “Qilin2”. The program reads the output file from the Univariate logistic regression analysis in SAS and discards the titles, storing only the amino acid positions and chi-squared values. Then, the program selects the highest chi-squared value within a single permutation and stores it in an output file.
Using Highest Value
Type "python highest_valuenew.py" in bash prompt to run Highest Value. The program then prompts the user to type the file path and name for the lst file to analyze and the number of chi-squared values in each permutation (this is equivalent to the number of polymorphic amino acids in the original alignment used for data analysis)
Output files
The first output of the program is the .lst original file without titles. It is usually named “originalfilename.lst.out”. This file is then used by the program to identify the highest chi-squared value of each set of amino acids. There are as many chi-squared highest values as permutations analyzed in the SAS program. The highest chi-squared value in each permutation is stored in the file “highest.out”. This can be easily imported in a word processing program.
DOWNLOAD
Program: highest_value.py
Sample input: output100peryeastclean.lst
Sample output: output100peryeastclean.lst.out , highest.out