AltHap Files

Python implementation

1. Prerequest

In python version of AltHap, we use python 2.7.12, numpy 1.10.4, scipy 0.17.0 and Anaconda 4.0.0 (which may not be necessary).

2. Usage

usage: python AltHap.py [OPTIONS]

The parameters to AltHap are given in -<parameter> <value> or
--<parameter>=<value> pairs if there are arguments or -<parameter> or
--<parameter> for boolean switches.

Example usage:

python AltHap.py -i sim0.txt -p 3

3. Required arguments

To get AltHap run, 2 parameters are required: input file name and ploidy, the easiest command line is as shown above in Usage part.

-i, --input <input file name>: 
Specify the path of input file the algorithm takes in

-p, --ploidy <ploidy number>:
Specify the number of haplotype sequences (e.g., 2 for humans) to recover.

4. Optional arguments

-o, --output <output file name>:
Specify the path of output file

-h, --help:
Print out the usage of this code and exit

-s, --sumproj:
Turn off the entry normalization for V during iteration (Only for ployploid ployallelic case)

-m, --maxiter <max iterations>:
Specify maximum number of iteration

-t, --threshold <threshold>:
Specify the threshold for iteration