The snpDensityMatrix script is used to read files from a snp pipeline output directory and output an interactive web page based visualization of snp density, depth of reads, and possible recombination represented with a phi statistic. This script takes the optional arguments window size, and step size, an argument for the snp pipeline format and a positional argument for the root directory of the snp pipeline output. The window size is the range in which a snp density will be captured per window, the step size is the length of spaces the window will be moved forward for the next density capture window, and the DIR is the location of the snp pipeline output that will be measured.
snpDensityMatrix is called with the following command line prompt:
$ snpDensityMatrix.py [-h, --help] [--window WINDOW] [--step STEP] [--nasp | --cfsan | --lyve | --snvphyl] DIR
The following is a list of arguments for snpDensityMatrix:
Displays the help menu for snpDensityMatrix before exiting.
Set size of capture window to measure snp density.
Set step size to move window down snp matrix.
[--nasp | --cfsan | --lyve | --snvphyl]
Flag used for snp pipeline format.
Root directory for snp pipeline output.
Running snpDensityMatrix to get the snp density visualization for snp pipeline output located at './example/snpOut/', with a window size of 1000 and a step size of 500:
$ snpDensityMatrix.py --window 1000 --step 500 --nasp ./example/snpOut/
Would result in the command line output:
====================( Job Starting: snpDensityMatrix.py )
(1/3) gathering coverage from BAM/VCF files
creating file "./snpDensityOut/snpPositions.txt"
creating file "./snpDensityOut/Sample1-Depth.txt" (1 of 10)
creating file "./snpDensityOut/Sample2-Depth.txt" (2 of 10)
creating file "./snpDensityOut/Sample3-Depth.txt" (3 of 10)
creating file "./snpDensityOut/Sample4-Depth.txt" (4 of 10)
creating file "./snpDensityOut/Sample5-Depth.txt" (5 of 10)
creating file "./snpDensityOut/Sample6-Depth.txt" (6 of 10)
creating file "./snpDensityOut/Sample7-Depth.txt" (7 of 10)
creating file "./snpDensityOut/Sample8-Depth.txt" (8 of 10)
creating file "./snpDensityOut/Sample9-Depth.txt" (9 of 10)
creating file "./snpDensityOut/Sample10-Depth.txt" (10 of 10)
(2/3) processing hash table
processing 1 of 1 contigs |▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉| (100%)
(3/3) writing results csv file
creating file "./snpDensityOut/snpDensityMatrix.csv"
====================( Total Time: 0:0:1:11 )
====================( Job Complete: snpDensityMatrix.py )