README.md

In PBGLMichaelHall/Py_QTL_Parser:

title: "Python QTL"

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Please SEE https://github.com/dblhlx/PyBSASeq for where the python script came frome and who developed it. In this tutorial I develop a generic parser in R which produces an CSV file used as an argument when calling python script PyBSASeq.py. It is another method to perform a Quantitative Trait Locus analysis.

For more efficient comupting of the algorithm please download Fisher's Exact Test.

Installation

Within this folder :

git clone git://github.com/brentp/fishers_exact_test.git
pip install .

From PyPI :

pip install fisher

Or install the development version :

pip install git+git://github.com/brentp/fishers_exact_test.git

For Read the Docs please visit:

https://py-qtl-parser.readthedocs.io/en/latest/Rice_BSA.html

Rice Cold Tolerance:

```{r QTL} devtools::install_github("PBGLMichaelHall/Py_QTL_Parser",force = TRUE) library(PyQTLParser) library(vcfR)

setwd("/home/michael/Desktop/RiceCold/")

file <- "wGQ-freebayes~bwa~IRGSP-1.0~both-segregant_bulks~filtered-default.vcf.gz"

vcf <- read.vcfR(file)

VCF_TIDY <- vcfR2tidy(vcf)

Py_QTL_Parser(vcf = VCF_TIDY, HighBulk = "ET-pool-385", LowBulk = "ES-pool-430")

Run this command in Terminal

python PyBSASeq.py -i Hall.csv -o RiceCold -p F2 -b 430,385 #Please refer to: https://github.com/dblhlx/PyBSASeq/tree/master/BulksOnly for more help #The analysis takes over 4 hours <<<<<<< HEAD

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![TerminalOutput](https://user-images.githubusercontent.com/93121277/156781414-34d8517f-10cc-4bf7-bc2a-f09bb1f2b678.png)
![PYQTL](https://user-images.githubusercontent.com/93121277/156782187-5c642bbb-a09a-4b62-84f0-cd44857c2c07.png)

# Sorghum Semi-Dwarfism:
```r

file <- "freebayes_D2.filtered.vcf"

vcf <- read.vcfR(file)

VCF_TIDY <- vcfR2tidy(vcf)

Py_QTL_Parser(vcf = VCF_TIDY, HighBulk = "D2_F2_tt" , LowBulk = "D2_F2_TT")

#Windows Power Shell Terminal on Windows
#Needed to download visual studio due to fisher exact test uses C++

PS C:\Users\micha\OneDrive\Desktop> python .\PyBSASeq.py -i Hall.csv -o Sorghum -p F2 --smooth TRUE -c 99,5,6,1 -b 45,38 -v .01,.01 -s 5000000,10000 -m 100,3

PBGLMichaelHall/Py_QTL_Parser documentation built on July 30, 2022, 6:15 a.m.