Add Usage and G25 score calculation instructions

README.md

@@ -5,6 +5,8 @@
 
 ## Table of Contents
 1. [Installation](#Installation)
+2. [Usage](#Usage)
+3. [How to convert the result into G25 scores](#How to convert the result into G25 scores)
 
 ## Installation
 
@@ -14,3 +16,45 @@ Currently, the best way to install Diablo G25 is to git clone the repository and
 git clone https://github.com/TheSergeyPixel/Diablo_G25
 conda env create -f /path/to/cloned/repo/diablo_g25.yml 
 ```
+You can also git clone the repository and manually install the required packages as follows:
+
+```
+git clone https://github.com/TheSergeyPixel/Diablo_G25
+conda install pandas>=1.5.1
+conda install numpy>=1.23.4
+pip install admix
+```
+
+
+We are currently working on creating conda package.
+
+## Usage
+
+Diablo G25 requires basic **gzipped** VCF file (for example, HaplotypeCaller + GenotypeGVCFs output) as input. The output 
+is always generated as tsv file. Run main.py from downloaded repository as follows:
+
+```
+python main.py -i /path/to/vcf/file.vcf -o /desired/output/direcotry/output.tsv -m model_name
+```
+```-i``` and ```-o``` arguments are always required.<br/>
+<br/>
+23andMe style tsv file with all genotypes will be generated in the directory of output file. <br/>
+<br/>
+For the ```-m``` option, enter the name of any model provided by [admix](https://github.com/stevenliuyi/admix#models).
+If ```-m``` is not provided, K36 model will be used by default.
+
+## How to convert the result into G25 scores
+
+After you have obtained the scores for the model you chose, you can convert them into G25 scores via visiting 
+[Allelocator calculator](https://allelocator.ovh/simulatedg25.html) and performing following steps:
+
+1. Paste your result from the Diablo G25 output into **Calculator results** field
+2. Choose the model you used from **Linear regression matrix** field
+3. **Simulated G25 coordinates** field will auto generate your simulated G25 scores
+4. You can proceed to [Vahaduo admixture calculator](https://vahaduo.github.io/vahaduo/) to estimate admixture 
+proportions and calculate Euclidean distances.<br\> 
+
+When you open Vahaduo admixture calculator, you would need to paste your G25 coordinates into **target** field, 
+G25 populations (can be downloaded from another [Vahaduo tool](https://vahaduo.github.io/g25download/)) into **source** 
+field followed by choice of desired options and running the tool at **single** tab if you have one 
+sample (line) in your target field or **multi** if you have multiple samples.

main.py

@@ -10,7 +10,7 @@
 
 parser.add_argument('-i', '--input', required=True, help='Input as vcf.gz file', type=str)
 parser.add_argument('-o', '--output', required=True, help='Output in txt file', type=str)
-parser.add_argument('-m', '--model', required=False, help='model to use in admix', type=str)
+parser.add_argument('-m', '--model', required=False, help='model to use for admixture', type=str, default='K36')
 
 args = parser.parse_args()
 

src.py

@@ -9,4 +9,3 @@ def admix(in_file, model):
     ser = df.iloc[:, -1].str.split(": ", expand=True)[1]
     admix_scores = ",".join(a.strip('%') for a in ser)
     return admix_scores
-