edit pass through the deepgoplus tutorial.

dataAnalysis/GenomeAnnotation/DeepGoPlus_AI_Functional_Prediction_of_Proteins.md

@@ -8,21 +8,25 @@ header:
   overlay_image: /assets/images/dna.jpg
 ---
 
-DeepGOPlus is a bioinformatics tool designed for protein function prediction using deep learning. It combines convolutional neural networks with sequence-based features to predict Gene Ontology (GO) terms for proteins. This tool is particularly useful for large-scale genome annotation and proteome analysis, though a webserver is currently availble for smaller requests: https://deepgo.cbrc.kaust.edu.sa/ . Frequently genome annotation projects will produce tens of thousands of genes, and depending upon the model status of your chosen species, many of these genes may lack significant homology to anything availabe in current databases. This software is not a replacement for identifying ontology terms using interproscan, but an alternative for novel gene candidates. 
+DeepGOPlus is a bioinformatics tool designed for protein function prediction using deep learning. It combines convolutional neural networks with sequence-based features to predict Gene Ontology (GO) terms for proteins. This tool is particularly useful for large-scale genome annotation and proteome analysis, though a [webserver](https://deepgo.cbrc.kaust.edu.sa/) is currently available for smaller requests. Frequently, genome annotation projects will produce tens of thousands of genes, and depending upon the model status of your chosen species, many of these genes may lack significant homology to anything available in current databases. This software is not a replacement for identifying ontology terms using interproscan, but an alternative for novel gene candidates. 
 
 
 **Software used in this tutorial**
 * Kulmanov, M., & Hoehndorf, R. (2020). DeepGOPlus: Improved protein function prediction from sequence. *Bioinformatics*, 36(2), 422–429. https://doi.org/10.1093/bioinformatics/btz595
 * Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. *Nature Methods*, 12(1), 59–60. https://doi.org/10.1038/nmeth.3176
+* [Github Repository](https://github.com/bio-ontology-research-group/deepgoplus)
 
 
+## Installation  of DeepGOPlus and prerequisite software
 
+#### Create conda environment in python 3.7.9
 
-### Installation
+* create conda environment
+* activate conda environment
+* create python virtual environment
+* upgrade pip and setuptools
 
-**Installation of DeepGOPlus**
-```
-#create conda environment in python 3.7.9
+```bash
 ml miniconda3
 conda create -n deepgoplus_env python=3.7.9
 
@@ -39,59 +43,106 @@ source DeepGoPlus_pyenv/bin/activate
 
 #upgrade pip and setuptools
 pip install --upgrade pip setuptools
+```
+
+
+
+#### Download the repository 
 
-#download the repository 
+* Download the repository
+* install the requirements
+
+```bash
 git clone https://github.com/bio-ontology-research-group/deepgoplus.git
 cd deepgoplus/
 pip install -r requirements.txt
 pip install deepgoplus
+```
+
+
+#### Download the metadata and training datasets
+
+* download datasets
+* copy metadata to data folder
 
-#download the metadata and training
+```bash
 wget http://deepgoplus.bio2vec.net/data/data.tar.gz
 
 #automatically unpacks into data folder if within deepgoplus
 tar -zxvf data.tar.gz
 
-
 cp -rf metadata/ data/.
 ```
 
-**Install Diamond BLAST to path**
-```
+#### Install Diamond BLAST
+
+* download tar ball
+* add to PATH variable
+
+```bash
 wget http://github.com/bbuchfink/diamond/releases/download/v2.1.9/diamond-linux64.tar.gz
 tar xzf diamond-linux64.tar.gz
 
 #add to .bashrc and source or run in terminal for temporary access
 export PATH="/work/gif3/masonbrink/Software/:$PATH"
 ```
 
-**I had to modify the update.py script to get around the check for the uniprot header. This header must not exist anymore.** 
-```
-# Release information
-Current version is 1.0.21. The model in the current release was trained using the Gene Ontology
-released on 2024-09-08 and the SwissProt data with version 2024_05.
+## Run the database update.py script
+
+In order for this to run properly, I had to modify the update.py script to get around the check for the uniprot header. This header is not required and is not found in the dataset we downloaded.
+
+
+* Release information
+  * Current version is 1.0.21
+    * Gene Ontology released on 2024-09-08
+    * SwissProt data with version 2024_05.
+
 
-python update.py
 
+The following lines need to be modified in the `update.py` script. 
+
+```python
 #allow check for header to pass
 if last_release_version == new_release_version:
-#to 
+```
+
+to 
+
+```python
+#allow check for header to pass
 if last_release_version != new_release_version:
+```
+
+And Updated uniprot address
 
-#Updated uniprot address
-#this line
+```python
 response = requests.get('https://www.uniprot.org')
-#to
+```
+
+to
+
+```python
 response = requests.get('https://rest.uniprot.org/uniprotkb/search')
+```
+
+Once these have been updated we can run 
 
-# this allows the update and retraining of the databases 
-python update.py 
+```python
+python update.py
 ```
 
 
-### Proceed with DeepGoPlus Run 
+
+
+## Run DeepGoPlus analysis
+
+* Download some fun data from a plant parasitic nematode
+* Format the data
+* Run DeepGoPlus
+* Format the output
+
 ```
-#get some fun data from a plant parasitic nematode
+
 wget https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS19/species/ditylenchus_dipsaci/PRJNA498219/ditylenchus_dipsaci.PRJNA498219.WBPS19.protein.fa.gz
 
 # this will save formatting steps later, reducing the fasta header to just the basic name (first column).
@@ -100,7 +151,7 @@ less ditylenchus_dipsaci.PRJNA498219.WBPS19.protein.fa |awk '{print $1}' >Cleand
 # use the same threshold as the online database
 ml miniconda3; conda activate deepgoplus_env; source bin/activate ; deepgoplus -if Cleanditylenchus_dipsaci.PRJNA498219.WBPS19.protein.fa -dr data/ -of results_DDipsaci -t 0.3
 
-
+# format the output
 awk 'NF>3' results_DDipsaci |sed 's/\t/#/1' |sed 's/\t/,/g' |sed 's/#/\t/g' >DeepGoPlusResults.tab
 ```