merge front to master

.gitignore

@@ -1,8 +1,5 @@
 # Byte-compiled / optimized / DLL files
-<<<<<<< HEAD
-=======
 cirDraw/cirDraw/__pycache__
->>>>>>> front
 __pycache__/
 *.py[cod]
 *$py.class
@@ -99,6 +96,8 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+django-env/
+d-env/
 
 # Spyder project settings
 .spyderproject
@@ -117,3 +116,28 @@ dmypy.json
 
 # Pyre type checker
 
+
+# vscode
+.vscode/
+
+# circDraw storage file
+density_result/
+md5_data/
+tops_result/
+
+# ignore genome decompress data
+RMBase_hg19_all_mod_snp_disease*
+RMBase_hg19_all_m1A_site*
+RMBase_hg19_all_m6A_site*
+gencode*
+gencode*
+RMBase_hg19_all_m5C_site*
+PMC-ids.csv
+
+# Django migration
+migrations/
+
+# Macos
+.DS_Store
+
+

README.md

@@ -2,50 +2,123 @@
 
 # CircDraw
 
-An online circRNA visualization and analysis tool. 
+An online circRNA visualization, analysis tool with epigentic annotation.
 
 Using [circDraw](http://www.circdraw.com)
 
-### Introduction
+## Introduction
 
 The circDraw allow visualization circRNA analysis results of circRNA analysis tools. It's user friendly and allow you to get your picture within few clicks. 
 
-<p align="center"><img src="home.png" alt="300" width="cover"></p>
+<p align="center"><img src="src/home.png" alt="300" width="cover"></p>
 
+##  
 
+## Manual
 
+### File Upload
 
-### Manual
+CiriDraw supports [.BED](https://www.ensembl.org/info/website/upload/bed.html) type file generated by any circRNA software. Each line will be intepretated as a circRNA. If you are not using a .BED file, you can try to modify it into the following format.
 
-#### File Upload
+The basic .BED file requires at least 3 columns.
 
-Supported circRNA software
+1. Chr: The chromosome location of circRNA.
+2. Start: The start site of circRNA.
+3. End: The end site of circRNA.
 
-- CIRI2
+If you have forth column that provide the Name of the circRNA, we will display it in the result.
+
+4. Name (Option): Name of circRNA
 
 
 
 Upload instruction:
 - Click the `GET START!` button from the main page or use navigation button `TOOLS` to go to upload page.
 
 
-- Use `+ Select File` and `Submit` button to upload file from your upstream processing software for circle RNA prediction, for example CIRI2. *Please note that we only support one file at a time for now.*
+- Use `+ Select File` and `Submit` button to upload file from your upstream processing software for circle RNA prediction.
+
+<p align="center"><img src="src/upload_blank.png" alt="300" width="uploadr"></p>
+
+- Wait for about 1-3 mins depending on your network speed.
+- When the `View Result` button arise, please remenber the link to retrieve your result, you result will be accessible in the next 24h. Now please enjoy the show!
+
+<p align=center><img src="src/example.png"></p>
+
+- You can also click `Example` button to load preloaded data to fast view on what circDraw can provided.
+
+
+### circRNA density distribution analysis
+By processing the uploaded file in backend, you will be able to __interactively__ view the circRNA density distribution on chromosome. Choose your interesting region and then click on it to display it in detailed map. Most of the region contain only 1 circRNA, so it will be a bit messy if you don't set the limit.
+
+<p align="center"><img src="src/density_nofilter.png" alt="300" width="cover"></p>
+
+
+[//]: # "### How to read Results?"
+
+When we set the limit to 15, the plot become much clear, it's easily for you to identify the hub gene with most isoforms.
+
+<p align='center'>
+  <img src='src/density_filter_15.png'>
+</p>
+
+
+### Detailed map of circRNA region.
+
+When the user choose no region from the density map, detailed map will display the first density region. Using the selector to select which gene or genes that you are interesting in. CircDraw provided epigenetic annotation for human circRNA. The data is from [RMBase](https://academic.oup.com/nar/article/46/D1/D327/4429298).
+
+<img src='src/isoformplot_ttn_m6A.png'>
 
-<p align="center"><img src="upload.png" alt="300" width="uploadr"></p>
+- How to read this map?
+  - **Black curve line**: The back-splicing of circRNA, link to the start and end.
+  - **Gene Block** and **Exon Block**: Click to display the name, if the name tags are overlapped, you can drag the name tags.
+  - **circRNA**: Display when clicking on the black curve line.
+    - Epigenetic Type: m6A, m1C, m5C, SNP
+    - Other functional region: ORF, MRE
 
-- Wait for about 1-3 mins depending on your network speed and enjoy the show!
 
 
-### Circle RNA density distribution analysis
-By processing the uploaded file in backend, you will be able to __interactively__ view the circle RNA density distribution results and explore your interest further.
+### General statistics of your circRNA data set
 
-<p align="center"><img src="density.png" alt="300" width="cover"></p>
+- Distrubution of circRNA length
 
+<img src="src/circLen.png">
+
+- Top 20 gene with most circRNA isoforms
+
+<img src="src/toplist.png">
+### Support for Further development
+- Scalibility was fully considered from the beginning of project, it includes:
+	- Extension of Upload Data Format. See details here.
+	- Extension of other annotation data. See details [here](https://github.com/Mr-Milk/circDraw/tree/front/related_genome_info) 
+
+- Easy reproduction server:
+	- CLI([command line interface](https://en.wikipedia.org/wiki/Command-line_interface)) for easy migrations and cleaning data in database for Develop-Testing-Optimize Paradigm. See details [here](https://github.com/Mr-Milk/circDraw/tree/front/process_watchdog)  
+	- CLI that integrates the whole process of inserting data into MySQL database is developed and tested for the use of circDraw processing. See details [here](https://github.com/Mr-Milk/circDraw/blob/front/related_genome_info/oneline.py)
+	- Virtualenv was used during the development and developers who want to re-build the server can use the requirment file in top directory to set up packages needed.
+
+
+
+
+
+### F&Q
+
+#### Will CircDraw store my data and use it in other purpose?
+
+Your data will be deleted from the server in 24 hour after you uploaded it. Any uploaded data will not be used in any kind of statistic service or any other purpose except the analysis and visualization by CircDraw.
+
+#### Is there any limite to the upload file size?
+
+Yes, not more than 30MB. We recommend you filter your data before uploading to have a better visualization result. A larger file will take more time for the server to process.
+
+#### Can CircDraw have more species? More epigenetic annotation?
+
+Yes, we will add more species gradually. But for epigenetic annotation, it depends on the related database, we could only provide such database.
 
-[//]: # (### How to read Results?)
 
 
 ### Used library
+
 #### Backend
 - Python 3: https://www.python.org/
 - Django: https://www.djangoproject.com/
@@ -69,14 +142,15 @@ By processing the uploaded file in backend, you will be able to __interactively_
 - Nginx: https://nginx.org/en/
 - uWSGI: https://uwsgi-docs.readthedocs.io/en/latest/
 
-[//]: # (## About)
+[//]: # "## About"
 
 
 ### More Information
 
 - Citation: 
-
-- Contact: 
+- Contact
+  - Milk [email protected]
+  - JackLi [email protected]
 
 
 Copyright: Qu Lab, School of Life School, Sun Yat-sen University

cirDraw/Dockerfile

@@ -0,0 +1,13 @@
+FROM tiangolo/uwsgi-nginx:python3.7
+
+ENV UWSGI_INI ./docker-deploy/django-uwsgi/uwsgi.ini
+
+
+COPY ./cirDraw /application
+
+WORKDIR /application
+
+
+
+
+

cirDraw/cirDraw/settings.py

@@ -27,7 +27,7 @@
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = False
 
-ALLOWED_HOSTS = ['144.202.111.235', '127.0.0.1', '144.202.101.9', 'www.circdraw.com']
+ALLOWED_HOSTS = ['*']
 
 
 # Application definition
@@ -36,6 +36,7 @@
     'download',
     'information',
     'tools',
+    'diy',
     'django.contrib.admin',
     'django.contrib.auth',
     'django.contrib.contenttypes',
@@ -83,11 +84,18 @@
 
 DATABASES = {
     'default': {
-        'ENGINE': 'django.db.backends.mysql',
+        #'ENGINE': 'django.db.backends.mysql',
+        'ENGINE': 'dj_db_conn_pool.backends.mysql',
         'NAME': 'circDraw',
         'USER': 'root',
-        'PASSWORD': '12345678',
-        'HOST': '127.0.0.1'
+        'PASSWORD': 'mypassword',
+        #'HOST': '167.179.90.87',
+        'HOST': '127.0.0.1',
+        'PORT': 6603,
+        'POOL_OPTIONS': {
+            'POOL_SIZE': 50,
+            'MAX_OVERFLOW': 10
+        }
     }
 }
 

cirDraw/cirDraw/urls.py

@@ -28,6 +28,7 @@
     url(r'^$', toolviews.render_index_page, name = 'home'),
     url(r'^admin/', admin.site.urls),
     url(r'^tools/', include('tools.urls')),
+    url(r'^diy/', include('diy.urls')),
     url(r'^download/', include('download.urls')),
     url(r'^information/', include('information.urls')),
 ]

cirDraw/diy/admin.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

cirDraw/diy/apps.py

@@ -0,0 +1,5 @@
+from django.apps import AppConfig
+
+
+class DiyConfig(AppConfig):
+    name = 'diy'

cirDraw/diy/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.