isoformQuantify can be used to compute relative abundances of different transcripts belonging to the same gene and visualize the result.
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install Django (https://www.djangoproject.com/download/)
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install scipy (http://www.scipy.org/SciPy)
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install samtools (http://sourceforge.net/projects/samtools/files/samtools/0.1.18/)
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clone the project repository to the location where you want to put
git clone https://github.com/jaxcs/charlie.git
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change line 20, 28, 29 in
/isoformQuantifyApp/getIsoformAbund.py
to appropriate directories in your server -
copy data files in the
/isoformQuantifyApp/data/
directory to the same directory in the server (right now, data files have been ignored by git repo commit) -
use command like
python manage.py runserver 0.0.0.0:8080
to kick off web service in the root folder that containsmanage.py
isoformQuantify
: configuration files for Django (Please refer to https://docs.djangoproject.com/en/1.4/)isoformQuantifyApp
: actual project code locates
*.py
: Python scripts that implement algorithm and do scientific computation/static/
: contains javascripts for visualization, css styling files/templates/
: index.html (our homepage)
- "views.py": respond to web request (which function responds to which request is determined by
/isoformQuantify/urls.py
) - "models.py": stores Python objects used in algorithm
- "getIsoformAbund.py": calculate relative abundances of transcripts (main script that implements the algorithm)
- "test.py": auto generated file by Django (demonstrates how to write a test)