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README
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README
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UCSC SuperPathway Database Toolkit
To get the dependencies
pip install pyaml
pip install networkx
To get the code:
git clone git://github.com/ucscCancer/pathway_tools.git
========================
Installation
========================
python setup.py build
python setup.py install
(Local install)
python setup.py install --user
========================
Developement
========================
Setup your PYTHONPATH
export PYTHONPATH=`pwd`/pathway_tools
Once you have the pathway toolkit:
========================
==The pathway_db tool
========================
----------
Synchronize local copy of HUGO
./scripts/pathway_db.py hugo_sync
----------
Compile to a superpathway (paradigm format)
./scripts/pathway_db.py build --paradigm > superpathway.pid
----------
Merge two paradigm files
./scripts/pathway_db.py build paradigm-file Five3_v3/pid_120912_pathway.tab paradigm-file RB1_v2.tab
----------
========================
==The network comparision tool
========================
Compare to the old super pathway
./scripts/network_compare.py <path/to/pid_110725_pathway.tab> pid_all_pathway.tab
========================
==The network converter tool
========================
Convert Superpathway file, with GMT file into XGMML
./network_convert.py --in-paradigm pid_110725_pathway.tab --in-gmt output.gmt --out-xgmml super.xgmml
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Convert XGMML file to paradigm network and gmt file
./network_convert.py --in-xgmml super.xgmml --out-gmt test.gmt --out-paradigm test.tab