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


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Installation
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python setup.py build
python setup.py install

(Local install)
python setup.py install --user


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Developement
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Setup your PYTHONPATH
export PYTHONPATH=`pwd`/pathway_tools
Once you have the pathway toolkit:

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==The pathway_db tool
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Synchronize local copy of HUGO
./scripts/pathway_db.py hugo_sync

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Compile to a superpathway (paradigm format)
./scripts/pathway_db.py build --paradigm > superpathway.pid 

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Merge two paradigm files
./scripts/pathway_db.py build paradigm-file Five3_v3/pid_120912_pathway.tab paradigm-file RB1_v2.tab 

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==The network comparision tool
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Compare to the old super pathway
./scripts/network_compare.py <path/to/pid_110725_pathway.tab> pid_all_pathway.tab


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==The network converter tool 
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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