GitHub - rbaertsch/pathway_tools: Tools for working with UCSC super pathway

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Tools for working with UCSC super pathway

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Name		Name	Last commit message	Last commit date
Latest commit History 184 Commits
build_scripts		build_scripts
data		data
galaxy		galaxy
pathway_tools		pathway_tools
project		project
sbt		sbt
scripts		scripts
src/main/scala/edu/ucsc/pathway		src/main/scala/edu/ucsc/pathway
tests		tests
web_viewer		web_viewer
.gitignore		.gitignore
Makefile		Makefile
README		README
build.sbt		build.sbt
setup.py		setup.py

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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:

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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 

----------


========================
==The network comparision tool
========================

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 
========================


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