Ancestral Reconstruction Pipeline

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This page is to document the Ancestral Reconstruction Pipeline by Chunfang Zheng

Master control is from her batch script: batchFile.txt 


#compile 
#gets gene pairs from SynMap output
javac TestGetGenomes.java
#run with config file
#config file:
#number of genomes and number
java TestGetGenomes data/inputInfoCoGe.txt


javac TestGetContigInput.java
java TestGetContigInput data/inputInfoAGRP.txt
cd outputFiles
python contigInput_8400_9050_10997_19515.py> contigOutput.txt
cd ..
javac TestGetContigOutputAndScaffoldInput.java
java TestGetContigOutputAndScaffoldInput data/inputInfoAGRP.txt
cd outputFiles
python scaffoldInput1.py > scaffoldOutput1.txt
python scaffoldInput2.py > scaffoldOutput2.txt
python scaffoldInput3.py > scaffoldOutput3.txt
python scaffoldInput4.py > scaffoldOutput4.txt
python scaffoldInput5.py > scaffoldOutput5.txt
python scaffoldInput6.py > scaffoldOutput6.txt
python scaffoldInput7.py > scaffoldOutput7.txt
cd ..
javac TestScaffoldOutput.java
java TestScaffoldOutput
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