Ancestral Reconstruction Pipeline: Difference between revisions
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Created page with 'This page is to document the Ancestral Reconstruction Pipeline by Chunfang Zheng Master control is from her batch script: batchFile.txt <pre>#compile #gets gene pairs from S...' |
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This page is to document the Ancestral Reconstruction Pipeline by Chunfang Zheng | This page is to document the Ancestral Reconstruction Pipeline by Chunfang Zheng | ||
Master control is from her batch script: batchFile.txt | Master control is from her batch script: batchFile.txt | ||
<br> | |||
<pre>#compile | <pre>#compile | ||
#gets gene pairs from SynMap output | #gets gene pairs from SynMap output | ||
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</pre> | |||
inputInfo example file (describes input from CoGe) | |||
<pre> | |||
#obvious | |||
numberOfGenomes 4 | |||
numberOfGenomePairs 9 | |||
8400 9050 data/8400_9050.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | |||
10997 8400 data/10997_8400.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | |||
10997 9050 data/10997_9050.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | |||
10997 19515 data/10997_19515.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.1.40.gcoords | |||
19515 8400 data/19515_8400.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac1.3.40.gcoords | |||
19515 9050 data/19515_9050.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac1.3.40.gcoords | |||
8400 8400 data/8400_8400.CDS-CDS.last.tdd10.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | |||
9050 9050 data/9050_9050.CDS-CDS.last.tdd10.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | |||
10997 10997 data/10997_10997.CDS-CDS.last.tdd10.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | |||
8400 3 | |||
9050 3 | |||
10997 3 | |||
19515 1 | |||
data/subGenomeRegions.txt | |||
</pre> | </pre> | ||
Revision as of 15:36, 24 April 2014
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
inputInfo example file (describes input from CoGe)
#obvious numberOfGenomes 4 numberOfGenomePairs 9 8400 9050 data/8400_9050.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords 10997 8400 data/10997_8400.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords 10997 9050 data/10997_9050.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords 10997 19515 data/10997_19515.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.1.40.gcoords 19515 8400 data/19515_8400.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac1.3.40.gcoords 19515 9050 data/19515_9050.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac1.3.40.gcoords 8400 8400 data/8400_8400.CDS-CDS.last.tdd10.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords 9050 9050 data/9050_9050.CDS-CDS.last.tdd10.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords 10997 10997 data/10997_10997.CDS-CDS.last.tdd10.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords 8400 3 9050 3 10997 3 19515 1 data/subGenomeRegions.txt