Ancestral Reconstruction Pipeline: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 42: | Line 42: | ||
numberOfGenomePairs 9 | numberOfGenomePairs 9 | ||
#synmap output with correct syntenic depth | |||
8400 9050 data/8400_9050.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | 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 8400 data/10997_8400.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | ||
| Line 51: | Line 52: | ||
9050 9050 data/9050_9050.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 | 10997 10997 data/10997_10997.CDS-CDS.last.tdd10.filtered.dag.all.go_D20_g10_A5.aligncoords.Dm0.ma1.qac3.3.40.gcoords | ||
#syntenic depth among the genomes | |||
#peach | |||
8400 3 | 8400 3 | ||
#grape | |||
9050 3 | 9050 3 | ||
Cacao | |||
10997 3 | 10997 3 | ||
#amborella | |||
19515 1 | 19515 1 | ||
#subgenome information | |||
data/subGenomeRegions.txt | data/subGenomeRegions.txt | ||
</pre> | </pre> | ||
Revision as of 15:38, 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 #synmap output with correct syntenic depth 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 #syntenic depth among the genomes #peach 8400 3 #grape 9050 3 Cacao 10997 3 #amborella 19515 1 #subgenome information data/subGenomeRegions.txt