pogview
Genome scale multiple alignment tool
For distribution
tar cvf - jars/pogvue.jar pogview pogview.galGal4 README.md perl/Maf2.pm perl/index_maf perl/get_maf.pl data/galGal4.* data/strCam.* maf/orgfile.dat data/ratites.nh|gzip -c > pogview.tgz
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tar zxvf pogview.tgz
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cd pogview
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Copy your maf files into the maf directory (They’re sitting in /scratch/mclamp/ratites/ on sandy2)
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Index your maf files
cd perl; perl ./index_maf
You should see lines like
Align ../maf/strCam.superscaffold21.maf ../maf/strCam.superscaffold21.maf.index
Check the index file isn’t empty
ls -l ../maf
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Back to the top dir
cd ..
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Test you can fetch the alignment pieces
perl perl/get_maf.pl strCam.superscaffold21 1 1000
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Run pogview
./pogview data/strCam.GeneWise.gff
I’m getting out of memory errors if I load up all the exons - maybe need to filter them.
Karyotype view keystrokes
ctrl left click - zoom in ctrl right click - zoom out
click - select features
Click the pogvue button to bring up the alignment window
With the mouse in the bottom window click s to fetch the sequence (keep an eye on the terminal window for wierdness)
Other keys
arrow keys <- -> scroll left and right click drag to scroll too
right clikc in top window to move the displayed region in the bottom window
i - increase track height d - decrease track height f - base level view
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- zoom in
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- zoom out
`,1,2,3,4 are different levels of zoom.
y - brings up tree
There are many other display options that aren’t hooked up yet.
ctrl-F is a find box but this is uber flaky
The display is a bit effed on my machine (I haven’t run this since 2009 or so) so I use i or d to refresh the screen.
It may be too buggy to use for too long in its current state. It needs some TLC.
Initializing keystore (github password)
keytool -genkey -alias mydomain -keyalg RSA -keystore KeyStore.jks -keysize 2048