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invert a partition in a batch file (Read 2080 times)

Jennifer Knies

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invert a partition in a batch file
Jun 20^th, 2006 at 6:41am

Hi,

I would like to be able enter one partition into the Hyphy batch file and then have a second partition that is the inverse of the first. Is this possible?
Currently, I have code like this:

DataSetFilter filteredData = CreateFilter (ds,1,"3-7,11-19,21-29,","");

(I have made the partition much smaller than actuality). Later in this batch file I run another analysis on the inversion of the partition and I want to be able to have a line that sets a new filter = ds - filteredData.

Thanks, Jen Knies

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Sergei

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Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male

Re: invert a partition in a batch file
Reply #1 - Jun 20^th, 2006 at 11:56am

Dear Jen,

Something like the code I paste below should do the trick.
The code builds and uses an associative array 'sitesIn' to mark all the sites to be excluded from the inverted partition.

Code:

RequireVersion ("0.9920060601beta");

GetURL 			(dataString,"http://www.hyphy.org/pubs/IntronExon.nex");
DataSet 		ds 			 = ReadFromString (dataString);
DataSetFilter	filteredData = CreateFilter (ds,1,"3-7,11-19,21-29","");

sitesIn	= {};
for (k=0; k<filteredData.sites; k=k+1)
{
	sitesIn[filteredData.site_map[k]] = 1;
}

DataSetFilter	invertedFilter = CreateFilter (ds,1,sitesIn[siteIndex] == 0,"");

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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