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HYPHY reading NEXUS charpartitions (Read 1777 times)
jamescotton
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HYPHY reading NEXUS charpartitions
Oct 21st, 2005 at 4:31am
 
Hi,

I'm having a bit of trouble getting hyphy to read in charpartitions from a nexus file.

MY nexus file darterfile.nex has the block
Code:
begin assumptions;
CHARPARTITION CodonPos = N: 759-1141,
		1: 1-127\3 129 132 133 135-756\3,
		2: 2-128\3 130 131 134 136-757\3,
		3: 3-126\3 137-758\3;
CHARPARTITION ATPasevs12S = ATPase:1-758,12S:759-1141;
end;
 



but when I run this HYPHY code:
Code:
DataSet ds	 = ReadDataFile ("darterfile.nex");
DataSetFilter filteredData = CreateFilter (ds,1);

fprintf(stdout,"MATRIX HAS ",Columns(DATA_FILE_PARTITION_MATRIX)," BY ",Rows(DATA_FILE_PARTITION_MATRIX),"\n");
for (i=0; i < Columns(DATA_FILE_PARTITION_MATRIX); i = i+1)
{
fprintf(stdout,DATA_FILE_PARTITION_MATRIX[i][1],"=",DATA_FILE_PARTITION_MATRIX[i][2],"\n");
}
 



I get told that the matrix has only a single row (1 BY 1)

I get the same thing if my charpartition command is in a "SETS" block or "PAUP" block. Any suggestions?

Cheers,
James
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Sergei
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Posts: 1658
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Re: HYPHY reading NEXUS charpartitions
Reply #1 - Oct 21st, 2005 at 8:43am
 
Dear James,

At this point, HyPhy recognizes only a few NEXUS block commands; if you think other blocks will be useful, please let me know which ones - they are not difficult to add in most cases.

At any rate, the only partitioning command HyPhy will read from NEXUS files is the CHARSET command as in:

Code:
BEGIN ASSUMPTIONS;
      CHARSET Intron = 1-89 276-552;
      CHARSET Exon = 90-140 147-152 180-185 198-275;
END;
 



Cheers,
Sergei
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