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Methodology Questions >> How to >> HYPHY reading NEXUS charpartitions
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Message started by jamescotton on Oct 21st, 2005 at 4:31am

Title: HYPHY reading NEXUS charpartitions
Post by jamescotton on 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;
[/code):



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

Title: Re: HYPHY reading NEXUS charpartitions
Post by Sergei on 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;
[/code]

Cheers,
Sergei

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