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HYPHY nj tree builder now also makes species-only-labeled trees as well

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as others.
This commit is contained in:
Daniel Blankenberg
2007-04-06 13:58:24 +00:00
parent bddbe4a68b
commit 323041dba0
1 changed files with 7 additions and 4 deletions
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tools/hyphy/hyphy_util.py
+7 -4
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@@ -17,6 +17,7 @@ HYPHY_EXECUTABLE = os.path.join(HYPHY_PATH,"HYPHY")
NJ_tree_shared_ibf = """
COUNT_GAPS_IN_FREQUENCIES = 0;
methodIndex = 1;
/*-----------------------------------------------------------------------------------------------------------------------------------------*/
@@ -133,7 +134,7 @@ function TreeMatrix2TreeString (doLengths)
if (n<ds.species)
{
GetString (nodeName, ds, n);
if (doLengths == 2)
if (doLengths != 1)
{
treeString*nodeName;
}
@@ -287,10 +288,11 @@ function _processAGene (_geneID, nwk_file, ps_file)
{
if (ds.species == 1)
{
fprintf (nwk_file, _geneID, "\\tNone\\tNone\\n");
fprintf (nwk_file, _geneID-1, "\\tNone \\tNone\\n");
return 0;
}
DataSetFilter filteredData = CreateFilter (ds,1);
/* do sequence to branch map */
@@ -300,7 +302,7 @@ function _processAGene (_geneID, nwk_file, ps_file)
for (k=0; k<ds.species; k=k+1)
{
GetString (thisName, ds,k);
shortName = (thisName^{{"\\\\..+",""}})&&1;
shortName = (thisName^{{"\\\\..+",""}});
taxonNameMap[shortName] = thisName;
SetParameter (ds,k,shortName);
}
@@ -309,7 +311,7 @@ function _processAGene (_geneID, nwk_file, ps_file)
DISTANCE_PROMPTS = (_geneID==1);
InferTreeTopology (0);
fprintf (nwk_file, _geneID, "\\t", TreeMatrix2TreeString (0), "\\t", TreeMatrix2TreeString (1), "\\n");
fprintf (nwk_file, _geneID-1, "\\t", TreeMatrix2TreeString (0), "\\t", TreeMatrix2TreeString (1), "\\n");
if (Abs(ps_file))
{
treeString = TreeMatrix2TreeString (2);
@@ -333,6 +335,7 @@ function _processAGene (_geneID, nwk_file, ps_file)
}
baseWidth = 40*baseWidth;
fprintf (stdout, _geneID, ":", givenTree,"\\n");
fprintf (ps_file, PSTreeString (givenTree, "STRING_SUPPLIED_LENGTHS",{{baseWidth,baseHeight}}));
}
return 0;