int
main (int argc, char * argv[])
{
struct pllPhylip * phylip;
if (argc != 2)
{
usage (argv[0]);
return (EXIT_FAILURE);
}
phylip = pllPhylipParse (argv[1]);
if (!phylip)
{
printf ("Error while parsing\n");
return (EXIT_FAILURE);
}
printf ("Taxa: %d SeqLen: %d\n", phylip->nTaxa, phylip->seqLen);
pllPhylipDump (phylip);
pllPhylipRemoveDuplicate (phylip);
pllPhylipDestroy (phylip);
return (EXIT_SUCCESS);
}
static void testProteinStuff()
{
pllAlignmentData * alignmentData;
pllInstance * tr;
pllNewickTree * newick;
partitionList * partitions;
struct pllQueue * parts;
int i;
for(i = 0; i < 5; i++)
{
//write a simple partition file with 3 partitions
//for dataset dna.phy.dat contained
//in this source directory
FILE *f = fopen("proteinPartitions", "w");
switch(i)
{
case 0:
fprintf(f, "WAG, p1 = 1-200\n");
fprintf(f, "WAG, p2 = 201-600\n");
fprintf(f, "WAG, p3 = 601-1104\n");
break;
case 1:
fprintf(f, "LG, p1 = 1-200\n");
fprintf(f, "LG, p2 = 201-600\n");
fprintf(f, "LG, p3 = 601-1104\n");
break;
case 2:
fprintf(f, "JTT, p1 = 1-200\n");
fprintf(f, "JTT, p2 = 201-600\n");
fprintf(f, "JTT, p3 = 601-1104\n");
break;
case 3:
case 4:
fprintf(f, "GTR, p1 = 1-200\n");
fprintf(f, "GTR, p2 = 201-600\n");
fprintf(f, "GTR, p3 = 601-1104\n");
break;
default:
assert(0);
}
fclose(f);
tr = pllCreateInstance (GAMMA, PLL_FALSE, PLL_FALSE, PLL_FALSE, 12345);
alignmentData = pllParsePHYLIP ("prot.phy");
/* or alternatively, parse a FASTA file */
// alignmentData = pllParseFASTA ("prot.phy");
newick = pllNewickParseFile("parsimonyTree");
parts = pllPartitionParse ("proteinPartitions");
/* Validate the partitions */
if (!pllPartitionsValidate (parts, alignmentData))
{
fprintf (stderr, "Error: Partitions do not cover all sites\n");
return (EXIT_FAILURE);
}
/* commit the partitions and build a partitions structure */
partitions = pllPartitionsCommit (parts, alignmentData);
/* destroy the intermedia partition queue structure */
pllQueuePartitionsDestroy (&parts);
/* eliminate duplicate sites from the alignment and update weights vector */
pllPhylipRemoveDuplicate (alignmentData, partitions);
pllTreeInitTopologyNewick (tr, newick, PLL_TRUE);
if (!pllLoadAlignment (tr, alignmentData, partitions, PLL_DEEP_COPY))
{
fprintf (stderr, "Incompatible tree/alignment combination\n");
return (EXIT_FAILURE);
}
//pllInitModel(tr, PLL_TRUE, alignmentData, partitions);
pllInitModel(tr, alignmentData, partitions);
switch(i)
{
case 0:
//all params unlinked
pllLinkAlphaParameters("0,1,2", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,2", partitions);
break;
case 1:
//link params in another way
pllLinkAlphaParameters("0,0,0", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,2", partitions);
break;
case 2:
//link params in yet another way
pllLinkAlphaParameters("0,0,0", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,0", partitions);
break;
case 3:
//also fiddle around with the Q matrices, make them to be non-GTR, but simpler
pllLinkAlphaParameters("0,1,2", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,2", partitions);
//these are GTR models
//pllSetSubstitutionRateMatrixSymmetries("0,1,2,3,4,5", partitions, 0);
//pllSetSubstitutionRateMatrixSymmetries("0,1,2,3,4,5", partitions, 1);
//this is a simpler model with 5 parameters, parameter a and f have
//the same value
//pllSetSubstitutionRateMatrixSymmetries("0,1,2,3,4,0", partitions, 2);
break;
case 4:
{
//test case to show how the model parameters can be set to fixed values
// set up arrays of user-defined base frequencies
// and a user defined q matrix
double
f[4] = {0.25, 0.25, 0.25, 0.25},
q[6] = {1.0, 1.0, 1.0, 1.0, 1.0, 0.5};
//unlink alpha parameters base frequencies and Q matrices
//across all partitions
pllLinkAlphaParameters("0,1,2", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,0,0", partitions);
//set alpha to a fixed value of 1.0 for partition 0 and
//parition 1
//pllSetFixedAlpha(1.0, 0, partitions, tr);
//pllSetFixedAlpha(1.0, 1, partitions, tr);
//fix the base frequencies to 0.25 for
//partitions 0 and 1
//pllSetFixedBaseFrequencies(f, 4, 0, partitions, tr);
//pllSetFixedBaseFrequencies(f, 4, 1, partitions, tr);
//set the Q matrix to fixed values for partition
//0
//pllSetFixedSubstitutionMatrix(q, 6, 0, partitions, tr);
}
break;
default:
assert(0);
}
evaluateGeneric(tr, partitions, tr->start, PLL_TRUE, PLL_FALSE);
printf("%f \n", tr->likelihood);
pllOptimizeModelParameters(tr, partitions, 1.0);
//print the model parameters
//printModelParameters(partitions);
printf("%f \n", tr->likelihood);
//cleanup
pllAlignmentDataDestroy (alignmentData);
pllNewickParseDestroy (&newick);
pllPartitionsDestroy (tr, &partitions);
pllTreeDestroy (tr);
}
}
int main (int argc, char * argv[])
{
pllAlignmentData *alignmentData1, *alignmentData2;
pllInstance * tr, *tr2;
pllNewickTree * newick;
partitionList * partitions, *partitions2;
struct pllQueue * parts;
int i;
if (argc != 4)
{
fprintf (stderr, "usage: %s [phylip-file] [newick-file] [partition-file]\n", argv[0]);
return (EXIT_FAILURE);
}
/* Create a PLL tree */
tr = pllCreateInstance (GAMMA, PLL_FALSE, PLL_FALSE, PLL_FALSE, 12345);
tr2 = pllCreateInstance (GAMMA, PLL_FALSE, PLL_FALSE, PLL_FALSE, 12345);
/* Parse a PHYLIP file */
alignmentData1= pllParsePHYLIP (argv[1]);
alignmentData2 = pllParsePHYLIP (argv[1]);
if (!alignmentData1)
{
fprintf (stderr, "Error while parsing %s\n", argv[1]);
return (EXIT_FAILURE);
}
/* Parse a NEWICK file */
newick = pllNewickParseFile (argv[2]);
if (!newick)
{
fprintf (stderr, "Error while parsing newick file %s\n", argv[2]);
return (EXIT_FAILURE);
}
if (!pllValidateNewick (newick)) /* check whether the valid newick tree is also a tree that can be processed with our nodeptr structure */
{
fprintf (stderr, "Invalid phylogenetic tree\n");
return (EXIT_FAILURE);
}
/* Parse the partitions file into a partition queue structure */
parts = pllPartitionParse (argv[3]);
/* Validate the partitions */
if (!pllPartitionsValidate (parts, alignmentData1))
{
fprintf (stderr, "Error: Partitions do not cover all sites\n");
return (EXIT_FAILURE);
}
/* commit the partitions and build a partitions structure */
partitions = pllPartitionsCommit (parts, alignmentData1);
partitions2 = pllPartitionsCommit (parts, alignmentData2);
/* destroy the intermedia partition queue structure */
pllQueuePartitionsDestroy (&parts);
/* eliminate duplicate sites from the alignment and update weights vector */
pllPhylipRemoveDuplicate (alignmentData1, partitions);
pllPhylipRemoveDuplicate (alignmentData2, partitions2);
/* Set the topology of the PLL tree from a parsed newick tree */
//pllTreeInitTopologyNewick (tr, newick, PLL_TRUE);
/* Or instead of the previous function use the next commented line to create
a random tree topology
pllTreeInitTopologyRandom (tr, phylip->nTaxa, phylip->label); */
pllTreeInitTopologyForAlignment(tr, alignmentData1);
/* Connect the alignment with the tree structure */
if (!pllLoadAlignment (tr, alignmentData1, partitions, PLL_DEEP_COPY))
{
fprintf (stderr, "Incompatible tree/alignment combination\n");
return (EXIT_FAILURE);
}
/* Initialize the model TODO: Put the parameters in a logical order and change the TRUE to flags */
pllInitModel(tr, alignmentData1, partitions);
/* TODO transform into pll functions !*/
/*
allocateParsimonyDataStructures(tr, partitions);
pllMakeParsimonyTreeFast(tr, partitions);
pllFreeParsimonyDataStructures(tr, partitions);
*/
pllComputeRandomizedStepwiseAdditionParsimonyTree(tr, partitions);
pllTreeToNewick (tr->tree_string, tr, partitions, tr->start->back, PLL_TRUE, PLL_TRUE, PLL_FALSE, PLL_FALSE, PLL_FALSE, PLL_SUMMARIZE_LH, PLL_FALSE, PLL_FALSE);
printf ("Tree: %s %d\n", tr->tree_string, tr->start->number);
evaluateGeneric(tr, partitions, tr->start, PLL_TRUE, PLL_FALSE);
double
firstTree = tr->likelihood;
printf("%f \n", tr->likelihood);
//computeBIGRAPID_Test(tr, partitions, PLL_TRUE);
printf("final like %f\n", tr->likelihood);
//pllInitModel(tr, PLL_TRUE, phylip, partitions);
pllTreeInitTopologyNewick (tr2, newick, PLL_TRUE);
if (!pllLoadAlignment (tr2, alignmentData2, partitions2, PLL_DEEP_COPY))
{
fprintf (stderr, "Incompatible tree/alignment combination\n");
return (EXIT_FAILURE);
}
pllInitModel(tr2, alignmentData2, partitions2);
pllTreeToNewick (tr2->tree_string, tr2, partitions2, tr2->start->back, PLL_TRUE, PLL_TRUE, PLL_FALSE, PLL_FALSE, PLL_FALSE, PLL_SUMMARIZE_LH, PLL_FALSE, PLL_FALSE);
printf ("Tree: %s %d\n", tr2->tree_string, tr2->start->number);
evaluateGeneric(tr2, partitions2, tr2->start, PLL_TRUE, PLL_FALSE);
printf("%f \n", tr2->likelihood);
double
secondTree = tr2->likelihood;
assert(firstTree == secondTree);
pllOptimizeModelParameters(tr2, partitions2, 10.0);
printf("%f \n", tr2->likelihood);
pllAlignmentDataDestroy (alignmentData1);
pllNewickParseDestroy (&newick);
pllPartitionsDestroy (tr, &partitions);
pllTreeDestroy (tr);
pllAlignmentDataDestroy (alignmentData2);
pllPartitionsDestroy (&partitions2, tr2->mxtips);
pllTreeDestroy (tr2);
for(i = 0; i < 5; i++)
{
//write a simple partition file with 3 partitions
//for dataset dna.phy.dat contained
//in this source directory
FILE *f = fopen("dummy", "w");
fprintf(f, "DNA, p1 = 1-200\n");
fprintf(f, "DNA, p1 = 201-400\n");
fprintf(f, "DNA, p1 = 401-705\n");
fclose(f);
tr = pllCreateInstance (GAMMA, PLL_FALSE, PLL_FALSE, PLL_FALSE, 12345);
alignmentData1= pllParsePHYLIP (argv[1]);
newick = pllNewickParseFile (argv[2]);
parts = pllPartitionParse ("dummy");
/* Validate the partitions */
if (!pllPartitionsValidate (parts, alignmentData1))
{
fprintf (stderr, "Error: Partitions do not cover all sites\n");
return (EXIT_FAILURE);
}
/* commit the partitions and build a partitions structure */
partitions = pllPartitionsCommit (parts, alignmentData1);
/* destroy the intermedia partition queue structure */
pllQueuePartitionsDestroy (&parts);
/* eliminate duplicate sites from the alignment and update weights vector */
pllPhylipRemoveDuplicate (alignmentData1, partitions);
pllTreeInitTopologyNewick (tr, newick, PLL_TRUE);
if (!pllLoadAlignment (tr, alignmentData1, partitions, PLL_DEEP_COPY))
{
fprintf (stderr, "Incompatible tree/alignment combination\n");
return (EXIT_FAILURE);
}
pllInitModel(tr, alignmentData1, partitions);
switch(i)
{
case 0:
//link params in one way
pllLinkAlphaParameters("0,1,2", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,2", partitions);
break;
case 1:
//link params in another way
pllLinkAlphaParameters("0,0,0", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,2", partitions);
break;
case 2:
//link params in yet another way
pllLinkAlphaParameters("0,0,0", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,0", partitions);
break;
case 3:
//also fiddle around with the Q matrices, make them to be non-GTR, but simpler
pllLinkAlphaParameters("0,1,2", partitions);
pllLinkFrequencies("0,1,2", partitions);
pllLinkRates("0,1,2", partitions);
//these are GTR models
pllSetSubstitutionRateMatrixSymmetries("0,1,2,3,4,5", partitions, 0);
pllSetSubstitutionRateMatrixSymmetries("0,1,2,3,4,5", partitions, 1);
//this is a simpler model with 5 parameters, parameter a and f have
//the same value
pllSetSubstitutionRateMatrixSymmetries("0,1,2,3,4,0", partitions, 2);
break;
case 4:
{
//test case to show how the model parameters can be set to fixed values
// set up arrays of user-defined base frequencies
// and a user defined q matrix
double
f[4] = {0.25, 0.25, 0.25, 0.25},
q[6] = {1.0, 1.0, 1.0, 1.0, 1.0, 0.5};
//unlink alpha parameters base frequencies and Q matrices
//across all partitions
pllLinkAlphaParameters("0,1,2", partitions);
pllLinkFrequencies("0,0,1", partitions);
pllLinkRates("0,1,2", partitions);
//set alpha to a fixed value of 1.0 for partition 0 and
//parition 1
pllSetFixedAlpha(1.0, 0, partitions, tr);
pllSetFixedAlpha(1.0, 1, partitions, tr);
//fix the base frequencies to 0.25 for
//partitions 0 and 1
pllSetFixedBaseFrequencies(f, 4, 0, partitions, tr);
pllSetFixedBaseFrequencies(f, 4, 1, partitions, tr);
//set the Q matrix to fixed values for partition
//0
pllSetFixedSubstitutionMatrix(q, 6, 0, partitions, tr);
}
break;
default:
assert(0);
}
evaluateGeneric(tr, partitions, tr->start, PLL_TRUE, PLL_FALSE);
printf("%f \n", tr->likelihood);
pllOptimizeModelParameters(tr, partitions, 10.0);
//print the model parameters
printModelParameters(partitions);
printf("%f \n", tr->likelihood);
//cleanup
pllAlignmentDataDestroy (alignmentData1);
pllNewickParseDestroy (&newick);
pllPartitionsDestroy (&partitions, tr->mxtips);
pllTreeDestroy (tr);
}
testProteinStuff();
return (EXIT_SUCCESS);
}
