void DoMakeTree()
{
if (g_pstrInFileName.get() == 0 || g_pstrOutFileName.get() == 0)
Quit("-maketree requires -in <msa> and -out <treefile>");
SetStartTime();
SetSeqWeightMethod(g_SeqWeight1.get());
TextFile MSAFile(g_pstrInFileName.get());
MSA msa;
msa.FromFile(MSAFile);
unsigned uSeqCount = msa.GetSeqCount();
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
SetMuscleInputMSA(msa);
Progress("%u sequences", uSeqCount);
Tree tree;
TreeFromMSA(msa, tree, g_Cluster2.get(), g_Distance2.get(), g_Root2.get());
TextFile TreeFile(g_pstrOutFileName.get(), true);
tree.ToFile(TreeFile);
Progress("Tree created");
}
void DoSP()
{
MuscleContext *ctx = getMuscleContext();
TextFile f(ctx->params.g_pstrSPFileName);
MSA a;
a.FromFile(f);
ALPHA Alpha = ALPHA_Undefined;
switch (ctx->params.g_SeqType)
{
case SEQTYPE_Auto:
Alpha = a.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid SeqType");
}
SetAlpha(Alpha);
a.FixAlpha();
SetPPScore();
const unsigned uSeqCount = a.GetSeqCount();
if (0 == uSeqCount)
Quit("No sequences in input file %s", ctx->params.g_pstrSPFileName);
MSA::SetIdCount(uSeqCount);
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
a.SetSeqId(uSeqIndex, uSeqIndex);
SetSeqWeightMethod(ctx->params.g_SeqWeight1);
Tree tree;
TreeFromMSA(a, tree, ctx->params.g_Cluster2, ctx->params.g_Distance2, ctx->params.g_Root2);
SetMuscleTree(tree);
SetMSAWeightsMuscle((MSA &) a);
SCORE SP = ObjScoreSP(a);
Log("File=%s;SP=%.4g\n", ctx->params.g_pstrSPFileName, SP);
fprintf(stderr, "File=%s;SP=%.4g\n", ctx->params.g_pstrSPFileName, SP);
}
void AlignSubFam(SeqVect &vAll, const Tree &GuideTree, unsigned uNodeIndex,
MSA &msaOut)
{
const unsigned uSeqCount = vAll.GetSeqCount();
const char *InTmp = "asf_in.tmp";
const char *OutTmp = "asf_out.tmp";
unsigned *Leaves = new unsigned[uSeqCount];
unsigned uLeafCount;
GetLeaves(GuideTree, uNodeIndex, Leaves, &uLeafCount);
SeqVect v;
for (unsigned i = 0; i < uLeafCount; ++i)
{
unsigned uLeafNodeIndex = Leaves[i];
unsigned uId = GuideTree.GetLeafId(uLeafNodeIndex);
Seq &s = vAll.GetSeqById(uId);
v.AppendSeq(s);
}
#if TRACE
{
Log("Align subfam[node=%d, size=%d] ", uNodeIndex, uLeafCount);
for (unsigned i = 0; i < uLeafCount; ++i)
Log(" %s", v.GetSeqName(i));
Log("\n");
}
#endif
TextFile fIn(InTmp, true);
v.ToFASTAFile(fIn);
fIn.Close();
char CmdLine[4096];
sprintf(CmdLine, "probcons %s > %s 2> /dev/null", InTmp, OutTmp);
// sprintf(CmdLine, "muscle -in %s -out %s -maxiters 1", InTmp, OutTmp);
system(CmdLine);
TextFile fOut(OutTmp);
msaOut.FromFile(fOut);
for (unsigned uSeqIndex = 0; uSeqIndex < uLeafCount; ++uSeqIndex)
{
const char *Name = msaOut.GetSeqName(uSeqIndex);
unsigned uId = vAll.GetSeqIdFromName(Name);
msaOut.SetSeqId(uSeqIndex, uId);
}
unlink(InTmp);
unlink(OutTmp);
delete[] Leaves;
}
void Refine()
{
SetOutputFileName(g_pstrOutFileName.get());
SetInputFileName(g_pstrInFileName.get());
SetStartTime();
SetMaxIters(g_uMaxIters.get());
SetSeqWeightMethod(g_SeqWeight1.get());
TextFile fileIn(g_pstrInFileName.get());
MSA msa;
msa.FromFile(fileIn);
const unsigned uSeqCount = msa.GetSeqCount();
if (0 == uSeqCount)
Quit("No sequences in input file");
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType.get())
{
case SEQTYPE_Auto:
Alpha = msa.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid SeqType");
}
SetAlpha(Alpha);
msa.FixAlpha();
SetPPScore();
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
SetPPScore(PPSCORE_SPN);
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
SetMuscleInputMSA(msa);
Tree GuideTree;
TreeFromMSA(msa, GuideTree, g_Cluster2.get(), g_Distance2.get(), g_Root2.get());
SetMuscleTree(GuideTree);
if (g_bAnchors.get())
RefineVert(msa, GuideTree, g_uMaxIters.get());
else
RefineHoriz(msa, GuideTree, g_uMaxIters.get(), false, false);
ValidateMuscleIds(msa);
ValidateMuscleIds(GuideTree);
// TextFile fileOut(g_pstrOutFileName.get(), true);
// msa.ToFile(fileOut);
MuscleOutput(msa);
}
void DoRefineW()
{
SetOutputFileName(g_pstrOutFileName);
SetInputFileName(g_pstrInFileName);
SetStartTime();
SetMaxIters(g_uMaxIters);
SetSeqWeightMethod(g_SeqWeight1);
TextFile fileIn(g_pstrInFileName);
MSA msa;
msa.FromFile(fileIn);
const unsigned uSeqCount = msa.GetSeqCount();
if (0 == uSeqCount)
Quit("No sequences in input file");
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
SetMuscleInputMSA(msa);
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType)
{
case SEQTYPE_Auto:
Alpha = msa.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid SeqType");
}
SetAlpha(Alpha);
msa.FixAlpha();
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
SetPPScore(PPSCORE_SPN);
MSA msaOut;
RefineW(msa, msaOut);
// ValidateMuscleIds(msa);
// TextFile fileOut(g_pstrOutFileName, true);
// msaOut.ToFile(fileOut);
MuscleOutput(msaOut);
}
