void DoMuscle() { SetOutputFileName(g_pstrOutFileName.get()); SetInputFileName(g_pstrInFileName.get()); SetMaxIters(g_uMaxIters.get()); SetSeqWeightMethod(g_SeqWeight1.get()); TextFile fileIn(g_pstrInFileName.get()); SeqVect v; v.FromFASTAFile(fileIn); const unsigned uSeqCount = v.Length(); if (0 == uSeqCount) Quit("No sequences in input file"); ALPHA Alpha = ALPHA_Undefined; switch (g_SeqType.get()) { case SEQTYPE_Auto: Alpha = v.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 seq type"); } SetAlpha(Alpha); v.FixAlpha(); // // AED 21/12/06: Moved matrix loading code inside the PP param function so it gets called for all alignment types // SetPPScore(); unsigned uMaxL = 0; unsigned uTotL = 0; for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) { unsigned L = v.GetSeq(uSeqIndex).Length(); uTotL += L; if (L > uMaxL) uMaxL = L; } SetIter(1); g_bDiags.get() = g_bDiags1.get(); SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount); SetMuscleSeqVect(v); MSA::SetIdCount(uSeqCount); // Initialize sequence ids. // From this point on, ids must somehow propogate from here. for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) v.SetSeqId(uSeqIndex, uSeqIndex); if (0 == uSeqCount) Quit("Input file '%s' has no sequences", g_pstrInFileName.get()); if (1 == uSeqCount) { TextFile fileOut(g_pstrOutFileName.get(), true); v.ToFile(fileOut); return; } if (uSeqCount > 1) MHackStart(v); // First iteration Tree GuideTree; if (0 != g_pstrUseTreeFileName.get()) { // Discourage users... if (!g_bUseTreeNoWarn.get()) fprintf(stderr, g_strUseTreeWarning); // Read tree from file TextFile TreeFile(g_pstrUseTreeFileName.get()); GuideTree.FromFile(TreeFile); // Make sure tree is rooted if (!GuideTree.IsRooted()) Quit("User tree must be rooted"); if (GuideTree.GetLeafCount() != uSeqCount) Quit("User tree does not match input sequences"); const unsigned uNodeCount = GuideTree.GetNodeCount(); for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex) { if (!GuideTree.IsLeaf(uNodeIndex)) continue; const char *LeafName = GuideTree.GetLeafName(uNodeIndex); unsigned uSeqIndex; bool SeqFound = v.FindName(LeafName, &uSeqIndex); if (!SeqFound) Quit("Label %s in tree does not match sequences", LeafName); unsigned uId = v.GetSeqIdFromName(LeafName); GuideTree.SetLeafId(uNodeIndex, uId); } } else TreeFromSeqVect(v, GuideTree, g_Cluster1.get(), g_Distance1.get(), g_Root1.get(), g_pstrDistMxFileName1.get()); const char *Tree1 = ValueOpt("Tree1"); if (0 != Tree1) { TextFile f(Tree1, true); GuideTree.ToFile(f); if (g_bClusterOnly.get()) return; } SetMuscleTree(GuideTree); ValidateMuscleIds(GuideTree); MSA msa; ProgNode *ProgNodes = 0; if (g_bLow.get()) ProgNodes = ProgressiveAlignE(v, GuideTree, msa); else ProgressiveAlign(v, GuideTree, msa); SetCurrentAlignment(msa); if (0 != g_pstrComputeWeightsFileName.get()) { extern void OutWeights(const char *FileName, const MSA &msa); SetMSAWeightsMuscle(msa); OutWeights(g_pstrComputeWeightsFileName.get(), msa); return; } ValidateMuscleIds(msa); if (1 == g_uMaxIters.get() || 2 == uSeqCount) { //TextFile fileOut(g_pstrOutFileName.get(), true); //MHackEnd(msa); //msa.ToFile(fileOut); MuscleOutput(msa); return; } if (0 == g_pstrUseTreeFileName.get()) { g_bDiags.get() = g_bDiags2.get(); SetIter(2); if (g_bLow.get()) { if (0 != g_uMaxTreeRefineIters.get()) RefineTreeE(msa, v, GuideTree, ProgNodes); } else RefineTree(msa, GuideTree); const char *Tree2 = ValueOpt("Tree2"); if (0 != Tree2) { TextFile f(Tree2, true); GuideTree.ToFile(f); } } SetSeqWeightMethod(g_SeqWeight2.get()); SetMuscleTree(GuideTree); if (g_bAnchors.get()) RefineVert(msa, GuideTree, g_uMaxIters.get() - 2); else RefineHoriz(msa, GuideTree, g_uMaxIters.get() - 2, false, false); #if 0 // Refining by subfamilies is disabled as it didn't give better // results. I tried doing this before and after RefineHoriz. // Should get back to this as it seems like this should work. RefineSubfams(msa, GuideTree, g_uMaxIters.get() - 2); #endif ValidateMuscleIds(msa); ValidateMuscleIds(GuideTree); //TextFile fileOut(g_pstrOutFileName.get(), true); //MHackEnd(msa); //msa.ToFile(fileOut); MuscleOutput(msa); }
bool RefineSubfams(MSA &msa, const Tree &tree, unsigned uIters) { MuscleContext *ctx = getMuscleContext(); CLUSTER &g_Cluster2 = ctx->params.g_Cluster2; DISTANCE &g_Distance2 = ctx->params.g_Distance2; ROOT &g_Root2 = ctx->params.g_Root2; bool &g_bAnchors = ctx->params.g_bAnchors; const unsigned uSeqCount = msa.GetSeqCount(); if (uSeqCount < 3) return false; const double dMaxHeight = 0.6; const unsigned uMaxSubfamCount = 16; //const unsigned uNodeCount = tree.GetNodeCount(); unsigned *Subfams; unsigned uSubfamCount; GetSubfams(tree, dMaxHeight, uMaxSubfamCount, &Subfams, &uSubfamCount); assert(uSubfamCount <= uSeqCount); if (ctx->params.g_bVerbose) LogSubfams(tree, Subfams, uSubfamCount); MSA *SubfamMSAs = new MSA[uSubfamCount]; unsigned *Leaves = new unsigned[uSeqCount]; unsigned *Ids = new unsigned[uSeqCount]; bool bAnyChanges = false; for (unsigned uSubfamIndex = 0; uSubfamIndex < uSubfamCount; ++uSubfamIndex) { unsigned uSubfam = Subfams[uSubfamIndex]; unsigned uLeafCount; GetLeaves(tree, uSubfam, Leaves, &uLeafCount); assert(uLeafCount <= uSeqCount); LeafIndexesToIds(tree, Leaves, uLeafCount, Ids); MSA &msaSubfam = SubfamMSAs[uSubfamIndex]; MSASubsetByIds(msa, Ids, uLeafCount, msaSubfam); DeleteGappedCols(msaSubfam); #if TRACE Log("Subfam %u MSA=\n", uSubfamIndex); msaSubfam.LogMe(); #endif if (msaSubfam.GetSeqCount() <= 2) continue; // TODO ///////////////////////////////////////// // Try using existing tree, may actually hurt to // re-estimate, may also be a waste of CPU & mem. ///////////////////////////////////////////////// Tree SubfamTree; TreeFromMSA(msaSubfam, SubfamTree, g_Cluster2, g_Distance2, g_Root2); bool bAnyChangesThisSubfam; if (g_bAnchors) bAnyChangesThisSubfam = RefineVert(msaSubfam, SubfamTree, uIters); else bAnyChangesThisSubfam = RefineHoriz(msaSubfam, SubfamTree, uIters, false, false); #if TRACE Log("Subfam %u Changed %d\n", uSubfamIndex, bAnyChangesThisSubfam); #endif if (bAnyChangesThisSubfam) bAnyChanges = true; } if (bAnyChanges) ProgressiveAlignSubfams(tree, Subfams, uSubfamCount, SubfamMSAs, msa); delete[] Leaves; delete[] Subfams; delete[] SubfamMSAs; return bAnyChanges; }
void DoMuscle(CompositeVect*CVLocation) { SetOutputFileName(g_pstrOutFileName); SetInputFileName(g_pstrInFileName); SetMaxIters(g_uMaxIters); SetSeqWeightMethod(g_SeqWeight1); TextFile fileIn(g_pstrInFileName); SeqVect v; v.FromFASTAFile(fileIn); const unsigned uSeqCount = v.Length(); if (0 == uSeqCount) Quit("No sequences in input file"); ALPHA Alpha = ALPHA_Undefined; switch (g_SeqType) { case SEQTYPE_Auto: Alpha = v.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 seq type"); } SetAlpha(Alpha); v.FixAlpha(); PTR_SCOREMATRIX UserMatrix = 0; if (0 != g_pstrMatrixFileName) { const char *FileName = g_pstrMatrixFileName; const char *Path = getenv("MUSCLE_MXPATH"); if (Path != 0) { size_t n = strlen(Path) + 1 + strlen(FileName) + 1; char *NewFileName = new char[n]; sprintf(NewFileName, "%s/%s", Path, FileName); FileName = NewFileName; } TextFile File(FileName); UserMatrix = ReadMx(File); g_Alpha = ALPHA_Amino; g_PPScore = PPSCORE_SP; } SetPPScore(); if (0 != UserMatrix) g_ptrScoreMatrix = UserMatrix; unsigned uMaxL = 0; unsigned uTotL = 0; for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) { unsigned L = v.GetSeq(uSeqIndex).Length(); uTotL += L; if (L > uMaxL) uMaxL = L; } SetIter(1); g_bDiags = g_bDiags1; SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount); SetMuscleSeqVect(v); MSA::SetIdCount(uSeqCount); // Initialize sequence ids. // From this point on, ids must somehow propogate from here. for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) v.SetSeqId(uSeqIndex, uSeqIndex); if (0 == uSeqCount) Quit("Input file '%s' has no sequences", g_pstrInFileName); if (1 == uSeqCount) { TextFile fileOut(g_pstrOutFileName, true); v.ToFile(fileOut); return; } if (uSeqCount > 1) MHackStart(v); // First iteration Tree GuideTree; if (0 != g_pstrUseTreeFileName) { // Discourage users... if (!g_bUseTreeNoWarn) fprintf(stderr, "%s", g_strUseTreeWarning); // Read tree from file TextFile TreeFile(g_pstrUseTreeFileName); GuideTree.FromFile(TreeFile); // Make sure tree is rooted if (!GuideTree.IsRooted()) Quit("User tree must be rooted"); if (GuideTree.GetLeafCount() != uSeqCount) Quit("User tree does not match input sequences"); const unsigned uNodeCount = GuideTree.GetNodeCount(); for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex) { if (!GuideTree.IsLeaf(uNodeIndex)) continue; const char *LeafName = GuideTree.GetLeafName(uNodeIndex); unsigned uSeqIndex; bool SeqFound = v.FindName(LeafName, &uSeqIndex); if (!SeqFound) Quit("Label %s in tree does not match sequences", LeafName); unsigned uId = v.GetSeqIdFromName(LeafName); GuideTree.SetLeafId(uNodeIndex, uId); } } else TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1, g_pstrDistMxFileName1); const char *Tree1 = ValueOpt("Tree1"); if (0 != Tree1) { TextFile f(Tree1, true); GuideTree.ToFile(f); if (g_bClusterOnly) return; } SetMuscleTree(GuideTree); ValidateMuscleIds(GuideTree); MSA msa; msa.SetCompositeVector(CVLocation); ProgNode *ProgNodes = 0; if (g_bLow) ProgNodes = ProgressiveAlignE(v, GuideTree, msa); else ProgressiveAlign(v, GuideTree, msa); SetCurrentAlignment(msa); if (0 != g_pstrComputeWeightsFileName) { extern void OutWeights(const char *FileName, const MSA &msa); SetMSAWeightsMuscle(msa); OutWeights(g_pstrComputeWeightsFileName, msa); return; } ValidateMuscleIds(msa); if (1 == g_uMaxIters || 2 == uSeqCount) { //TextFile fileOut(g_pstrOutFileName, true); //MHackEnd(msa); //msa.ToFile(fileOut); MuscleOutput(msa); return; } if (0 == g_pstrUseTreeFileName) { g_bDiags = g_bDiags2; SetIter(2); if (g_bLow) { if (0 != g_uMaxTreeRefineIters) RefineTreeE(msa, v, GuideTree, ProgNodes); } else RefineTree(msa, GuideTree); const char *Tree2 = ValueOpt("Tree2"); if (0 != Tree2) { TextFile f(Tree2, true); GuideTree.ToFile(f); } } SetSeqWeightMethod(g_SeqWeight2); SetMuscleTree(GuideTree); if (g_bAnchors) RefineVert(msa, GuideTree, g_uMaxIters - 2); else RefineHoriz(msa, GuideTree, g_uMaxIters - 2, false, false); #if 0 // Refining by subfamilies is disabled as it didn't give better // results. I tried doing this before and after RefineHoriz. // Should get back to this as it seems like this should work. RefineSubfams(msa, GuideTree, g_uMaxIters - 2); #endif ValidateMuscleIds(msa); ValidateMuscleIds(GuideTree); //TextFile fileOut(g_pstrOutFileName, true); //MHackEnd(msa); //msa.ToFile(fileOut); MuscleOutput(msa); }
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); }