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#include "muscle.h"
#include "textfile.h"
#include "seqvect.h"
#include "distfunc.h"
#include "msa.h"
#include "tree.h"
#include "profile.h"
extern void MHackStart(SeqVect &v);
extern void MHackEnd(MSA &msa);
static char g_strUseTreeWarning[] =
"\n******** WARNING ****************\n"
"\nYou specified the -usetree option.\n"
"Note that a good evolutionary tree may NOT be a good\n"
"guide tree for multiple alignment. For more details,\n"
"please refer to the user guide. To disable this\n"
"warning, use -usetree_nowarn <treefilename>.\n\n";
static void Muscle()
{
SetOutputFileName(g_pstrInFileName);
SetInputFileName(g_pstrInFileName);
SetStartTime();
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_Nucleo:
Alpha = ALPHA_Nucleo;
break;
default:
Quit("Invalid seq type");
}
SetAlpha(Alpha);
v.FixAlpha();
if (ALPHA_Nucleo == Alpha)
{
SetPPScore(PPSCORE_SPN);
g_Distance1 = DISTANCE_Kmer4_6;
}
if (g_bVerbose)
ListParams();
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 (uSeqCount > 1)
MHackStart(v);
if (0 == uSeqCount)
Quit("Input file '%s' has no sequences", g_pstrInFileName);
if (1 == uSeqCount)
{
TextFile fileOut(g_pstrOutFileName, true);
v.ToFile(fileOut);
return;
}
// First iteration
Tree GuideTree;
if (0 != g_pstrUseTreeFileName)
{
// Discourage users...
if (!g_bUseTreeNoWarn)
fprintf(stderr, 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);
}
// Set ids
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
const char *SeqName = v.GetSeqName(uSeqIndex);
unsigned uLeafIndex = GuideTree.GetLeafNodeIndex(SeqName);
GuideTree.SetLeafId(uLeafIndex, uSeqIndex);
}
}
else
TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1);
const char *Tree1 = ValueOpt("Tree1");
if (0 != Tree1)
{
TextFile f(Tree1, true);
GuideTree.ToFile(f);
if (g_bCluster)
return;
}
SetMuscleTree(GuideTree);
ValidateMuscleIds(GuideTree);
MSA msa;
ProgNode *ProgNodes = 0;
if (g_bLow)
ProgNodes = ProgressiveAlignE(v, GuideTree, msa);
else
ProgressiveAlign(v, GuideTree, msa);
SetCurrentAlignment(msa);
ValidateMuscleIds(msa);
if (1 == g_uMaxIters || 2 == uSeqCount)
{
TextFile fileOut(g_pstrOutFileName, true);
MHackEnd(msa);
msa.ToFile(fileOut);
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);
}
void Run()
{
Log("Started %s\n", GetTimeAsStr());
for (int i = 0; i < g_argc; ++i)
Log("%s ", g_argv[i]);
Log("\n");
if (g_bRefine)
Refine();
else if (g_bSW)
Local();
else if (0 != g_pstrSPFileName)
DoSP();
else if (g_bProfile)
Profile();
else if (g_bPPScore)
PPScore();
else
Muscle();
ListDiagSavings();
Log("Finished %s\n", GetTimeAsStr());
}
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