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/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
==========================================================================*/
#include <seqan/basic.h>
#include <seqan/graph_msa.h>
#include <seqan/modifier.h>
#include <seqan/arg_parse.h>
#include <seqan/stream.h>
#include <iostream>
using namespace seqan;
//////////////////////////////////////////////////////////////////////////////////
template <typename TMat, typename TNames, typename TForwardIter>
void readPhylipMatrix(TMat & matrix,
TNames & names,
TForwardIter & iter)
{
//typedef typename Value<TFile>::Type TValue;
typedef typename Value<TMat>::Type TFloat;
typedef typename Size<TMat>::Type TSize;
//typedef typename Value<TNames>::Type TName;
typedef typename Iterator<TMat, Standard>::Type TMatIter;
if (atEnd(iter))
throw UnexpectedEnd();
// Parse the file and convert the internal ids.
CharString buffer;
while (!atEnd(iter))
{
clear(buffer);
// Read "<blanks><num>\n"
skipUntil(iter, NotFunctor<IsBlank>());
readUntil(buffer, iter, OrFunctor<NotFunctor<IsGraph>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Nothing> >());
TSize nseq = lexicalCast<TSize>(buffer);
skipLine(iter);
// Allocate memory in matrix and names.
resize(matrix, nseq * nseq);
resize(names, nseq);
TMatIter it = begin(matrix, Standard());
for (TSize row = 0; row < nseq; ++row)
{
readUntil(names[row], iter, NotFunctor<IsGraph>());
skipUntil(iter, OrFunctor<NotFunctor<IsSpace>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Nothing> >());
for (TSize col = 0; col < nseq; ++col, ++it)
{
clear(buffer);
readUntil(buffer, iter, NotFunctor<IsGraph>());
*it = lexicalCast<TFloat>(buffer);
if (col + 1 < nseq)
skipUntil(iter, OrFunctor<NotFunctor<IsSpace>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Nothing> >());
else
skipLine(iter);
}
}
}
}
//////////////////////////////////////////////////////////////////////////////////
int main(int argc, const char *argv[])
{
// -----------------------------------------------------------------------
// Setup argument parser
// -----------------------------------------------------------------------
seqan::ArgumentParser parser("tree_recon");
// Set short description, version, date.
setShortDescription(parser, "Tree reconstruction");
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
setDate(parser, SEQAN_DATE);
setCategory(parser, "Phylogeneny");
// Usage line and description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fB-m\\fP \\fIIN.DIST\\fP");
addDescription(parser, "Reconstruct phylogenetic tree from Phylip matrix \\fIIN.DIST\\fP.");
addSection(parser, "Input / Output");
addOption(parser, seqan::ArgParseOption("m", "matrix", "Name Phylip distance matrix file. Must contain at least three species.", seqan::ArgParseArgument::INPUT_FILE, "FILE"));
setRequired(parser, "matrix");
setValidValues(parser, "matrix", "dist");
addOption(parser, seqan::ArgParseOption("o", "out-file", "Path to write output to.", seqan::ArgParseArgument::OUTPUT_FILE, "FILE"));
setDefaultValue(parser, "out-file", "tree.dot");
setValidValues(parser, "out-file", "dot newick");
addSection(parser, "Algorithm Options");
addOption(parser, seqan::ArgParseOption("b", "build", "Tree building method. \\fInj\\fP: neighbour-joining, \\fImin\\fP: UPGMA single linkage, \\fImax\\fP: UPGMA complete linkage, \\fIavg\\fP: UPGMA average linkage, \\fIwavg\\fP: UPGMA weighted average linkage. Neighbour-joining creates an unrooted tree. We root that tree at the least joined pair.", seqan::ArgParseArgument::STRING, "METHOD"));
setValidValues(parser, "build", "nj min max avg wavg");
setDefaultValue(parser, "build", "nj");
addTextSection(parser, "Contact and References");
addListItem(parser, "For questions or comments, contact:", "Tobias Rausch <rausch@embl.de>");
addListItem(parser, "SeqAn Homepage:", "http://www.seqan.de");
// Parse command line.
seqan::ArgumentParser::ParseResult res = seqan::parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR;
// Tree reconstruction
typedef double TDistanceValue;
typedef String<char> TName;
typedef Size<TName>::Type TSize;
// Read the options
::std::string infile;
getOptionValue(infile, parser, "matrix");
::std::string outfile;
getOptionValue(outfile, parser, "out-file");
TSize build = 0;
String<char> meth;
getOptionValue(meth, parser, "build");
if (meth == "nj") build = 0;
else if (meth == "min") build = 1;
else if (meth == "max") build = 2;
else if (meth == "avg") build = 3;
else if (meth == "wavg") build = 4;
String<char> format;
String<char> tmp = outfile;
toLower(tmp);
if (endsWith(tmp, ".dot"))
format = "dot";
else
format = "newick";
// Read the distance matrix
String<TName> names;
String<TDistanceValue> matrix;
VirtualStream<char, Input> inPhylip(infile.c_str());
DirectionIterator<VirtualStream<char, Input>, Input>::Type iter(directionIterator(inPhylip, Input()));
readPhylipMatrix(matrix, names, iter);
// Create the tree
Graph<Tree<TDistanceValue> > tree;
switch (build)
{
case 0:
njTree(matrix, tree);
break;
case 1:
upgmaTree(matrix, tree, UpgmaMin());
break;
case 2:
upgmaTree(matrix, tree, UpgmaMax());
break;
case 3:
upgmaTree(matrix, tree, UpgmaAvg());
break;
case 4:
upgmaTree(matrix, tree, UpgmaWeightAvg());
break;
default:
SEQAN_FAIL("unknown build method.");
}
VirtualStream<char, Output> oStream(outfile.c_str());
if (format == "dot")
{
TSize nameLen = length(names);
resize(names, numVertices(tree));
// Add the label prefix for leaves
for (TSize i = 0;i < nameLen; ++i)
{
TName tmpName = "label = \"";
append(tmpName, names[i], Generous());
appendValue(tmpName, '"');
names[i] = tmpName;
}
// Append emty names for internal vertices
for (; nameLen < length(names); ++nameLen)
names[nameLen] = "label = \"\"";
// Write the result
writeRecords(oStream, tree, names, DotDrawing());
}
else if (format == "newick")
{
// If nj tree collapse the root
if (build == 0)
writeRecords(oStream, tree, names, true, NewickFormat());
else
writeRecords(oStream, tree, names, false, NewickFormat());
}
return 0;
}
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