Reads a phylogenetic tree or data file and prints out the taxa labels one per line

newick2taxalist.cpp

//	Copyright (C) 2012 Mark T. Holder
//
//	Based on example/splitsinfile/splitsinfile.cpp in NEXUS class library
//
//	After NCL has been installed at ${NCL_PREFIX}
//
//		g++ newick2taxalist.cpp -o newick2taxalist -I "${NCL_PREFIX}/include" -lncl -L "${NCL_PREFIX}/lib/ncl"
//
//	Takes a newick file and prints out the taxa labels, one per line.
//
//	This script is free software; you can redistribute it and/or modify
//	it under the terms of the GNU General Public License as published by
//	the Free Software Foundation; either version 2 of the License, or
//	(at your option) any later version.
//
//	This script 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 General Public License for more details.
//
//	You should have received a copy of the GNU General Public License
//	along with NCL; if not, write to the Free Software Foundation, Inc.,
//	59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//

#include "ncl/ncl.h"
#include "ncl/nxsblock.h"
#include "ncl/nxspublicblocks.h"
#include "ncl/nxsmultiformat.h"
#include <cassert>

using namespace std;
long gStrictLevel = 2;
long gInterleaveLen = -1;
bool gVerbose = false;
void processContent(PublicNexusReader & nexusReader, ostream *out);






////////////////////////////////////////////////////////////////////////////////
// Takes NxsReader that has successfully read a file, and processes the
//	information stored in the reader.
//
// The caller is responsibel for calling DeleteBlocksFromFactories() to clean
//	up (if the reader uses the factory API).
////////////////////////////////////////////////////////////////////////////////
void processContent(PublicNexusReader & nexusReader, ostream *out)
{
	if (!out)
		return;
	BlockReaderList blocks = nexusReader.GetUsedBlocksInOrder();

	for (BlockReaderList::const_iterator bIt = blocks.begin(); bIt != blocks.end(); ++bIt)
		{
		NxsBlock * b = *bIt;
		if (b->GetID() == "TAXA")
		    {
			NxsTaxaBlockAPI * tb = (NxsTaxaBlockAPI *)b;
			std::vector<std::string> labVec = tb->GetAllLabels();
			std::vector<std::string>::const_iterator vIt = labVec.begin();
			for (; vIt != labVec.end(); ++vIt)
			    {
			    *out << *vIt << '\n';
			    }
			}

		}

}

////////////////////////////////////////////////////////////////////////////////
// Creates a NxsReader, and tries to read the file `filename`.  If the
//	read succeeds, then processContent will be called.
////////////////////////////////////////////////////////////////////////////////
void processFilepath(
	const char * filename, // name of the file to be read
	ostream *out, // output stream to use (NULL for no output). Not that cerr is used to report errors.
	MultiFormatReader::DataFormatType fmt) // enum indicating the file format to expect.
	{
	assert(filename);
	try
		{
		MultiFormatReader nexusReader(-1, NxsReader::WARNINGS_TO_STDERR);
		if (gStrictLevel != 2)
			nexusReader.SetWarningToErrorThreshold((int)NxsReader::FATAL_WARNING + 1 - (int) gStrictLevel);
		nexusReader.SetWarningOutputLevel(NxsReader::SUPPRESS_WARNINGS_LEVEL);
		NxsCharactersBlock * charsB = nexusReader.GetCharactersBlockTemplate();
		NxsDataBlock * dataB = nexusReader.GetDataBlockTemplate();
		charsB->SetAllowAugmentingOfSequenceSymbols(true);
		dataB->SetAllowAugmentingOfSequenceSymbols(true);
		if (gInterleaveLen > 0)
			{
			assert(charsB);
			charsB->SetWriteInterleaveLen(gInterleaveLen);
			dataB->SetWriteInterleaveLen(gInterleaveLen);
			}
		NxsTreesBlock * treesB = nexusReader.GetTreesBlockTemplate();
		assert(treesB);
		if (gStrictLevel < 2)
			treesB->SetAllowImplicitNames(true);
		if (gStrictLevel < 2)
			{
			NxsStoreTokensBlockReader *storerB =  nexusReader.GetUnknownBlockTemplate();
			assert(storerB);
			storerB->SetTolerateEOFInBlock(true);
			}
		try {
			nexusReader.ReadFilepath(filename, fmt);
			processContent(nexusReader, out);
			}
		catch(...)
			{
			nexusReader.DeleteBlocksFromFactories();
			throw;
			}
		nexusReader.DeleteBlocksFromFactories();
		}
	catch (const NxsException &x)
		{
		cerr << "Error:\n " << x.msg << endl;
		if (x.line >=0)
			cerr << "at line " << x.line << ", column (approximately) " << x.col << " (and file position "<< x.pos << ")" << endl;
		exit(2);
		}
	}

void readFilepathAsNEXUS(const char *filename, MultiFormatReader::DataFormatType fmt)
	{
	cerr << "[Reading " << filename << "	 ]" << endl;
	try {
		ostream * outStream = 0L;
		outStream = &cout;
		processFilepath(filename, outStream, fmt);
		}
	catch (...)
		{
		cerr << "Parsing of " << filename << " failed (with an exception)" << endl;
		exit(1);
		}
	}

void readFilesListedIsFile(const char *masterFilepath, MultiFormatReader::DataFormatType fmt)
	{
	ifstream masterStream(masterFilepath, ios::binary);
	if (masterStream.bad())
		{
		cerr << "Could not open " << masterFilepath << "." << endl;
		exit(3);
		}
	char filename[1024];
	while ((!masterStream.eof())  && masterStream.good())
		{
		masterStream.getline(filename, 1024);
		if (strlen(filename) > 0 && filename[0] != '#')
			readFilepathAsNEXUS(filename, fmt);
		}
	}

void printHelp(ostream & out)
	{
	out << "newick2taxalist takes a file and prints out the taxa labels, one per line.\n";
	out << "\nThe most common usage is simply:\n    newick2taxalist <path to NEXUS file>\n";
	out << "\nCommand-line flags:\n\n";
	out << "    -h on the command line shows this help message\n\n";
	out << "    -v verbose output\n\n";
	out << "    -l<path> reads a file and treats each line of the file as a path to NEXUS file\n\n";
	out << "    -s<non-negative integer> controls the NEXUS strictness level.\n";
	out << "        the default level is equivalent to -s2 invoking the program with \n";
	out << "        -s3 or a higher number will convert some warnings into fatal errors.\n";
	out << "        Running with -s1 will cause the parser to accept dangerous constructs,\n";
	out << "        and running with -s0 will cause the parser make every attempt to finish\n";
	out << "        parsing the file (warning about very serious errors).\n\n";
	out << "        Note that when -s0 strictness level is used, and the parser fails to\n";
	out << "        finish, it will often be the result of an earlier error than the \n";
	out << "        error that is reported in the last message.\n";
	out << "    -f<format> specifies the input file format expected:\n";
	out << "            -fnexus     NEXUS (this is also the default)\n";
	out << "            -faafasta   Amino acid data in fasta\n";
	out << "            -fdnafasta  DNA data in fasta\n";
	out << "            -frnafasta  RNA data in fasta\n";
	out << "        The complete list of format names that can follow the -f flag is:\n";
	std::vector<std::string> fmtNames =  MultiFormatReader::getFormatNames();
	for (std::vector<std::string>::const_iterator n = fmtNames.begin(); n != fmtNames.end(); ++n)
		{
		out << "            "<< *n << "\n";
		}
	}

int main(int argc, char *argv[])
	{
	MultiFormatReader::DataFormatType f(MultiFormatReader::NEXUS_FORMAT);

	bool readfile = false;
	for (int i = 1; i < argc; ++i)
		{
		const char * filepath = argv[i];
		const unsigned slen = strlen(filepath);
		if (strlen(filepath) > 1 && filepath[0] == '-' && filepath[1] == 'h')
			printHelp(cout);
		else if (strlen(filepath) == 2 && filepath[0] == '-' && filepath[1] == 'v')
			gVerbose = true;
		else if (slen > 1 && filepath[0] == '-' && filepath[1] == 's')
			{
			if ((slen == 2) || (!NxsString::to_long(filepath + 2, &gStrictLevel)))
				{
				cerr << "Expecting an integer after -s\n" << endl;
				printHelp(cerr);
				return 2;
				}
			}
		else if (slen > 1 && filepath[0] == '-' && filepath[1] == 'f')
			{
			f = MultiFormatReader::UNSUPPORTED_FORMAT;
			if (slen > 2)
				{
				std::string fmtName(filepath + 2, slen - 2);
				f =  MultiFormatReader::formatNameToCode(fmtName);
				}
			if (f == MultiFormatReader::UNSUPPORTED_FORMAT)
				{
				cerr << "Expecting a format after after -f\n" << endl;
				printHelp(cerr);
				return 2;
				}
			}
		else
			{
			if (strlen(filepath) > 2 && filepath[0] == '-' && filepath[1] == 'l')
				{
				readfile = true;
				readFilesListedIsFile(filepath+2, f);
				}
			else
				{
				readfile = true;
				readFilepathAsNEXUS(filepath, f);
				}
			}
		}
	if (!readfile)
		{
		cerr << "Expecting the path to NEXUS file as the only command line argument!\n" << endl;
		printHelp(cerr);
		return 1;
		}
	return 0;
	}