int main(int argc, char *argv[])
{
time_t rawtime;
struct tm * timeinfo;
time ( &rawtime );
timeinfo = localtime ( &rawtime );
// std::cout << "Start " << asctime (timeinfo);
/////////////////////////////////////////
// Setup
if( argc < 10 || argc > 12){
std::cout << "Wrong number of input arguments (" << argc << "), should have format:\n";
std::cout << "\ttree_to_matrix <infile> <tmpfile> <prunedfile> <refalignment> <outfile> <starting_row> <ending_row> <format M=matrix E=esprit> <Do_Pruning 0=no 1=yes 2=only prune> [outfile_freq] [maxdistance(E format only)]\n";
}
char* infilename = argv[1]; // (input) Tree file with reference sequences
char* tempfilename = argv[2]; // (output) Half-pruned file (after pruning, before cleaning up single-child nodes and internal nodes which have become leaves
char* prunedfilename = argv[3]; // (in/out) Pruned file name, input if not pruning, output if pruning
char* refalignname = argv[4]; // (input) reference fasta file, only uses the sequence identifiers for pruning
char* outfilename = argv[5]; // (output) Output distance matrix/list file name
int startrow = atoi(argv[6]); // (input) First row to print for the distance matrix (0 for all)
int endrow = atoi(argv[7]); // (input) Last row to print for the distance matrix (0 for all)
char format = argv[8][0]; // (input) Format of distance, M=matrix, E=ESPRIT list
int do_pruning = atoi(argv[9]); // (input) 0=no 1=yes 2=only prune
// M = matrix format, used by mothur
// E = ESPRIT list format
char* frqfilename;
float maxdist=0.1;
if( argc == 12 ){
frqfilename = argv[10]; // (Optional output) Frequency file name, used when running ESPRIT
maxdist = atof(argv[11]); // (Optional input) Maximum distance to print in the distance list (ESPRIT format only)
std::cout << frqfilename << " " << maxdist << std::endl;
} else {
if( format == 'E' ){
std::cerr << "maximum distance required for ESPRIT printout; quitting\n";
return EXIT_FAILURE;
}
}
int srow = startrow;
char* inname;
if( do_pruning>0 ){
// Read in raw file, then prune it
inname = infilename;
} else {
// Read in pruned file directly
inname = prunedfilename;
}
if( format == 'E' ){
std::cout << "Printing output in ESPRIT list format\n";
} else if( format == 'M' ){
std::cout << "Printing output in Mothur matrix format\n";
} else {
std::cerr << "Unknown format " << format << ". Quitting\n";
return EXIT_FAILURE;
}
std::list<TreeNode>::iterator startit;
std::list<TreeNode>::iterator endit;
/////////////////////////////////////////
// READ IN TREE FROM FILE
std::cout << "Reading in " << inname << std::endl;
PhyloTree<TreeNode>* tr = new PhyloTree<TreeNode>();
std::ifstream infile;
infile.open(inname);
if( !infile.is_open() ){ std::cout << "Unable to open file " << inname << std::endl; }
tr->readTree(infile);
std::cout << "LEAVES: " << tr->getNleaves() << std::endl;
tr->check_root();
/////////////////////////////////////////
// Prune tree (if necessary)
if( do_pruning>0 ){
std::cout << "Pruning tree\n";
// Read in reference alignment file and grab reference file names
std::ifstream reffile;
reffile.open(refalignname);
if( !reffile.is_open() ){ std::cout << "Unable to open file " << refalignname << std::endl; }
char line[100];
reffile >> line;
while( !reffile.eof() ){
if( line[0] == '>' ){
// Clean-up the file name
std::string name(line);
int slash = (int)name.find("/");
name = name.substr(1, slash-1);
int bar = (int)name.find("|");
if ( bar != name.npos ){
name = name.replace(bar, 1, "_");
}
// Remove this leaf from the tree
tr->deleteLeaf(name.c_str());
}
reffile >> line;
}
reffile.close();
// Print to tmp file, just in case
std::ofstream treeout;
treeout.open( tempfilename );
if( !treeout.is_open() ){ std::cout << "Unable to open file " << tempfilename << std::endl; }
treeout.precision(5);
treeout.setf(std::ios::fixed,std::ios::floatfield);
tr->writeTree( treeout );
treeout.close();
std::cout << "Printed to file " << tempfilename << std::endl;
// Remove internal nodes that are now leaves
while( tr->deleteLeaf("") > 0 );
// Smooth to remove single child nodes
while( tr->smooth() > 0 );
// Check that the root doesn't have only one node
tr->check_root();
// Print pruned file, for use by parallel jobs
treeout.open( prunedfilename );
if( !treeout.is_open() ){ std::cout << "Unable to open file " << prunedfilename << std::endl; }
treeout.precision(6);
treeout.setf(std::ios::fixed,std::ios::floatfield);
tr->writeTree( treeout );
treeout.close();
std::cout << "Printed to file " << prunedfilename << std::endl;
// If I only needed to prune then I'm done
if( do_pruning>1 ){
std::cout << "Done pruning tips, ready to launch parallel tree_to_matrix jobs\n";
return EXIT_SUCCESS;
}
}
