void LodExtract::createInterpolatedAlignment(AlignmentConstPtr inAlignment,
AlignmentPtr outAlignment,
double scale,
const string& tree,
const string& rootName,
bool keepSequences,
bool allSequences,
double probeFrac,
double minSeqFrac)
{
_inAlignment = inAlignment;
_outAlignment = outAlignment;
_keepSequences = keepSequences;
_allSequences = allSequences;
_probeFrac = probeFrac;
_minSeqFrac = minSeqFrac;
string newTree = tree.empty() ? inAlignment->getNewickTree() : tree;
createTree(newTree, rootName);
cout << "tree = " << _outAlignment->getNewickTree() << endl;
deque<string> bfQueue;
bfQueue.push_front(_outAlignment->getRootName());
while (!bfQueue.empty())
{
string genomeName = bfQueue.back();
bfQueue.pop_back();
vector<string> childNames = _outAlignment->getChildNames(genomeName);
if (!childNames.empty())
{
convertInternalNode(genomeName, scale);
for (size_t childIdx = 0; childIdx < childNames.size(); childIdx++)
{
bfQueue.push_back(childNames[childIdx]);
}
}
}
}
int main(int argc, char** argv)
{
CLParserPtr optionsParser = hdf5CLParserInstance();
optionsParser->setDescription("Retrieve basic statistics from a hal database");
optionsParser->addArgument("halFile", "path to hal file to analyze");
optionsParser->addOptionFlag("genomes", "print only a list of genomes "
"in alignment", false);
optionsParser->addOption("sequences", "print list of sequences in given "
"genome", "\"\"");
optionsParser->addOption("sequenceStats", "print stats for each sequence in "
"given genome", "\"\"");
optionsParser->addOption("bedSequences", "print sequences of given genome "
"in bed format",
"\"\"");
optionsParser->addOptionFlag("tree", "print only the NEWICK tree", false);
optionsParser->addOptionFlag("branches", "print list of branches. "
"Each branch is specified by the child genome",
false);
optionsParser->addOption("span", "print branches on path (or spanning tree) "
"between comma "
"separated list of genomes", "\"\"");
optionsParser->addOption("spanRoot", "print genomes on path"
"(or spanning tree) between comma "
"separated list of genomes. Different from --span"
"only in that the spanning tree root is also "
"given", "\"\"");
optionsParser->addOption("children", "print names of children of given "
"genome", "\"\"");
optionsParser->addOptionFlag("root", "print root genome name", false);
optionsParser->addOption("parent", "print name of parent of given genome",
"\"\"");
optionsParser->addOption("branchLength", "print branch length between "
"given genome and its parent in the tree",
"\"\"");
optionsParser->addOption("numSegments", "print numTopSegments "
"numBottomSegments for given genome.",
"\"\"");
optionsParser->addOption("baseComp", "print base composition for given "
"genome by sampling every step bases. Parameter "
"value is of the form genome,step. Ex: "
"--baseComp human,1000. The ouptut is of the form "
"fraction_of_As fraction_of_Gs fraction_of_Cs "
"fraction_of_Ts.",
"\"\"");
optionsParser->addOption("genomeMetaData", "print metadata for given genome, "
"one entry per line, tab-seperated.", "\"\"");
optionsParser->addOption("chromSizes", "print the name and length of each"
" sequence in a given genome. This is a subset"
" of the"
" information returned by --sequenceStats but is"
" useful because it is in the format used by"
" wigToBigWig",
"\"\"");
optionsParser->addOption("percentID",
"print % ID of a genome with all other genomes."
"Only non-duplicated and unambiguous sites are"
"considered",
"\"\"");
optionsParser->addOption("coverage",
"print histogram of coverage of a genome with"
" all genomes", "\"\"");
optionsParser->addOption("topSegments",
"print coordinates of all top segments of given"
" genome in BED format.", "\"\"");
optionsParser->addOption("bottomSegments",
"print coordinates of all bottom segments of given"
" genome in BED format.", "\"\"");
optionsParser->addOptionFlag("allCoverage",
"print histogram of coverage from all genomes to"
" all genomes", false);
string path;
bool listGenomes;
string sequencesFromGenome;
string sequenceStatsFromGenome;
string bedSequencesFromGenome;
string spanGenomes;
string spanRootGenomes;
bool tree;
bool branches;
string childrenFromGenome;
string parentFromGenome;
bool printRoot;
string nameForBL;
string numSegmentsGenome;
string baseCompPair;
string genomeMetaData;
string chromSizesFromGenome;
string percentID;
string coverage;
string topSegments;
string bottomSegments;
bool allCoverage;
try
{
optionsParser->parseOptions(argc, argv);
path = optionsParser->getArgument<string>("halFile");
listGenomes = optionsParser->getFlag("genomes");
sequencesFromGenome = optionsParser->getOption<string>("sequences");
sequenceStatsFromGenome = optionsParser->getOption<string>("sequenceStats");
bedSequencesFromGenome = optionsParser->getOption<string>("bedSequences");
tree = optionsParser->getFlag("tree");
spanGenomes = optionsParser->getOption<string>("span");
spanRootGenomes = optionsParser->getOption<string>("spanRoot");
branches = optionsParser->getFlag("branches");
childrenFromGenome = optionsParser->getOption<string>("children");
parentFromGenome = optionsParser->getOption<string>("parent");
printRoot = optionsParser->getFlag("root");
nameForBL = optionsParser->getOption<string>("branchLength");
numSegmentsGenome = optionsParser->getOption<string>("numSegments");
baseCompPair = optionsParser->getOption<string>("baseComp");
genomeMetaData = optionsParser->getOption<string>("genomeMetaData");
chromSizesFromGenome = optionsParser->getOption<string>("chromSizes");
percentID = optionsParser->getOption<string>("percentID");
coverage = optionsParser->getOption<string>("coverage");
topSegments = optionsParser->getOption<string>("topSegments");
bottomSegments = optionsParser->getOption<string>("bottomSegments");
allCoverage = optionsParser->getFlag("allCoverage");
size_t optCount = listGenomes == true ? 1 : 0;
if (sequencesFromGenome != "\"\"") ++optCount;
if (tree == true) ++optCount;
if (sequenceStatsFromGenome != "\"\"") ++optCount;
if (bedSequencesFromGenome != "\"\"") ++optCount;
if (spanGenomes != "\"\"") ++optCount;
if (spanRootGenomes != "\"\"") ++optCount;
if (branches) ++ optCount;
if (childrenFromGenome != "\"\"") ++optCount;
if (parentFromGenome != "\"\"") ++optCount;
if (printRoot) ++optCount;
if (nameForBL != "\"\"") ++optCount;
if (numSegmentsGenome != "\"\"") ++optCount;
if (baseCompPair != "\"\"") ++optCount;
if (genomeMetaData != "\"\"") ++optCount;
if (chromSizesFromGenome != "\"\"") ++optCount;
if (percentID != "\"\"") ++optCount;
if (coverage != "\"\"") ++optCount;
if (topSegments != "\"\"") ++optCount;
if (bottomSegments != "\"\"") ++optCount;
if (allCoverage) ++optCount;
if (optCount > 1)
{
throw hal_exception("--genomes, --sequences, --tree, --span, --spanRoot, "
"--branches, --sequenceStats, --children, --parent, "
"--bedSequences, --root, --numSegments, --baseComp, "
"--genomeMetaData, --chromSizes, --percentID, "
"--coverage, --topSegments, --bottomSegments, "
"--allCoverage "
"and --branchLength options are exclusive");
}
}
catch(exception& e)
{
cerr << e.what() << endl;
optionsParser->printUsage(cerr);
exit(1);
}
try
{
AlignmentConstPtr alignment = openHalAlignmentReadOnly(path, optionsParser);
if (listGenomes == true && alignment->getNumGenomes() > 0)
{
printGenomes(cout, alignment);
}
else if (sequencesFromGenome != "\"\"")
{
printSequences(cout, alignment, sequencesFromGenome);
}
else if (tree == true)
{
cout << alignment->getNewickTree() << endl;
}
else if (sequenceStatsFromGenome != "\"\"")
{
printSequenceStats(cout, alignment, sequenceStatsFromGenome);
}
else if (bedSequencesFromGenome != "\"\"")
{
printBedSequenceStats(cout, alignment, bedSequencesFromGenome);
}
else if (spanGenomes != "\"\"")
{
printBranchPath(cout, alignment, chopString(spanGenomes, ","), false);
}
else if (spanRootGenomes != "\"\"")
{
printBranchPath(cout, alignment, chopString(spanRootGenomes, ","), true);
}
else if (branches == true)
{
printBranches(cout, alignment);
}
else if (childrenFromGenome != "\"\"")
{
printChildren(cout, alignment, childrenFromGenome);
}
else if (parentFromGenome != "\"\"")
{
printParent(cout, alignment, parentFromGenome);
}
else if (printRoot == true)
{
printRootName(cout, alignment);
}
else if (nameForBL != "\"\"")
{
printBranchLength(cout, alignment, nameForBL);
}
else if (numSegmentsGenome != "\"\"")
{
printNumSegments(cout, alignment, numSegmentsGenome);
}
else if (baseCompPair != "\"\"")
{
printBaseComp(cout, alignment, baseCompPair);
}
else if (genomeMetaData != "\"\"")
{
printGenomeMetaData(cout, alignment, genomeMetaData);
}
else if (chromSizesFromGenome != "\"\"")
{
printChromSizes(cout, alignment, chromSizesFromGenome);
}
else if (percentID != "\"\"")
{
printPercentID(cout, alignment, percentID);
}
else if (coverage != "\"\"") {
printCoverage(cout, alignment, coverage);
}
else if (topSegments != "\"\"") {
printSegments(cout, alignment, topSegments, true);
}
else if (bottomSegments != "\"\"") {
printSegments(cout, alignment, bottomSegments, false);
} else if (allCoverage) {
printAllCoverage(cout, alignment);
}
else
{
HalStats halStats(alignment);
cout << endl << "hal v" << alignment->getVersion() << "\n" << halStats;
}
}
catch(hal_exception& e)
{
cerr << "hal exception caught: " << e.what() << endl;
return 1;
}
catch(exception& e)
{
cerr << "Exception caught: " << e.what() << endl;
return 1;
}
return 0;
}
int main(int argc, char** argv)
{
CLParserPtr optionsParser = hdf5CLParserInstance();
optionsParser->setDescription("Rertrieve basic statics from a hal database");
optionsParser->addArgument("halFile", "path to hal file to analyze");
optionsParser->addOptionFlag("genomes", "print only a list of genomes "
"in alignment", false);
optionsParser->addOption("sequences", "print list of sequences in given "
"genome", "\"\"");
optionsParser->addOption("sequenceStats", "print stats for each sequence in "
"given genome", "\"\"");
optionsParser->addOptionFlag("tree", "print only the NEWICK tree", false);
optionsParser->addOptionFlag("branches", "print list of branches. "
"Each branch is specified by the child genome",
false);
optionsParser->addOption("span", "print branches on path (or spanning tree) "
"between comma "
"separated list of genomes", "\"\"");
optionsParser->addOption("spanRoot", "print genomes on path"
"(or spanning tree) between comma "
"separated list of genomes. Different from --path"
"only in that the spanning tree root is also "
"given", "\"\"");
string path;
bool listGenomes;
string sequencesFromGenome;
string sequenceStatsFromGenome;
string spanGenomes;
string spanRootGenomes;
bool tree;
bool branches;
try
{
optionsParser->parseOptions(argc, argv);
path = optionsParser->getArgument<string>("halFile");
listGenomes = optionsParser->getFlag("genomes");
sequencesFromGenome = optionsParser->getOption<string>("sequences");
sequenceStatsFromGenome = optionsParser->getOption<string>("sequenceStats");
tree = optionsParser->getFlag("tree");
spanGenomes = optionsParser->getOption<string>("span");
spanRootGenomes = optionsParser->getOption<string>("spanRoot");
branches = optionsParser->getFlag("branches");
size_t optCount = listGenomes == true ? 1 : 0;
if (sequencesFromGenome != "\"\"") ++optCount;
if (tree == true) ++optCount;
if (sequenceStatsFromGenome != "\"\"") ++optCount;
if (spanGenomes != "\"\"") ++optCount;
if (spanRootGenomes != "\"\"") ++optCount;
if (branches) ++optCount;
if (optCount > 1)
{
throw hal_exception("--genomes, --sequences, --tree, --span, "
"--spanRoot, --branches "
"and --sequenceStats "
"options are mutually exclusive");
}
}
catch(exception& e)
{
cerr << e.what() << endl;
optionsParser->printUsage(cerr);
exit(1);
}
try
{
AlignmentConstPtr alignment = openHalAlignmentReadOnly(path, optionsParser);
if (listGenomes == true && alignment->getNumGenomes() > 0)
{
printGenomes(cout, alignment);
}
else if (sequencesFromGenome != "\"\"")
{
printSequences(cout, alignment, sequencesFromGenome);
}
else if (tree == true)
{
cout << alignment->getNewickTree() << endl;
}
else if (sequenceStatsFromGenome != "\"\"")
{
printSequenceStats(cout, alignment, sequenceStatsFromGenome);
}
else if (spanGenomes != "\"\"")
{
printBranchPath(cout, alignment, chopString(spanGenomes, ","), false);
}
else if (spanRootGenomes != "\"\"")
{
printBranchPath(cout, alignment, chopString(spanRootGenomes, ","), true);
}
else if (branches == true)
{
printBranches(cout, alignment);
}
else
{
HalStats halStats(alignment);
cout << endl << "hal v" << alignment->getVersion() << "\n" << halStats;
}
}
catch(hal_exception& e)
{
cerr << "hal exception caught: " << e.what() << endl;
return 1;
}
catch(exception& e)
{
cerr << "Exception caught: " << e.what() << endl;
return 1;
}
return 0;
}
