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ClassSequenceDataCreatorApplication.hpp
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ClassSequenceDataCreatorApplication.hpp
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#ifndef CLASSSEQUENCEDATACREATORAPPLICATION_HPP
#define CLASSSEQUENCEDATACREATORAPPLICATION_HPP
#include <ApplicationInterface.hpp>
#include <string>
#include <SequenceMatrixCreator.hpp> // SequenceMatrixCreator::methods
/*!
* \brief The ClassSequenceDataCreatorApplication is a wrapper
* around a ClassSequenceDataCreator that creates a sequence
* matrix containing the data assigned to a given class, given
* a partition of these data.
*
* ClassSequenceDataCreator is an autonomous application that extracts the data
* that have been assigned to a given class K.
*
* Given posterior probabilities and a sequence matrix, the corresponding
* class models can be computed. They are the weighted aggregations of the
* DNA sequences assigned to each given class. However, because DNA sequences
* cannot be summed, the aggregation are represented as probability matrices
* or consensus sequence (A+C is represented as 50%A, 50%C, 0%G, 0%T). Instead
* of this, this program creates the unfolded matrix that, if summed over the
* columns, gives the model of class K.
*
* For a hard clustering methods, this procedure would simply correspond to the
* creation of a matrix of dimensions N'xL where N'<=N is the number sequences
* assigned to class K among the N overall sequences and L the length of
* the each sequence.
*
* In the case of a soft clustering methods, this procedure creates a 3D matrix of
* dimensions NxL'x4. This matrix contains N probability matrices, each one of
* dimensions L'x4 where L'=L-S+1, 4 corresponds to A, C, G, T and S is the
* shifting freedom allowed during the classification. The resulting matrix
* contains as many rows as the starting matrix because in soft clustering, all
* sequences (rows) are assigned to all classes
*
* To construct a final matrix M3 of dimensions NxL3 where L3 covers a given
* range <from>/<to>, the original matrix M1 of dimensions NxL is computed and
* extended into a matrix M2 NxL2 with L2>=L1. The final M3 of dimensions NxL
* is eventually computed, for class K, using the given posterior probabilities.
* A row of the final matrix M3 is the weighted average of each of the S
* possibles slices of the corresponding row in M2, represented as a probability
* matrix. The weights used are the probabilities with which this row was assigned
* to class K, for each of the S shift states, in each flip state.
*
* The original matrix M1 that was partitionned with shifting freedom S is
* generated using the BED and fasta files that were originally used to
* create it.
* The posterior probabilities should be a 4D matrix in binary format, with
* dimensions :
* 1) number of sequences
* 2) number of classes
* 3) number of shift states
* 4) number of flip states
* The results is returned as a 3D binary matrix of dimensions :
* 1) number of sequences
* 2) length of the sequences, as defined by the <from>/<to> range
* 3= 4 for A, C, G, T
*/
class ClassSequenceDataCreatorApplication : public ApplicationInterface
{
public:
ClassSequenceDataCreatorApplication() = delete ;
ClassSequenceDataCreatorApplication(
const ClassSequenceDataCreatorApplication& app) = delete ;
/*!
* \brief Constructs an object from the command line
* options.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
*/
ClassSequenceDataCreatorApplication(int argn, char** argv) ;
/*!
* \brief TODO
* \return an exit code EXIT_SUCCESS or EXIT_FAILURE
* to return to the OS.
*/
virtual int run() override ;
private:
/*!
* \brief Parses the program command line options and
* sets the object field accordingly.
* If the help option is detected, the "runnable"
* field is set to false and subsequent calls to
* run() will produce nothing.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
* \throw std::invalid_argument if an error is found
* in the program options.
*/
void parseOptions(int argn, char** argv) ;
/*!
* \brief the path to the bed file.
*/
std::string file_bed ;
/*!
* \brief the path to the fasta file.
*/
std::string file_fasta ;
/*!
* \brief the path to the posterior probability
* file (the partition).
*/
std::string file_prob ;
/*!
* \brief the path to the file in which the
* results will be written.
*/
std::string file_out ;
/*!
* \brief the coordinate of the most upstream
* position that was in the original matrix, in
* relative coordinate.
*/
int from ;
/*!
* \brief the coordinate of the most downstream
* position that was in the original matrix, in
* relative coordinate.
*/
int to ;
/*!
* \brief the class of interest (0-based).
*/
size_t class_k ;
/*!
* \brief a flag indicating whether the core of run() can be
* run or not.
*/
bool runnable ;
} ;
#endif // CLASSSEQUENCEDATACREATORAPPLICATION_HPP

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