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/***************************************************************************
* PHAST: PHylogenetic Analysis with Space/Time models
* Copyright (c) 2002-2005 University of California, 2006-2010 Cornell
* University. All rights reserved.
*
* This source code is distributed under a BSD-style license. See the
* file LICENSE.txt for details.
***************************************************************************/
/** @file tfbs.h
Transcription Factor binding sites functions.
Identitifes Transcription Factor Binding Sites (TFBS) given a set of sequences
that might contain TFBS and a set of Transcription Factors to search for.
Transcription Factors are specified as MEME files containing Position Weight Matrices (PWMs)
@ingroup motif
*/
#ifndef TFBS_H
#define TFBS_H
#include <ms.h>
/** Convert a double to a charstring
@param num Double to convert to charstring
@result Charstring containing double
*/
char *dtoa(double num);
/** Create a new MS object to hold sequences that are not nececssairly aligned
@param seqs 2D array, one entry per sequence containing the bases.
@param names 2D array, one entry per sequence containing name
@param nseqs number of sequences in this MS
@param alphabet characters thare are valid bases
@param rangeLow Lower bound of %GC content this bin will hold (between 0 and 1)
@param rangeHigh Upper bound of %GC content this bin will hold (between 0 and 1)
@result New GC bin to hold sequences
*/
MS *ms_new(char **seqs, char **names, int nseqs, const char *alphabet, double rangeLow, double rangeHigh);
/** Free a MS object
@param toFree the MS object to free
*/
void ms_free(MS *toFree);
/** Read a MEME text format file and extract Position Weight Matrix (PWM)
@param filename Full Path to MEME formated file containing at least one PWM
@result List of PWMs found in file
*/
List *pwm_read(const char *filename);
/** Read in non-aligned Multiple Sequences.
@param filename Full path to file of type FASTA
@param alphabet Characters allowed in sequences (normally 'ACGT')
@result List of MSA objects with one sequence per MSA.
*/
MS *ms_read(const char *filename, const char *alphabet);
/** Helper function for building Markov Matrix of order N
@param inputMS MS object containing sequences used to make Markov Model
@param norder Specifies order of the markov MATRIX to construct
@param pseudoCount Number of counts to add for each possible entry (smoothing parameter)
@param considerReverse If TRUE also take into account reverse complement frequencies
@result Markov Matrix of order 'norder'
*/
Matrix *mm_build_helper(MS *inputMS, int norder, int pseudoCount, int considerReverse);
/** Reverse complement a DNA PWM
@param m PWM to reverse complement
@result Reverse complement of m
*/
Matrix *mat_reverse_complement(Matrix *m);
/** Calculate Markov Models for all groups
@param inputMS Multiple Sequences object containing sequences used to make Markov Model
@param norderP Order of the Markov MODEL to construct
@param pseudoCount Number of counts to add for each possible entry (smoothing parameter)
@param considerReverse If TRUE also take into account reverse complement frequencies
@result Markov Model (List of Markov Matrices)
@note Each Markov Model contains norder Markov Matrices i.e. norder=3 matrices of norder 1, 2, 3
*/
List *mm_build(MS *inputMS, int norder, int pseudoCount, int considerReverse);
/** Identifies column of a PWM or Markov Matrix corrisponding to a single base.
@param base Single character i.e. 'A' or 'T'
@result Integer 0 to 3 specifying column that contains data for that base
*/
int basetocol(char base);
/** Lookup row of Markov Matrix corrisponding to bases i.e 'AT' == 3
@param norder Order of Markov Matrix represented
@param alph_size Alphabet size of data represented in Markov Matrix
@param Integer specifying row of Markov Matrix mapped to given bases
*/
int basesToRow(int *previousBases, int norder, int alph_size);
/** Prints MS to file in FASTA format.
@param F File pointer where to output FASTA file
@param ms MS object containing sequences & names to write out
*/
void ms_print(FILE *F, MS *ms);
void ms_print_fasta(FILE *F, MS *ms);
/** Prints MS to file in FASTA format. (wrapper for ms_print)
@param filename Full Path to where file should be written
@param ms MS object containing sequences & names to write out
*/
void ms_print_to_file(const char *filename, MS *ms);
/** Compute GC content of each sequence in an ms
@param ms MS object
@return A vector of the same length as the number of sequences in ms,
containing the GC fraction of each sequence.
*/
Vector *ms_gc_content(MS *ms);
/* Scores a markov model on a specific sequence.
@param seqData Sequence being scored
@param base Current base for testing
@param MarkovMatrices Markov Model source
@param conservative Whether to treat regions containing 'N' as possible binding sites
*/
double calcMMscore(char *seqData, int base, List *MarkovMatrices, int conservative);
/** Scores sequences for matches to motif represented as PWM.
@param seqName Name of the sequence being scored
@param seqData Sequence data (bases) of the sequence being scored
@param seqLen Length of the sequence being scored
@param seqIdxOff Index offset of the sequence being scored
@param seqAlphLen Length of the alphabet for the sequence being scored
@param MarkovMatrices Markov Model (list of Markov Matrices) of GC content group sequence belongs to
@param pwm Position Weight Matrix representing a Motif to scan for
@param reverseCmpPwm Reverse complemented version of pwm parameter
@param conservative If == 1 and encounters an 'N' base, the site gets a -Inf score
@param threshold Score threshold that any score must be above to be part of the returned feature set
@param strand Which strands to score and which results to return ("best", "both", "+", "-") more info in R docs
@result List of scores as a Feature Set
*/
GFF_Set *ms_score(char *seqName, char *seqData, int seqLen, int seqIdxOff, int seqAlphLen, List *MarkovMatrices, Matrix *pwm, Matrix *reverseCmpPWM, int conservative, double threshold, char *strand);
/** Simulate a sequence given a Markov Model
@param mm Markov Model containing probabilities used to generate sequence
@param norder Order of Markov Model mm
@param alph_size Alphabet size of data used to generate mm
@param length Length of sequence to generate
@result Char string containing generated sequence i.e. "ATAGCGC" for length 7
*/
char *ms_simulate(List *mm, int norder, int alph_size, int length);
#endif
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