MatrixREDUCE [options] -sequence=file_name -expression=file_name

  Required parameters:
    -sequence=file_name    --- name of a file containing IDs and sequence in FASTA format
    -expression=file_name  --- the expression data file in tab-delimited format, or a file
                               containing a list of such expression data files

  Optional parameters:
    [-output=dir_name]     --- path to the output directory (./, i.e., current directory)
    [-model=string]        --- path to the directory containing matrices to be added to
                                   the model before starting ("", i.e., no models)
    [-filtered=file_name]  --- file name containing a list of matrices to be filtered
    [-corrected=sequence]  --- sequence(s) to be filtered out: single sequence can be in
                                   included in either "" or '', or plain text when no
                                   such file exists, in which case, the sequences are
                                   read in from the file. The sequence can be any
                                   combination of IUPAC characters ACGTUWRKYSMBHDVN
    [-univariate]          --- switch to treat each matrix/motif separately from above
    [-mseq=sequence]       --- use IUPAC sequence as seed for optimization
    [-mmtx=file_name]      --- optimize the initial matrix contained in file_name
    [-damid]               --- a shortcut for -filter=\"gatc\"
#    [-keep_original]       --- a switch to keep original residuals etc.
    [-p_value=float]       --- p-value threshold to stop looking for new motifs (0.001)
    [-dyad_length=integer] --- the length of each oligo in the dyad (3)
    [-min_gap=integer]     --- minimum gap length between the two oligos in the dyad (0)
    [-max_gap=integer]     --- maximum gap length between the two oligos in the dyad (10)
    [-flank=integer]       --- # of nucleotides to either side of the dyad core (3)
#    [-min_counts=integer]  --- minimum # of motif counts to be included in regression (5)
    [-max_motif=integer]   --- maximum # of motifs to search (20)
#    [-max_iter=integer]    --- maximum # of iterations in matrix optimization (inf.)
#    [-num_print=integer]   --- # of iterations to print optimized function value (50)
    [-single_strand]       --- switch for scoring only forward strand
#    [-simplex]             --- switch for matrix optimization with downhill simplex
    [-motif=[n1|n1-n2|file] --- scan motif from length n1 to n2 (1..15) or from a file
                                If a file is given, IUPAC wild cards are allowed and
                                no length limit. (1-7, corresponding to d7 in REDUCE).
    [-runlog=[stderr|stdout|file]
                           --- direct running diagnostics message to stderr, stdout or a
                               file in the *output* directory (stderr)
    [-no_optimization]     --- without matrix optimization
    [-help]                --- print out this help message

    NB: o the parameters must follow the -name=value format, except for the
          four switches -single_strand, -simplex, -no_optimization and -help.
        o you may use unambiguous abbreviations for the option names
            e.g., -se=seq_file; -b=1 etc.
        o value in () are the default values, e.g., p_value is default to 0.001

    Run script "MatrixREDUCE_setup" for installation and setting up instructions

  Usage:
    Suppose your are at $MATRIXREDUCE/examples, run "mkdir my_test" to set up my_test as
    your output directory:
      MatrixREDUCE -e=../data/Spellman1998Alpha -se=../sequences/Y5_600_Bst.fa -o=my_test

      MatrixREDUCE -e=../data/Spellman1998Alpha -se=../sequences/Y5_600_Bst.fa \
                   -max_g=0 -flank=0 -single -o=my_test -ru=run_log

      MatrixREDUCE -e=../data/Spellman1998Alpha -se=../sequences/Y5_600_Bst.fa -o=my_test \
                   -motif=1-7 -no_opt
                   # this has the same functionality as the original REDUCE