mcxdump(1)                      USER COMMANDS                       mcxdump(1)



  NAME
      mcxdump - dump matrices, optionally map indices to labels

  SYNOPSIS
      mcxdump [-imx <fname> (matrix file)] [-icl <fname> (cluster file to be
      dumped line-wise)] [-tf <spec> (apply unary transformations to input
      matrix)] [-imx-cat <fname> (concatenation matrix file)] [-imx-tree
      <fname> (concatenation cone file)] [--skeleton (read empty matrix,
      honour domains)] [-o <fname> (output file name ('-' for stdout))]
      [-digits <num> (output precision)] [-tab <fname> (row/column tab (label)
      file)] [-tabc <fname> (column tab file)] [-tabr <fname> (row tab file)]
      [--lazy-tab (allow tab/domain mismatch)] [--transpose (work with the
      transpose)] [--no-values (omit values)] [--omit-empty (omit empty
      columns)] [--no-loops (omit loops)] [--force-loops (force loops)]
      [--dump-pairs (emit pairs per line)] [--dump-table (dump table format)]
      [-dump-sif <tag> (dump sif format)] [-dump-sifx <tag> (dump extended sif
      format with weights)] [--dump-lines (emit rows per line)] [--dump-rlines
      (omit leading identifier)] [--dump-vlines (add leading identifier
      values)] [--dump-lead-off (omit leading identifier)] [--dump-lower (dump
      lower part excluding diagonal)] [--dump-loweri (dump lower part
      including diagonal)] [--dump-upper (dump upper part excluding diagonal)]
      [--dump-upperi (dump upper part including diagonal)] [--write-tabc (dump
      tab file on column domain)] [--write-tabr (dump tab file on row domain)]
      [--dump-domc (dump column domain)] [--dump-domr (dump row domain)]
      [-table-nfields <num> (output first <num> fields)] [-table-nlines <num>
      (output first <num> lines)] [--newick (output newick format)] [-newick
      [NBI]+ (exclude Number|Branch-length|Indent)] [--write-matrix
      ((deconcatenate) write matrices)] [-split-stem <str> ((deconcatenate)
      matrices file name stem)] [-cat-max <num> ((deconcatenate) write first
      <num> matrices)] [-sep-value <str> (node/value separator)] [-sep-field
      <str> (field separator)] [-sep-lead <str> (lead separator)] [-sep-cat
      <str> (concatenation separator)] [-prefixc <str> (prefix column indices
      with <str>)] [-sort size-{ascending,descending} (vector sort mode)] [-h
      (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version
      (print version, exit)]

  DESCRIPTION
      mcxdump reads a data file satisfying the mcl input format (refer to
      mcxio(5)). It outputs a line-based format. The --dump-pairs option
      yields a single matrix entry per line, identified by the respective
      column and row identifiers (either index or label) separated by the
      field separator.  The --dump-lines and --dump-rlines result in the
      joining of all row entries on a single line, separated by the field
      separator. For both formats, the matrix value corresponding with a
      particular entry is by default output as well.

      mcxdump can also act on files that contain concatenated matrices. Refer
      to the group of options headed by -imx-cat fname.

  OPTIONS
      -imx <fname> (matrix file)
        Input matrix.

      -icl <fname> (cluster file)
        This specifies the input matrix, and sets up a cluster-wise line-based
        label dump.  This option is fully equivalent to the combination of
        --dump-rlines and --no-values.

      -tf <spec> (apply unary transformations to input matrix)
        Applies the specified transformation to the matrix before it is
        output.  Refer to mcxio(5) for a description of the transformation
        syntax.

      --transpose (work with the transpose)
        Work with the tranpsose of the input matrix.

      --skeleton (read empty matrix, honour domains)
        No entries are read, only domains.

      -o <fname> (output file name)
        Output stream. Use - for STDOUT.

      -digits <num> (output precision)
        Specify the precision to use in native interchange format.

      -tab <fname> (row/column tab (label) file)
        Substitute column indices and row indices by labels from the tab file.
        Since the same tab file is used for both, this implies that the matrix
        domains are identical.

      -tabc <fname> (column tab file)
        Substitute column indices by labels from the tab file.

      -tabr <fname> (row tab file)
        Substitute row indices by labels from the tab file.

      --lazy-tab (allow tab/domain mismatch)
        If used, the tab file domain(s) do not necessarily need to match the
        corresponding domain in the input matrix. Entries missing in the tab
        files will be replaced by a question mark.

      --no-values (omit values)
        Do not emit values.

      --omit-empty (omit empty columns)
        Do not output line data (with --dump-table or --dump-lines or related
        options) for those columns that are empty.

      --no-loops (omit loops)
        Do not output entries for which the row index equals the column index,
        if present.  Applies only to matrices for which column and row domains
        are equal.

      --force-loops (force loops)
        For each column, force output of a row entry that matches the column
        index.  Applies only to matrices for which column and row domains are
        equal.

      --dump-pairs (emit pairs per line)
      -dump-sif <tag> (dump sif format)
      -dump-sifx <tag> (dump extended sif format with weights)
      --dump-lines (emit rows per line)
      --dump-rlines (omit leading column node)
      --dump-vlines (add leading column values)
      --dump-lead-off (do not dump leading identifiers)
      --dump-lower (dump lower part excluding diagonal)
      --dump-loweri (dump lower part including diagonal)
      --dump-upper (dump upper part excluding diagonal)
      --dump-upperi (dump upper part including diagonal)
        --dump-pairs is the default mode of output. Each matrix entry is
        output as a single pair of column-identifier and row-identifier per
        line, optionally followed by the value of the corresponding matrix
        entry.  All fields are separated by the field separator.

        Use -dump-sif <tag> to dump SIF format.  The argument <tag> will be
        used as the edge type (the second column in SIF format). The option
        -dump-sifx <tag> is similar except that an extended format is produced
        where the label is followed by the colon character and the edge
        weight.

        With --dump-lines, each matrix column is output on a single line, with
        row identifiers separated by the field separator and values attached
        to the row identifier by the node/value separator.  In this format,
        the column identifier is output as the leading field.

        --dump-rlines is as --dump-lines, except that the column identifier is
        not output.  Use --dump-lead-off to preclude the output of the leading
        identifiers (for line-based outputs).

        --dump-vlines is as --dump-lines. The leading identifiers are followed
        by a value associated with the entire column. This can be used to dump
        the output given by clm vol. The value provided is a measure for the
        stability of the cluster that follows.

        The options pertaining to lower and upper dumps currently only work
        with --dump-pairs. They act to only output the specified part of the
        matrix.

      --dump-table (dump table format)
      -table-nfields (field limit)
      -table-nlines (line/row limit)
        Output table format. In table format no indices are printed by default
        and all values are printed including zeroes. The options -table-
        nfields and -table-nlines can be used to limit the number of fields
        and lines to be printed. Note that fields correspond to MCL matrix
        rows and that lines correspond to MCL matrix columns, as MCL calls its
        primary indices column indices.  Use --dump-lead-off to preclude the
        output of the leading identifiers (for line-based outputs).

      --newick (output newick format)
      -newick [NBI]+ (newick, exclude Number|Branch-length|Indent)
        Output a hierarchical clustering specified by -imx-tree in Newick tree
        format.

      --write-tabc (dump tab file on column domain)
      --write-tabr (dump tab file on row domain)
      --dump-domc (dump column domain)
      --dump-domr (dump row domain)
        These options work in conjunction with the -ixm fname option.  Only
        the domains from the input matrix are read as if --skeleton was
        specified.  --write-tabc assumes the input tab file envelopes the
        matrix column domain, and it outputs a new tab file restricted to that
        domain.  --write-tabr acts analogously for the row domain.  --dump-
        domc and --dump-domr respectively dump the column or row domain as a
        regular dump, outputting labels in case a tab file is specified.

        These options are implemented as ensembles of other options.  For
        example, --dump-domr -imx fname corresponds with --dump-lines
        --transpose --skeleton.

      -imx-cat <fname> (concatenation matrix file)
      -imx-tree <fname> (concatenation cone file)
      --write-matrix ((deconcatenate) write matrices)
      -split-stem <str> ((deconcatenate) matrices file name stem)
      -cat-max <num> ((deconcatenate) write first <num> matrices)
        -imx-cat is like -imx except that the input is assumed to contain
        multiple concatenated matrices.  The matrices are dumped separated by
        the cat separator (cf. -sep-cat).  Alternatively, the matrices can be
        written to different files using the -split-stem option.  In this case
        it is possible to output each matrix in native format rather than as a
        dump by specifying --write-matrix.  This makes mcxdump effectively act
        as a deconcatenator.  In all cases (respectively dumping and writing
        matrices to either the same stream or multiple files) the number of
        matrices to be dumped can be limited with -cat-max.

        -imx-tree is like -imx-cat except that the input is assumed to be in
        cone format (the format output by mclcm).  This format encodes a tree
        as a concatenation of matrices with nested domains. mcxdump will
        project all levels of this tree so that all row domains are the same
        as the bottom row domain.  This implies that a set of nested
        clusterings (on different node sets, as the set of clusters of a given
        level is the node set of the next level) is transformed into a set of
        flattened clusterings, all on the same node set.  If you do not want
        this to happen, simply use -imx-cat.

      -sep-value <str> (node/value separator)
        Set the node/value separator for line based row ensemble output.

      -sep-field <str> (field separator)
        Set the field separator for different row indices in a given column.

      -sep-lead <str> (lead separator)
        Set the lead separator. In the --dump-lines format it separates the
        leading column index from the following ensembl of row indices. It can
        be useful to make this different from the field separator. One can for
        example grep for columns that have more than one entry in a matrix
        mapping nodes to clusters. This will find nodes in overlap.

      -sep-cat <str> (concatenation separator)
        Set the separator that is used between matrix dumps when a
        concatenation of matrices is dumped.

      -prefixc <str> (prefix column indices with <str>)
        This can be useful when external row names cannot be numbers and when
        a label dictionary is not available or not appropriate.

      -sort size-{ascending,descending} (concatenation separator)
        Reorder the matrix columns prior to dumping, based on the number of
        nonzero entries in each column.  Do not use this in conjunction with a
        tab file for the column domain.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mcxload(1), mcl(1), mclfaq(7), and mclfamily(7) for an overview of all
      the documentation and the utilities in the mcl family.



  mcxdump 14-137                    16 May 2014                       mcxdump(1)
