


  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)] [-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))] [-dig-
      its  <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)]  [--no-loops  (omit   loops)]
      [--force-loops  (force  loops)]  [--dump-pairs  (emit  pairs  per line)]
      [--dump-lines (emit rows per line)] [--dump-rlines (omit leading identi-
      fier)]  [--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)] [--dump-table (dump
      table format)]  [--dump-lead-off  (do  not  dump  leading  identifiers)]
      [-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 ((decon-
      catenate) 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 col-
      umn 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



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  mcxdump(1)                USER COMMANDS                mcxdump(1)


        --dump-rlines and --no-values.

      --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.

      --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-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 out-
        put as a single pair of column-identifier and row-identifier per line,



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  mcxdump(1)                USER COMMANDS                mcxdump(1)


        optionally  followed  by  the value of the corresponding matrix entry.
        All fields are separated by the field separator.

        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 speci-
        fied.   --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 --trans-
        pose --skeleton.

      -imx-cat <fname> (concatenation matrix file)



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      -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 mul-
        tiple 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 pro-
        ject 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 concatena-
        tion 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.





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  mcxdump(1)                USER COMMANDS                mcxdump(1)


  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.






















































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