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  std-
      out))] [-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 for-
      mat)] [-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 sepa-
      rator. 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.

      --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 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)
      -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  effec-
	tively	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 12-068						      8 Mar 2012							  mcxdump(1)