The mcxdump manual
Keywords: manual

4 Nov 2009 mcxdump 1.008, 09-308

1.
NAME
2.
SYNOPSIS
3.
DESCRIPTION
4.
OPTIONS
5.
AUTHOR
6.
SEE ALSO

## 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))] [-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)] [--no-loops (omit loops)] [--force-loops (force loops)] [--dump-pairs (emit pairs per line)] [--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)] [--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 ((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). 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.

--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 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.

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, mcl, mclfaq, and mclfamily for an overview of all the documentation and the utilities in the mcl family.