mcxassemble(1)                  USER COMMANDS                   mcxassemble(1)



  NAME
      mcxassemble - transform raw cooccurrence data to mcl matrix format.

  SYNOPSIS
      mcxassemble -b base (base name) [-o fname (write to file fname)]
      [--write-binary (write output in binary format)] [--map (apply
      base.map)] [-raw-tf (apply transform spec to input)] [-rv MODE (repeated
      vectors)] [-re MODE (repeated entries)] [-ri MODE (adding mirror image)]
      [-r MODE (repeated entries/vectors/images)] [-prm-tf (apply transform
      spec to primary matrix)] [-sym-tf (apply transform spec to symmetrified
      matrix)] [-q (quiet mode)]

      The options above embody the default setup when using mcxassemble.
      There are many more options which mostly provide subtly different ways
      of doing input/output, set warning levels, or regulate how repeated
      entries and vectors should be treated.  The full list of options is
      shown below.  Read DESCRIPTION for learning about mcxassemble
      input/output and the functionality it provides.

      NOTE
      As of release 05-314 mcl(1) is able to cluster label-type input on the
      fly. In most cases, this will be sufficient. Alternatively, mcxload(1)
      can be used to map label-type input onto mcl matrices. Consequently,
      there are likely fewer scenarios nowadays where mcxassemble is the best
      solution. Consider first whether mcl in label mode or mcxload can do the
      job as well.

      mcxassemble [-b base (base name)] [-hdr fname (read header file)] [-raw
      fname (read raw file)] [--map (apply base.map)] [--cmap (apply
      base.cmap)] [--rmap (apply base.rmap)] [-map fname (apply fname)] [-rmap
      fname (apply fname)] [-cmap fname (apply fname)] [-tag tag (apply
      base.tag)] [-rtag tag (apply base.tag)] [-ctag tag (apply base.tag)]
      [-skw fname (write skew matrix)] [-prm fname (write primary result
      matrix)] [--skw (write base.skw)] [--prm (write base.prm)] [-xo suf
      (write base.suf)] [-o fname (write to file fname)] [-n (do not write
      default symmetrized result)] [-i (read from single data file)] [-digits
      int (digits width)] [-s (check for symmetry)] [-raw-tf (apply transform
      spec to input)] [-rv <mode> (action for repeated vectors)] [-re <mode>
      (action for repeated entries)] [-ri <mode> (adding mirror image)] [-r
      <mode> (same for entries and vectors)] [-prm-tf (apply transform spec to
      primary matrix)] [-sym-tf (apply transform spec to symmetrified matrix)]
      [--quiet-re (quiet for repeated entries)] [--quiet-rv (quiet for
      repeated vectors)] [-q (the two above combined)] [-h (print synopsis,
      exit)] [--apropos (print synopsis, exit)] [--version (print version,
      exit)]

  DESCRIPTION
      mcxassemble enables easy matrix creation from an intermediate raw matrix
      format that can easily be constructed from a one-pass-parse of
      cooccurrence data. The basic setup is as follows.

      o Parse cooccurrence data from some external format.
      o Transform cooccurrence data to raw mcl data as you parse.
      o When done, write out required header and domain information to a
        separate file. The domain information can be built during the parsing
        stage.
      o Use mcxassemble to construct a valid matrix from the raw data and the
        header information.
      o Nodes can optionally be relabeled by writing a separate map file to be
        read by mcxassemble, which takes the form of a very thin matrix file.

      The easiest thing to do is to group all input/output files under the
      same base name, say base. A standard way of proceeding, which will lead
      to a concise mcxassemble command line, is by creating the input files
      base.raw and base.hdr, and optionally the file base.map. The default
      behaviour of mcxassemble is then to create base.sym as the resulting
      matrix file, containing the symmetrized matrix constructed from the raw
      input.

      Example
      Suppose blastresult is a file containing blast results.  The following
      two commands construct an mcl matrix file from the file.

         mcxdeblast --score=e --sort=a blastresult
         mcxassemble -b blastresult -r max --map

      mcxdeblast will generate the files blastresult.hdr, blastresult.raw, and
      blastresult.map.  The --sort=a option will create a map file
      corresponding with alphabetic ordering. These files are processed by
      mcxassemble and it will generate the file blastresult.sym. The -r option
      tells mcxassemble that repeated entries should be maxed; each time the
      largest entry seen thus far will be taken.

      Header file
      This file contains a header as usually found in generic mcl matrix
      files, i.e. the required header part, and optionally the domain part(s)
      if not all domains are canonical. Refer to mcxio(5) for more
      information.  The domain information in the header file will be used to
      pre-construct a skeleton matrix and to validate the entries in the raw
      data file as they fill the skeleton matrix.

      Raw input format
      The file from which raw input is read should have the raw format as
      described in mcxio(5). Simply put; no header specification, no domain
      specification, and no matrix introduction syntax is used. The file just
      contains a listing of vectors. An example fragment is the following:

      2  4:0.34 1:2.8838 4:2.328 1:4.238 1:12 $
      1  2:7.8 $
      2  1:0.01 4:20.3 3:2 $

      The listing of vectors need not be sorted, and neither does a vector
      itself need to be sorted - the mcl generic matrix format is actually not
      different in this respect.  Furthermore, duplicate entries and duplicate
      vectors are allowed.  This is in fact again allowed in the generic
      format, except that where applications expect generic format warnings
      will be issued and duplicate entries will be disregarded. mcxassemble
      allows customizable behaviour dictating how to merge repeated entries.
      Refer to the -re, -rv, -r options below.

      The vectors read by mcxassemble do have to match the domains specified
      in the header file. The leading index that specifies the column index
      has to be present in the column domain; all subsequent indices that
      specify column entries have to be present in the row domain.

      If one concatenates the contents of the header file and the data file,
      the result is almost but not quite a file containing a matrix in
      syntactically correct mcl generic matrix format. The parts missing are
      the (mclmatrix introduction token, (followed by) the begin token, and
      the closing ) token.

      Map file
      This file must contain a map matrix, which is a matrix with the
      following properties:

      o The column domain and row domain are of the same cardinality.
      o Each column has exactly one entry.
      o Each row domain index occurs in exactly one column.

      Such a matrix is used to relabel the nodes as found in the raw data. A
      situation that might occur when parsing some external format (and
      producing raw matrix format), is that ID's (indices) are handed out on
      the fly during the parse. Afterwards, one may want to relabel the IDs
      such that they correspond with an alphabetic listing of the quantity
      that is represented by the node domain, or by some other sort criterion.
      A map file is then typically generated by the parser, as that is the
      utility in charge of the IDs. A small example of a map file for a graph
      containing five nodes is the following:

      (mclheader
      mcltype matrix
      dimensions 5x5
      )
      (mclmatrix
      begin
      0  4  $  #  mno
      1  2  $  #  ghi
      2  1  $  #  def
      3  3  $  #  jkl
      4  0  $  #  abc
      )

      This corresponds to a relabeling such that the associated strings will
      be ordered alphabetically. Note that comments can be used to link string
      identifiers with indices. This map file says e.g. that the string
      identifier "mno" is represented by index 0 in the raw data, and by index
      4 in the matrix output by mcxassemble.

  OPTIONS
      -b base (base name)
        Base name of files to be processed and output. Refer to DESCRIPTION
        above and the entries of other options below.
      -hdr fname (read header file)
      -raw fname (read raw file)
        Explicitly specify the header file and the data file (rather than
        constructing the file names from a base name and suffixes).
      --map (apply base.map)
      --cmap (apply base.cmap)
      --rmap (apply base.rmap)
      -map fname (apply fname)
      -rmap fname (apply fname)
      -cmap fname (apply fname)
      -tag tag (apply base.tag)
      -rtag tag (apply base.tag)
      -ctag tag (apply base.tag)
        Map options. --cmap combines with the -b option, and says that the map
        file in base.cmap (where base was specified with -b base) should be
        applied to the column domain only. --rmap works the same for the row
        domain, and --map can be used to apply the same map to both the column
        and row domains.

        -cmap and its siblings are used to explicitly specify the map file to
        be used, rather than combining a base name with a fixed suffix.  -tag
        and its siblings work in conjuction with the -b option, and require
        that a tag be specified from which to construct the map file (by
        appending it to the base name).
      -skw fname (write skew matrix)
      -prm fname (write primary result matrix)
      --prm (write base.prm)
      --skw (write base.skw)
      -n (do not write default symmetrized result)
        Options for writing matrices other than the default symmetrized
        result.  The primary result matrix is the matrix constructed from
        reading in the raw data and adding entries to the skeleton matrix as
        specified with the -r, -re, and -rv options.  This matrix can be
        written using one of the prm options.  Calling the primary matrix A,
        the skew matrix (as defined here) is the matrix A - A^T, i.e. A minus
        its transposed matrix.  It can be written using one of the skw
        options.

        If for some reason the symmetrized result is not needed, its output
        can be prevented using the -n option.
      -xo suf (write base.suf)
      -o fname (write to file fname)
      -i (read from single data file)
      -digits int (digits width)
      --write-binary (write output in binary format)
        The -xo option is used in conjunction with the -b option in order to
        change the suffix for the file in which the symmetrized result matrix
        is written. Use e.g. -xo mci to change the suffix from the default
        value sym to mci. Use -o to explicitly specify the filename in full.
        Use -digits to set the number of digits written for matrix entries
        (c.q. edge weights).

        The -i option is special. It causes mcxassemble to read both the
        header information and the raw data from the same file, where the
        syntax should be fully conforming to generic mcl matrix format.
      -s (check for symmetry)
        This will check whether the primary result matrix was symmetric.  It
        reports the number of failing (or skew) edges.
      -raw-tf <tf-spec> (apply transform spec to input)
      -prm-tf (apply transform spec to primary matrix)
      -sym-tf (apply transform spec to symmetrified matrix)
        The first applies its transformation spec to the values as found in
        the raw data. The second applies its transformation spec to the
        primary matrix. The third applies its transformation step to the
        symmetrified matrix.  Refer to mcxio(5) for documentation on the
        transformation spec syntax.
      -rv add|max|min|mul|left|right (action for repeated vectors)
      -re add|max|min|mul|left|right (action for repeated entries)
      -ri add|max|min|mul (adding mirror image)
      -r add|max|min|mul|left|right (same for entries and vectors)
        Merge options, dictating the behaviour when repeated entries are
        found. A distinction is made between entries that are repeated within
        the same column listing, and entries that are repeated between
        different column listings. An entry can be a repeat of both kinds
        simultaneously as well.  Additionally, the final result is by default
        symmetrized by combining with the mirror image (in matrix terminology,
        the transposed matrix). This symmetrization can be done in the same
        variety of ways.

        The re option, for repeats within the same column, is carried out
        first. It is applied after the column has its entries sorted, so the
        left and right options are not garantueed to follow the order found in
        the raw input. The rv option, for repeats over different columns, is
        carried out second.

        The option -ri min can assist in implementing a (top-list) best
        reciprocal hit criterion.

        Examples
        The column

        0 1:30 1:50 2:60 4:70 3:20 1:40 2:40 $

        is encountered in the input, listing entries for the vector labeled
        with index 0. If -re add or -r add is used, it will transform to the
        vector

        0 1:120 2:60  3:20 4:70 $

        If -re max or -r add is used instead, it will transform to the vector

        0 1:40 2:60 3:20 4:70 $

        Suppose add mode is used, and that later on another vector
        specification for the index 0 is found, leading to this transformed
        vector:

        0 1:60 2:80 4:40 $

        If -rv max was specified, this new vector is combined with the
        previous vector by taking the entry wise maximum:

        0 1:120 2:60 3:20 4:70 $      # first (transformed) vector
        0 1:60 2:80 4:40 $            # second vector

        0 1:120 2:80 3:20 4:70 $      # entry wise maximum

        Finally, suppose that somewhere one or more vector listings were
        specified for index 3, which eventually led to an entry 0:50.  The
        final symmetrization step will take the [0,3] entry of weight 20 and
        combine it with the [3,0] entry of weight 50. The resulting matrix
        will then have the [0,3] and the [3,0] entry both equal to either the
        maximum, the sum, or the product of the two quantities 50 and 20.
      --quiet-re (quiet for repeated entries)
      --quiet-rv (quiet for repeated vectors)
      -q (the two above combined)
        Warning options. Turn these on if you expect the raw data to be free
        of repeats.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mcxio(5), mcl(1), mcxload(1) and mclfamily(7) for an overview of all the
      documentation and the utilities in the mcl family.



  mcxassemble 1.008, 09-308         4 Nov 2009                    mcxassemble(1)
