mclpipeline(1)                  USER COMMANDS                   mclpipeline(1)



  NAME
      mclpipeline - a generic pipeline for generating and scrutinizing mcl
      clusterings.

      NOTE
      mcl has acquired the ability to manipulate label input directly. This
      enables a very lightweight mechanism of generating clusterings by
      teaming up mcl with a lightweight parser. You might want to use this
      mechanism.  Example invocations using the mcxdeblast BLAST parser are
      documented in the mcl manual.

  SYNOPSIS
      mclpipeline [options] <file-name>

      where <file-name> is either the name of the data input file, or its base
      name. In the latter case the --xi-dat option is required. In case
      mclpipeline is indeed used to control all stages from the data input
      file onwards, usage will often be like this:

         mclpipeline [prepare options] --prepare-mcl <file-name>
         mclpipeline [cluster options 1] --start-mcl <file-name>
         mclpipeline [cluster options 2] --start-mcl <file-name>
         .. etc

      mclpipeline can also be used to control shorter pipelines, i.e. in case
      the input matrix was already created or in case pre-assembled parts of
      the input matrix were already created. In this case, usage will often be
      like this:

         mclpipeline [cluster options 1] --start-mcl=<fname>
         mclpipeline [cluster options 2] --start-mcl=<fname>
      or
         mclpipeline [assembly options] --start-assemble=<fname> --prepare-mcl

      NOTE
      It is possible to make mclpipeline output a large arrary of performance
      measures related to nodes and clusters in hyperlinked output by
      supplying the --fmt-fancy option.  This can be useful if one wants to
      scrutinize a clustering in greater detail and navigate within the
      clustering. The output then includes listings of external nodes that are
      relevant/close to a given cluster, and vice versa, listings of external
      clusters that are relevant/close to a given node.

      Generating this more intricate output requires the presence of the zoem
      macro processor. Refer to the SEE ALSO section and the clmformat manual
      for more information on zoem. By default zoem is not required, and the
      return result is a file where each line contains a clustering consisting
      of tab-separated labels.

      If this program does not work as expected, please file a bug report with
      the developer and/or subscribe to mcl-devel as indicated on
      http://micans.org/mcl/. The problem will then be fixed.

      The full list of pipeline options is given below. Start simple, and if
      you need some behaviour, try to see if there is an option that fits your
      needs.  If you use a wrapper pipeline such as mclblastline(1), you can
      ignore the --parser and --parser-tag options as they are provided by the
      wrapper.

      mclpipeline --parser=application (data parser) --parser-tag=str (parse
      option transporter)

      [--whatif (do not execute)]
      [--start-assemble (skip parse stage)]
      [--start-mcl (skip earlier stages)]
      [--start-format (skip earlier stages)]
      [--prepare-mcl (do preparatory stages)]
      [--help (summary of options)]
      [--xi=suf (strip suf from input file)]
      [--xo-dat=suf (attach suf to parse output)]
      [--xo-ass=suf (attach suf to assembly output)]
      [--xi-mcl=suf (use with --start-mcl)]
      [--xo-mcl=suf (replace mcl output suffix)]
      [--xa-mcl=str (append to mcl output suffix)]
      [--xe-mcl=suf (append to mcl output)]
      [--xo-fmt=suf (attach suf to clmformat output)]
      [--ass-repeat=str (assembly repeat option)]
      [--ass-nomap (ignore map file)]
      [--ass-opt=val (assembly option transporter)]
      [--mcl-te=num (#expansion threads)]
      [--mcl-I=float (mcl inflation value)]
      [--mcl-i=float (mcl initial inflation value)]
      [--mcl-l=float (mcl initial loop length)]
      [--mcl-c=float (mcl center value)]
      [--mcl-pi=float (mcl pre-inflation value)]
      [--mcl-scheme=i (mcl scheme index)]
      [--mcl-o=fname (do not use)]
      [--mcl-opt=val (mcl option transporter)]
      [--fmt-lump-count=num (collect formatted output)]
      [--fmt-opt val (clmformat option transporter)]
      [--fmt-tab fname (use this tab file)]
      [--fmt-notab (ignore tab file)]
      <file-name>

  DESCRIPTION
      mclpipeline encapsulates a sequence of programs to be run on some input
      data in order to obtain clusterings and formatted output representing
      the clusterings, while maintaining unique file names and file name
      ensembles corresponding with differently parametrized runs.

      The script can behave in several ways. By default, the pipeline consists
      of the stages of parsing, assembly, clustering, and formatting.  The
      parsing stage is to be represented by some parser script obeying the
      interface rules described below. The assembly stage is done by
      mcxassemble(1), the clustering stage is done by mcl(1), and the
      formatting stage is done by clmformat(1).

      The script can also be put to simpler uses, e.g. letting the script take
      care of unique file names for differently parametrized mcl runs. In this
      case there is no need to specify either the parser or the data file, and
      subsequent invocations might look like this:


         mclpipeline --start-mcl=<fname> --mcl-I=1.6 --mcl-scheme=4
         mclpipeline --start-mcl=<fname> --mcl-I=2.0 --mcl-scheme=4
         mclpipeline --start-mcl=<fname> --mcl-I=2.4 --mcl-scheme=4
         .. etc

      It is easiest if for each parser a wrapper script is written
      encapsulating the parser and mclpipeline. A mechanism is provided
      through which mclpipeline can recognize options that are meant to be
      passed to the parser. An example of such a wrapper script is the BLAST
      pipeline mclblastline that basically calls mclpipeline with the
      parameters --parser=mcxdeblast --parser-tag=blast.  In this case the
      parser is mcxdeblast, and mclpipeline will pass any options of the forms
      --blast-foo and --blast-bar=zut to the parser (respectively as --foo and
      --bar=zut).

      For a given data set the stages of parsing and assembling will often not
      need to be repeated, especially if there is a well established way of
      creating a matrix from the input data. In this case, usage will look
      like


         mclpipeline [parse/assembly options] --prepare-mcl <file-name>
         mclpipeline [cluster options 1] --start-mcl <file-name>
         mclpipeline [cluster options 2] --start-mcl <file-name>
         mclpipeline [cluster options 3] --start-mcl <file-name>
         ...

      Note that mclpipeline will store the output of those runs in unique file
      names derived from the parametrizations.

      There are some options that affect the file names of intermediate
      results. In the above setup of repeated runs, if used in one run, they
      must be used in all runs, as mclpipeline uses them to compute the file
      names it needs.  For the setup above, these options are --xi=suf, --xo-
      dat=suf, and --xo-ass=suf.

      There are other ways of resuming the pipeline, and one must always take
      care that options starting with --xi-, --xo-, --xa, or --xe are repeated
      among preparatory and subsequent runs.  These tags respectively
      mnemonize extension in, extension out, extension append, and extension
      extra.

      Should one want to experiment with various ways of creating input
      matrices, then mclpipeline supplies options to create unique file names
      and file name ensembles corresponding with different setups and
      parametrizations. These are --xo-dat=suf for the parsing stage and --xo-
      ass=suf for the assembly stage. mclpipeline automatically generates
      unique file names for the cluster results, but it does not do so for the
      parse and assembly results.

      Parser interface requirements
      The parser should recognize its last argument as a file name or as the
      base name of a file.  It should produce the files base.raw, base.hdr,
      and preferably base.tab and base.map, where the base name base is
      determined as described below.

      mclpipeline will pass its last argument <file-name> to the parser.  The
      parser should recognize the --xi-dat=suf and --xo-dat=suf options. If
      the first is present, it should try to strip <file-name> of the suffix
      specified in the value and use the result as the initial part of the
      base name for the files it constructs. If stripping does not succeed, it
      must interpret <file-name> as the base name and append the suffix in
      order to construct the name of the file it will try to read.  If the
      --xo-dat=suf option is present, it must append the suffix specified in
      the value to the base part as described above.  The result is then the
      full base name to which the raw, hdr, and other suffixes will be
      appended.

      Parser interface examples

      <parser> --xi-dat=abc --xo-dat=xyz foo
       *  parser reads foo.abc, writes foo.xyz.raw, foo.xyz.hdr et cetera.
      <parser> --xi-dat=abc --xo-dat=xyz foo.abc
       *  idem
      <parser> --xo-dat=xyz foo.abc
       *  parser reads foo.abc, writes foo.abc.xyz.raw et cetera.
      <parser> --xi-dat=abc foo.abc
       *  parser reads foo.abc, writes foo.raw, foo.hdr et cetera.
      <parser> foo.abc
       *  parser reads foo.abc, writes foo.abc.raw, foo.abc.hdr et cetera.

      Output file names construction
      The files of primary interest are the mcl output file and the formatted
      output produced by clmformat.  The pipeline constructs a file name for
      the mcl output in which several parameters are encoded. The first part
      of the file name is either the base name for the assembly stage, or
      simply the name of the input file, depending on whether the option --xo-
      ass=suf was used or not.

      A suffix encoding key-value pairs is appended. By default it has the
      form I..s., e.g. I20s2. The latter examples denotes primary inflation
      value 2.0 and scheme 2.  The pipeline will automatically append several
      other mcl parameters if they are used. These correspond with the
      pipeline options --mcl-i=f, --mcl-l=i, --mcl-c=f, and --mcl-pi=f, which
      in turn correspond with the mcl options -i f, -l i, -c f, and -pi f.
      The order of appending is alphabetical with capitals preceding
      lowercase, so a full example is I25c30i35l2pi28s3.

  OPTIONS
      --whatif (do not execute)
        Shows only what would be done without executing it.  Hugely useful!

      --start-assemble (skip parse stage)
        Skip the parse stage, assume the necessary files have been created in
        a previous run.

      --prepare-mcl (do preparatory stages)
        Do the parsing and assembly stage, then quit. Useful if you want to do
        multiple cluster runs for a given graph - use --start-mcl

      --start-mcl (skip earlier stages)
        Immediately start the mcl stage.  Assume the necessary files have been
        created in a previous run.

        NOTE
        This option can be used as --start-mcl=fname.  In this case, no final
        file name argument need be given, and mcl will use fname as the file
        name for its input.

        The difference with --start-mcl is that the latter will assume it is
        picking up the results of a previous run.  The names of those results
        might include suffixes corresponding with the parse and assembly stage
        (cf. --xo-dat and --xo-ass).  If you are not clear on this (and you
        should not be), exercise the --whatif option to be sure.

      --start-format (skip earlier stages)
        Immediately start the format stage.  Assume the necessary files have
        been created in a previous run.

      --help (summary of options)
        Print a terse summary of options.

      --xi suf (strip suffix from data file)
        In normal usage, this will strip the specified suffix from the data
        file to obtain the base name for further output.  When used with
        --start-mcl=fname the same behaviour is applied to the mcl input file
        name specified in fname.

      --xo-dat suf (attach suf to parse output)
        This suffix will be attached to the base name of the parse output.  It
        can be used to distinguish between different parse parametrizations if
        this is applicable.

      --xo-ass suf (attach suf to assembly output)
        This suffix will be attached to the base name of the assembly output.
        It can be used to distinguish between different assembly
        parametrizations if this is applicable.

      --xo-mcl suf (replace mcl output suffix)
        This suffix will be used instead of the suffix by default created by
        the pipeline.

      --xa-mcl str (append to mcl output suffix)
        This string will be appended to the suffix by default created by the
        pipeline.

      --xe-mcl suf (append to mcl output)
        This string will be appended as a single suffix to the output base
        name before mclpipeline appends its own suffix.

      --xo-fmt suf (attach suf to clmformat output)
        This suffix will be used instead of the suffix by default used by the
        formatting stage.

      --ass-repeat str (assembly repeat option)
        Corresponds with the mcxassemble -r mode option.  Refer to the
        mcxassemble(1) manual.

      --ass-opt val (assembly option transporter)
        Transfer -opt val to mcxassemble.

      --ass-nomap (ignore map file)
        Either no map file is present or it should be ignored.  For parsers
        that don't write map files.

      --mcl-I float (mcl inflation value)
        The (main) inflation value mcl should use.  This is the primary mcl
        option.

      --mcl-scheme i (mcl scheme index)
        The scheme index to use. This options is also important.  Refer to the
        mcl(1) manual.

      --mcl-te num (#expansion threads)
        The number of threads mcl should use.

      --mcl-i float (mcl initial inflation value)
        The initial inflation value mcl should use.  Only for fine-tuning or
        testing.

      --mcl-l float (mcl initial loop length)
        The length of the loop in which initial inflation is applied. By
        default zero.

      --mcl-c float (mcl center value)
        The center value. One may attempt to affect granularity by exercising
        this option, which controls the loop weights in the input matrix.
        Refer to the mcl(1) manual.

      --mcl-pi float (mcl pre-inflation value)
        Pre-inflation, another option which may possibly affect granularity by
        changing the input matrix. It makes the edge weight distribution
        either more or less homogeneous.  Refer to the mcl(1) manual.

      --mcl-o fname (do not use)
        Set the mcl output name.

      --mcl-opt val (mcl option transporter)
        Transfer -opt val to mcl.

      --fmt-dump-stats (add simple measures to dump file)
        This adds some simple performance measures to the dump file. For each
        cluster, five columns proceed the label listing. These are the cluster
        ID, the number of elements in the cluster, the projection (percentage
        of within-cluster edge weight relative to total outgoing edge weight),
        the efficiency of the cluster (which is the average of the efficiency
        of all its nodes), and the maximum efficiency (average of the max-
        efficiency of all the nodes). Look into the clmformat manual for more
        information on and references to the efficiency measures.

      --fmt-fancy (create detailed output (requires zoem))
        Creates extensive description of node/cluster and cluster/cluster
        relationships.

      --fmt-lump-count num (collect formatted output)
        Collect clusters in the same file until the total number of nodes has
        exceeded num (in the formatted output).  Only meaninful when --fmt-
        fancy is given.

      --fmt-tab (use this tab file)
        Explicitly specify the tab file to use.

      --fmt-notab (ignore tab file)
        Either no tab file is present or it should be ignored.  For parsers
        that don't write tab files.

      --fmt-opt val (clmformat option transporter)
        Transfer -opt val to clm format.

  AUTHOR
      Stijn van Dongen

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

      With default settings, mclpipeline depends on the presence of zoem. It
      can be obtained from http://micans.org/zoem/ .



  mclpipeline 14-137                16 May 2014                   mclpipeline(1)
