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 sup-
      plying the --fmt-fancy option.  This can be useful if one wants to scrutinize a clustering in greater detail and navigate within	the  clus-
      tering. 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  pro-
      vided 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 represent-
      ing 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 mcx-
      assemble(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 mcxde-
      blast, 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 exten-
      sion 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 suf-
      fix 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 speci-
      fied 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 clus-
	ter  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 12-068						      8 Mar 2012						      mclpipeline(1)