mclblastline(1) 						  USER COMMANDS 						   mclblastline(1)

  NAME
      mclblastline - a pipeline for clustering from BLAST files.

  SYNOPSIS
      mclblastline file-name

      mclblastline [deblast options] [pipeline options] file-name

      NOTE
      mcl  has acquired the ability to proceed from label input as produced by mcxdeblast. This enables a very lightweight mechanism of generating
      clusterings from BLAST files.  You might want to use this mechanism, documented in the mcl manual.

      NOTE
      mclblastline used to require (given default parameters) the presence of the zoem macro processor to produce detailed  output.   This  is	no
      longer the case. By default mclblastline now creates a line-based tab-separated dump file.  Zoem will be invoked when the --fmt-fancy option
      is supplied.  In that case, zoem obviously has to be installed.

  DESCRIPTION
      mclblastline wraps around mclpipeline. It supplies the --parser=app and --parser-tag=str options, setting them  respectively  to	mcxdeblast
      and  blast.  This  tells	mclpipeline  to use mcxdeblast as the parse script in its pipeline.  The significance of the blast tag is that any
      mcxdeblast option can be passed through mclblastline and mclpipeline by inserting this tag into the option.  For example, mcxdeblast accepts
      the  --score=x option.  When using mclblastline, you specify it as --blast-score=x.  There are two exceptions to this rule, namely the --xi-
      dat=str and --xo-dat=str options. Refer to the mclpipeline manual for more information.

      Additionally, all mclpipeline options are acceptable to mcxdeblast as well. The --whatif is useful for getting a feel for the pipeline.  The
      --mcl-I=f  inflation  option  and --mcl-scheme=i scheme index options are your basic means for respectively manipulating cluster granularity
      and allocating resources. Read the mcl manual entries for a description of the corresponding -I and -scheme mcl options.

      The best advice is to glance over the mcxdeblast and mclpipeline options in order to get a feeling for which of those may come in handy  for
      you. Then start experimenting. Use the --whatif option, it will tell you what would happen without actually doing it.

  OPTIONS
      All mcxdeblast and mclpipeline options.  mcxdeblast options must be passed using the mechanism described above.

  EXAMPLES
	 mclblastline --blast-score=b
	    --blast-sort=a --blast-bcut=5 --mcl-I=2.5 myblastfile

      This  will use bit scores, sort cluster indices such that the corresponding labels are ordered alphabetically, ignore bit scores not exceed-
      ing 5, and use inflation value 2.5. In this case, the output clustering will be in the file named  myblastfile.I25s2  (I25  identifying  the
      inflation value and s2 identifying the resource scheme) and the formatted output will be in the file myblastfile.I25s2.fmt.

	 mclblastline --prepare-mcl myblastfile
	 mclblastline --start-mcl --mcl-I=1.2 myblastfile
	 mclblastline --start-mcl --mcl-I=1.6 myblastfile
	 mclblastline --start-mcl --mcl-I=2.0 myblastfile
	 mclblastline --start-mcl --mcl-I=2.4 myblastfile
	 mclblastline --start-mcl --mcl-I=2.8 myblastfile
	 etc ..

      The  first  run  prepares  an input matrix to be read by mcl.  In this case its file will be named myblastfile.sym.  The subsequent runs use
      this matrix.  CAVEAT there are some options that you need to repeat when executing such a resumed  run.  They  are  clearly  marked  in  the
      mclpipeline manual - namely those options that affect names of (intermediate) files. Most importantly, this concerns the mclpipeline options
      that have prefix --xo or --xi. For example,

	 mclblastline --prepare-mcl --blast-score=b --xo-dat=b myblastfile
	 mclblastline --start-mcl --xo-dat=b --mcl-I=1.2 myblastfile
	 mclblastline --start-mcl --xo-dat=b --mcl-I=1.6 myblastfile
	 mclblastline --start-mcl --xo-dat=b --mcl-I=2.0 myblastfile
	 mclblastline --start-mcl --xo-dat=b --mcl-I=2.4 myblastfile
	 mclblastline --start-mcl --xo-dat=b --mcl-I=2.8 myblastfile
	 etc ..

      In this case, the matrix file will be named myblastfile.b.sym, and the --xo-dat options must be repeated in all runs so  that  the  pipeline
      reconstructs the correct file name(s).

  AUTHOR
      Stijn van Dongen

  SEE ALSO
      mcxdeblast, mclpipeline, mcxassemble.

  mclblastline 12-068						      8 Mar 2012						     mclblastline(1)