mclindex(7) MISCELLANEOUS mclindex(7)
NAME
mclindex - a list of the utilities and modules present in the MCL distribution.
For more information, consult mclfamily(7).
Generic stuff
mcl(1)
the mcl manual page
mclfaq(7)
the mcl FAQ
mcxio(5)
the mcl matrix format specification
mclpipeline(1)
generic pipeline (parsing/matrix creation/clustering/display)
mcx(1)
interface to basic matrix operations
mcxassemble(1)
prepare input matrix from cooccurrence scores
mcxdump(1)
dump matrices, optionally map indices to labels
mcxarray(1)
transform array data to MCL matrices
mcxconvert(1)
convert between ascii/binary storage types
Dealing with clustering results
clmformat(1)
display clusterings in browsable format
clmdist(1)
compute distances between clusterings
clminfo(1)
performance measures for clusterings
clmmeet(1)
compute intersection of clusterings
clmmate(1)
compute best matches between two clusterings
clmimac(1)
Interpret Matrices (c.q. MCL iterands) As Clusterings
clmresidue(1)
extend subgraph clusterings onto encompassing graph
clmorder(1)
reorder indices to represent blocks from different clusterings
clmclose(1)
fetch connected components from graphs or subgraphs
Dealing with matrices
mcxio(5)
the mcl matrix format specification
mcx(1)
interface to basic matrix operations
mcxsubs(1)
extract submatrices by specifiying sets of nodes and clusters
mcxmap(1)
remap matrix indices / relabel graph nodes
mcxassemble(1)
prepare input matrix from cooccurrence scores
Application specific parsers and wrappers
BLAST package - Documentation only available if installed with --enable-blast
__________________
mclblastline(1)
pipeline for clustering from blast files
mcxdeblast(1)
prepare input from blast files
mclindex 12-068 8 Mar 2012 mclindex(7)
Check Out this Related Man Page
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)