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ChangeLog
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Thu, 8 Mar 2012
* mcl-12-068 released.
* Stopgap release to fix a segmentation fault. Triggered in abc mode
due to absent initialisation of new SIF functionality. Now fixed.
* mcxrand has a new -pa <V>/<m> mode. This uses the standard preferential attachment
model to randomly generate a scale-free network.
Wed, 7 Dec 2011
* mcl-11-335 released.
* For a long time now MCL has shipped with many siblings in what is intended to
be a coherent set of network analysis tools. What this collection has lacked is
some way of refering to it without creating confusion. This void is now filled,
and MCL-edge is the new name. The unadorned name MCL will not go away, and the
source code will still be shipped using a name of the format mcl-YY-DDD.
* mcxload can now read SIF (Simple Interaction File) format with -sif <filename>.
The second column (relationship type) is ignored. To ensure
that an undirected graph is read, use the --stream-mirror option.
* mcxdump can now output SIF format with -dump-sif <relationship-type>.
The argument indicates the, yes, relationship type.
* mcl can now read SIF format with the --sif option.
With this option, the input file is assumed to be in SIF format.
* mcl can now read etc format with the --etc option. This is similar to
SIF format except that the second column, identifying the relationship
type, is dropped.
* mcx query now can read label format in its default mode. Not yet
in other modes.
* 'efficiency' criterion added to mcx query -vary-threshold,
-vary-knn, et cetera.
* minor fix in clm enstrict; on some occassions it would not clean up
empty clusters left by the removal of overlap.
Fri, 20 Jul 2010
* mcl-10-201 released.
* The speed of the clustering program mcl was improved.
It now utilises vanilla matrix/vector multiplication where this is faster
than sparse matrix/vector multiplication. It chooses between an
O(k^2 + N) algorithm with very low hidden constant and an O(k^2) algorithm
with significantly higher hidden constant, using the algorithm with least
expected run-time. Here k is a constant that bounds the number of
resources allocated to a node in the graph.
* The speed optimization code acquired a more logical option for adjustment
(-sparse) with a sane default setting that should work satisfactorily
across a wide range of graphs.
* The memory management code for vectors and sets was improved to work
better under malloc implementations that do not cope well with high
memory churn and large shrinking realloc requests.
* mcx query acquired --edges, --edges-sorted, and -edges-hist options.
They respectively output an unsorted list, sorted list, and histogram of
edge weights. Despite 'edges' being part of the names of these option,
the output contains a weight for each arc. For undirected graphs each
edge will be represented twice.
* mcx query acquired --output-table option. With -vary-threshold or
--vary-correlation the output will be a tab-separated table with row
names and without key.
* Got rid of the version tag (i.e. 1.008). It never acquired any meaning.
* Documentation was fixed and upated.
Fri, 28 May 2010
* mcl-10-148 released.
* mcl has become faster. It chooses between different matrix/vector multiplication
algorithms depending on the sparsity level of the vector.
* mcx erdos now works for directed graph, requiring the option --is-directed.
* clm adjust has a new option --force-connected. If
the input clustering does not induce connected subgraphs a subclustering
is output that does have that property.
* mcx clcf has been parallelized and now accepts -t <num> option.
* All -knn and -ceil-nb command line options are gone. The functionality
is still available in a more general fashion as new modes to the -tf
transformation option. As an example, '-knn 40' is now specified as -tf
'#knn(40)'. This is more general since the k-NN transformation
can be one among a list of transformations, where the user is
free to choose and order.
* All -tf style options allow new modes:
#max() make a graph symmetric using max
#min() make a graph symmetric using min
#add() make a graph symmetric using add
#arcmax() reduce two arcs to one arc using max
$arcsub() compute G[->] - G[<-]
#arcmcl(<num>) cluster a directed graph with inflation <num>
#tug() perturb edge weights to break ties (uses neighbourhood information)
#shrug() perturb edge weights to break ties (randomly)
#mcl(<num>) cluster an undirected graph with inflation <num>
#knn(<num>) reduce graph using k-Nearest-Neighbour selection
#ceilnb(<num>) reduce graph using ceil-nb selection
#tp() replace graph/matrix by inverse relationship
#step(<num>) replace graph by <num>-step relation
#thread() set thread count for parallelizable transformations (e.g. #knn)
Modes that start with the octothorpe (#) operate on entire graphs/matrices.
Other modes, e.g. ceil(), lt(), add(), operate on edges.
* A bug in clm enstrict was removed.
* clm dist has a new mode --index, in which it outputs the Rand index,
the adjusted (Hubert Arabie) Rand index, and the Jaccard index.
* Esoteric options and logging code were removed from mcl, to improve
readability and maintainability of its source.
* mcx clcf, mcx diameter, and mcx ctty all output column headers.
mcx collect by default expects column headers.
mcx --paste concatenates rows from different tables, requiring that the
first column is identical.
* mcx query --node-attr outputs a table of network node attributes.
* mcx diameter, mcx ctty, mcx clcf, and mcxarray all accept the same parallelization
interface. Jobs can split over multiple threads as well as over
multiple machines. The latter is done by the concept of 'thread group'.
- Use -t to specify the number of threads.
mcxarray -t 4
will run with 4 threads.
- Use -J to specify the number of groups/machines to use,
use -j to specify the group index.
It is important that all jobs use the same -t value, as all jobs
assume all other jobs use the same number while figuring out which
tasks they should run. The collection of tasks will only be
consistent if the jobs work from the same number of threads and
the same number of groups.
In the future different jobs will be able to run different numbers of
threads by having multiple group IDs.
mcxarray:
machine 1: mcxarray -t 3 -J 4 -j 0 -o d0.cor
machine 2: mcxarray -t 3 -J 4 -j 1 -o d1.cor
machine 3: mcxarray -t 3 -J 4 -j 2 -o d2.cor
machine 4: mcxarray -t 3 -J 4 -j 3 -o d3.cor
mcx collect -o result.cor d0.cor d1.cor d2.cor d3.cor
This last command combines the partial results and writes
to the file called result.cor .
mcx diameter/ctty:
machine 1: mcx diameter -t 8 -J 4 -j 0 -o d0.diam
machine 2: mcx diameter -t 8 -J 4 -j 1 -o d1.diam
machine 3: mcx diameter -t 8 -J 4 -j 2 -o d2.diam
machine 4: mcx diameter -t 8 -J 4 -j 3 -o d3.diam
mcx collect --two-column -o result.diameter d0.diam d1.diam d2.diam d3.diam
- The previous -start and -end options to mcx ctty and mcx diameter
have been removed.
- By default mcx collect expects matrix arguments. The two-column output
generated by mcx diameter/ctty should be specified using the
mcx collect --two-column option.
* mcxarray has seen many changes and improvements.
- It can use multiple cores. It uses pthreads and accepts the option -t
<num> to specify that <num> threads/cores should be used.
- It only accepts tab characters as separators. Spaces
no longer work.
- Parse errors are pinpointed precisely within the input file.
- It can handle missing data. Missing data is introduced
either by 'NA' or 'NaN' or 'inf' values in the tabular data, or by an
empty column. When computing correlations, rows are only compared on
those positions where neither of them has missing data.
- It has a new option --zero-as-na. With this, zeroes are treated
as NA (not available/applicable), and during the calculation of
correlations vectors are only considered on positions where neither is
NA. This works for modes --pearson (default) and --spearman. This
mode has very specialized uses. One example is when the input is
constructed using mcxload and read in mcxarray with -imx. In this
case missing data cannot be specified as 'NA' or empty columns, so
other means are necessary.
* clm order should write an output tree in its default mode,
but it did not. Now fixed.
* mcxdump --dump-table would err for graphs with sparse domains. Now fixed.
* mcx query has mode -vary-knn, to analyse different levels of
knn-selection (k-Nearest-Neighbours).
* Code clean-up: the taurus library for integer set manipulation
was finally discarded.
* A bug in the mcxi max and min operators was fixed, and both max and min
can now operate on matrices.
Wed, 04 Nov 2009
* mcl-09-308 released.
* The mcl cluster interpretation function did not deal correctly with
graphs that were encoded in gappy representations. Fixed. This would not
have been an issue for normal mcl usage, as mcl itself never constructs
such graphs (e.g. from label input).
* The 'q' mode to mcx (invoked as 'mcx q') has been renamed as 'mcx query'.
The new mode --vary-correlation triggers analysis of a correlation graph
at a series of thresholds, e.g. the number of connected components,
statistics (median, average, iqr) on node degrees and edge weights,
and a graph plotting the log(k) / log(#nodes of degree >=k) R^2 value
(high for scale-free-ish networks).
* mcl has had many not-so-interesting options removed or hidden.
* mcl has a new option, -knn-mutual <num>.
This considers the <num> best neighbours for each node, then only keeps
edges that occur in both best-neighbour lists for the two incident nodes.
* clm has a new mode 'stable', which outputs a (possibly overlapping) clustering
derived from a set of input clusterings. Each output cluster has a
stability value associated with it. If it is high, it means that
the output cluster occurred in some form in many of the input clusterings.
Such a matrix can be dumped with inclusion of the stability score
using the mcxdump option --dump-vlines.
* clm dist has new option --chain and --sort. The first causes only
consecutive comparisons to be made, the second sorts the clusterings
in order of (descending) granularity.
* If automatic naming of output files is employed (by not using the -o
option), mcl will only use the trailing part of the input file name.
Output will accordingly be written in the current directory, rather than
the directory in which the input file resides, as was previously the
case. The latter behaviour can be obtained by using the new unary --d
option.
* clm order and mcxarray have received polishing and upgrades.
- mcxarray now preserves negative correlations and
makes them available for later transformation (i.e. either
discarding or absolute value replacement).
- clm order finally outputs sensible output, namely a clustering
ordered in a manner consistent with the received set of nesting
clusterings, with largest clusters first, recursively,
starting from the coarsest clustering. It is possible to
halt this procedure at any level in the hierarchy using
the new -level option.
- clm order used to accept just a cluster hierarchy (such as produced
by mclcm or simple concatenating of cluster files). It now accepts
multiple separate clusterings as well, and one can even mix hierarchies
and clusterings all at the same time.
* The mcxplotlines.R script shipped with mcl has been improved and can
display a coarse experiment ordering (derived from clustering experiments
rather than probes) such as provided by 'clm order' on the expression
plots. The script should be regarded as a template for further
customization, although it does accept a number of parameters.
The expression plots now plot expression for all probes in a given
cluster, as well as the median value of expression of all probes
across a given experiment.
It is possible to let mcxplotlines.R handle a secondary coarser
clustering encoded by 'clm order'. The script will group together
information for the clusters within each supercluster, and plot
the medians of expression for all the subclusters as well as the
median of expression across the supercluster.
* mcx alter and mcxarray have both acquired the -tf option common in
several other programs. Use this option to transform values; e.g.
mcxarray -data t.expr -co 0.7 -tf 'abs(),add(-0.7)' -o t.mci
takes expression data, computes the pearson correlation coefficient,
takes values >= 0.7 and <= -0.7, takes the absolute value,
and maps the interval [0.7-1.0] to [0-0.3].
* The mcl options --adapt-smooth and --adapt-local have been turned
to no-ops. The implementation of these experimental options was not
sufficiently supported and not sufficiently elegant.
* Fixed a bug in mcxload, where mcxload -etc-ai would consistently crash.
Fri, 18 Sep 2009
* mcl-09-261 released.
* And a bug it did have (cf entry Wed 12 Jul 2009). When a resulting
clustering contains overlap, mcl tries to split off the overlapping part.
However, since the last release it has been doing this in a botched way,
causing erratic results. Bug reported by Tao Yue, now fixed.
* The mcxarray --transpose option now transposes the input data matrix,
rather than the result matrix, and -write-tab finds and writes the
correct labels in the presence of --transpose. Bugs were reported by
Jose Afonso Guerra Assuncao. The mcxarray --teartp option has been
removed.
* Added -resource <num> flag to mcl. Throughout the process, each
node will only keep track of at most <num> neighbours.
Use -ceil-nb <num> if you want to reduce the input graph in
the same manner.
Wed, 12 Jul 2009
* mcl-09-182 released.
* Lint modes have been removed from mcl. Linting can now be achieved
using 'clm adjust'.
* Analysis modes (and lint modes, now removed) would crash when combined
with --abc. Bug reported by David MacIver, now fixed.
* The interpretation routines were rewritten to be more compact and at a
somewhat higher-level of expressiveness, and should accordingly be
more understandable, maintainable, and extensible. They might have new
bugs too.
* mcl and 'mcx alter' and 'mcx erdos' have acquired the option -ceil-nb
to remove edges of lowest weight from highly connected nodes.
* volatility measures reported by 'clm dist' were wrong. Fixed.
* changed clm dist output to key=value format.
* 'mcx erdos' can now read label input with the -abc <fname> option.
* Added -ceil-nb <num> (cap neighbours) option to remove edges with
lowest weight from nodes with more than <num> edges. Consider it a poor
man's hub removal. Edges are removed in both directions, starting with
nodes that have the most neighbours and going down the list. This option
should help in obtaining more balanced clusterings. It reduces the
impact of sticky (having many neighbours) nodes, which generally have the
effect of pulling in many nodes, contributing to large clusters.
Breaking up those clusters otherwise requires increased inflation, which
increases cluster granularity throughout the entire graph. The -ceil-nb
option encodes a localized approach that should take the stick out of
sticky nodes.
* The output format of 'mcx erdos' was streamlined to some extent.
It is now in a pseudo s-expression syntax. mcx erdos can also read label
input with the customary -abc option. In interactive mode it is possible
to transform a graph in various ways, and additionally, to reread the
graph from file.
* Option -pp <num> (simple pre-pruning mode) has been removed seeing
that -ceil-nb should do a better job.
* mcx has a new mode, 'alter'. Currently supports -ceil-nb similar as
above.
Fri, 07 Nov 2008
* mcl-08-312 released (fixes bug in mcxdeblast).
* Fixed a bug in mcxdeblast, reported by Zhenxiang Xi.
* clm and mcx have acquired a help mode, for example
clm help info
will invoke the manual page for the info mode. It is fully equivalent to
'man clminfo'. All the modes that have a manual page are listed if mcx or
clm is invoked without arguments. This does require that the manual
pages are installed either in a directory listed in MANPATH or in
a standard location known to the 'man' program.
* Both mcx ctty (betweenness centrality) and mcx diameter can be run in
multiple threads with the -t option. In addition, the computation can
be split among different machines (each machine optionally running
multiple threads). The correct result is obtained by adding the partial
results of all the distributed runs, using 'mcx collect' (for diameter
subsequently, the maximum has to be taken over the resulting values).
This implies that mcx ctty and mcx diameter can now be sped up
arbitrarily by increasing the computation resources. Example:
HOST1: mcx ctty -imx graph.mci -t 4 -start 0 -end 1000 > graph.ctty1
HOST2: mcx ctty -imx graph.mci -t 4 -start 1000 -end 2000 > graph.ctty2
HOST3: mcx ctty -imx graph.mci -t 4 -start 2000 -end 3000 > graph.ctty3
HOST4: mcx ctty -imx graph.mci -t 4 -start 3000 -end 4000 > graph.ctty4
mcx collect graph.ctty1 graph.ctty2 graph.ctty3 graph.ctty3 > graph.CTTY
* clm close has new modes of output: The number of components,
and the list of component sizes.
* clm close accepts label type input with the -abc option
similar to mcx diameter, mcx ctty, mcx clcf and others.
* Added reference to Ulrik Brandes' paper on centrality betweenness
update algorithm.
* fixed bug in mcxdump that causes --dump-upper, --dump-upperi, --dump-lower,
and --dump-loweri to be ignored.
* A small R script called mcxplotlines.R was added to the scripts
directory. Use it to visualize per-cluster expression profiles
for clusterings of networks derived from expression data.
* mcxdump in newick mode has a modality to output singleton
labels without enclosing parentheses; -newick S.
* The layer responsible for handling label input (including
the format where each line consists of LABEL1 LABEL2 WEIGHT) was
rewritten. It is now in a more maintainable state, although
work still needs to be done.
Thu, 05 Jun 2008
* mcl-08-057 released.
- mcxarray reads in gene expression data in table format and
converts it to an mcl input graph.
- mcl now uses a simplified way of adding loops to the input graph. The
loop edge weight for a node is now set to the maximum of the weights
of edges connecting the node to its neighbours. This may cause small
changes in clustering results. These changes should generally be of
the same (small) magnitude as changes resulting from perturbing the
input data (edge weights).
- Added a program to compute, in various modes, for each node its
clustering coefficient, its eccentricity, and its betweenness
centrality. Also, to compute the diameter of a graph (i.e. the
maximum eccentricity): mcx clcf, mcx diameter, and mcx ctty.
- The number of applications has decreased substantially.
See below.
- The mcl suite is moving towards a wider focus on general purpose
large scale graph utilities, with the emphasis so far on basic
measures and transformations.
* mcx diameter compute diameter
* mcx ctty compute centrality
* mcx clcf compute clustering coefficient
* mcx erdos compute shortest paths
* mcxrand randomly shuffle, add, create, perturb edges
* mclcm hierarchical clustering with mcl
* clm dist compute cluster distance
* clm meet compute maximal joint subclustering
* clm close compute (subgraph) connected components
* ... and more.
* mcxi (formerly mcx) basic matrix operations
The binaries installed are
mcl mcxarray mcxrand clmformat
mclcm mcxassemble mcxsubs
clm mcxdump
mcx mcxload
mcxi mcxmap
The scripts installed are mclpipeline, along with mcxdeblast and
mclblastline if configure was instructed with --enable-blast.
Currently all programs in the mcl suite use one of the three
prefixes "mcl", "mcx", or "clm".
- first basic support for tree structures in the library.
- new --shadow-vl mcl preprocessing option.
- new mcl logging framework.
- speed ups in many applications.
- binary format can now be streamed over STDOUT/STDIN.
* Added mclcm, which implements hierarchical clustering with mcl.
It supports several modes:
contraction progress from fine to coarse
subcluster progress from coarse to fine
dispatch compute and combine different
* The mcl option --shadow-vl aids in creating well-balanced hierarchies
by adding dummy (shadow) nodes to a graph, which throttles flow between
denser and sparser parts. This prevents rapid absorption of sparse parts
by dense parts.
Possibly useful in standalone mode as well.
* New experimental mcl options --adapt-local and --adapt-smooth. They
adapt inflation according to local density characteristics of the input
graph.
* The number of applications has decreased substantially.
Most of the clm**** applications are now dispatched by the new
program clm, and most of the mcx**** applications are now dispatched
by the program mcx:
clm MODE clm encapsulates
dist order vol mate meet imac info close residue
mcx MODE mcx encapsulates
convert clcf diameter
Use
clm dist [options] <files>
clm order [options] <files>
mcx convert [options] <files>
et cetera.
The functionality formerly in mcx is now offered by mcxi.
* Interchange format now uses scientific notation except within a
limited range around zero (by using the fprintf %g conversion
specifier). This makes interchange format less lossy.
* binary format can now be streamed over STDOUT/STDIN. implying
very fast and lossless communication between mcl programs. Binary
format is lossless compared to interchange format in that the text
representations used by the latter are currently not garantueed to
result in the exact same value when read back.
* Lots of optimization work on graph and set related operations.
Many operations have been sped up for canonical matrices. These speed
ups do not affect mcl itself. Sped up: clmclose.
* mcl verbosity output is now largely controlled by a new logging
framework. Use the -q option or set environment variable TINGEA_LOG_TAG.
Use -q x -V all to thoroughly silence mcl.
* mcl emits more graph and cluster-related quantities in its
progress/log output.
* mcxarray:
It can now read flat-file array files with the -data option.
+ Skipping leading rows and leading columns is supported
(-skipr/-skipc). missing data is not yet supported.
+ Labels can be written to a tab file
* Renamed -cache-graph, -cache-graphx, -cache-tab to -write-graph,
-write-graphx, -write-tab. This is to avoid terminological confusion
with the process-level caching sometimes employed by mcl within a single
run to accomodate postprocessing.
Similarly the mcxload -cache-xxx options were all renamed to -write-xxx.
* mcl is accessible as a C library call. It is very undocumented
and lacking is an interface to build up a matrix. There are not yet
convenient installation tools.
* mcxdump by default read from STDIN and -imx is no longer
required.
* Fixed bug in mcxassemble where it would crash when presented
with a corrupted format.
* Added -lint-k and -lint-l options. Either will reread the input matrix and
do postprocessing on the clustering, reallocating nodes that seem to
have siphoned the wrong way.
When applied to networks with inhomogenously distributed edge density
characteristics the mcl process will sometimes cause smaller
clusters/sparse areas to suck in border nodes which 1) have only few
edges to that cluster/area and 2) seem to have been sucked out of a much
denser cluster into which they would fit beautifully. This is fully in
line with the flow characteristics of mcl but a largely unwanted
phenomenon. The postprocessing steps were added to remedy this.
-lint-l <num> considers all nodes in clusters of size not exceeding
<num> and optionally moves them to a larger cluster. Each
node is considered separately.
-lint-k <num> will try to have small clusters (up to a given size k)
assimilated in their entirety by a larger cluster if a suitable suitor
can be found.
* Fixed bug in mcxload -etc -etc-ai functionality. Singletons
would cause mayhem.
* The code underlying the analysis framework was largely reimplemented
and reorganized.
* --keep-overlap=y/n was removed and replaced by -overlap
<keep|remove|split>, remove being the default as before.
The split mode is new and causes all maximally consistent
overlapping fragments to be put in new clusters. This mode
is used in mclcm to cover theoretical fringe cases.
* If label data is tab-separated labels may contain spaces.
The code switches to tab-separated values if it finds a tab
in the input.
* Fixed bug in label loading where transformed values set to zero
were kept.
* Changed default output format in clminfo.
* GRATUITOUS. Bumped the gratuitous version tag to 1.007.
Mon, 27 Feb 2006
* mcl-06-058 released.
* Added scripts/minimcl, a 200-line fully functional mcl
implementation in perl. It only accepts label input and
has no parameters except inflation. The implementation is
hash-based rather than array, which may or may not leverage
sparseness properties.
Sat, 21 Jan 2006
* mcl-06-021 released.
* This release flushes some work before embarking on a big
mcxsubs overwrite. Analysis and cache modes have been improved.
* mcxsubs excepts path(<index-list>) top-level spec. It sets
the domain to all nodes participating in all shortest path
between all members of (the comma-separated) <index-list>.
* mcxsubs now works by default on the nil matrix. This makes it
easy to create domain templates with mcxsubs, e.g.
mcxsubs 'dom(cr, i(2,3,4))'
creates an empty matrix on the specified domains.
* mcxsubs did not recognize --from-disk and 'ext(disc())' specifications
cannot be combined and would dereference a NULL pointer. Fixed.
* Fixed weed-related bug in mcxsubs (removing rows/columns).
* Cleaned up the postprocess/analysis/caching frameworks.
Exceptions, limitations, and user-second-guessing were removed. By
default mcl does not append the log (it used to do this *sometimes*).
* Analysis modes try to read a cached graph if it exists.
* Added -cache-graphx <fname>. This caches a graph after transformations
have been applied.
* Caching of the input graphs is now done before matrix transformations
have been applied, but necessarily after stream transformations (if any)
have been applied in case input is streamed.
* Added -etc option to mcxload to load simple graphs from label-data
in a line-based format.
Use -etc-ai to load matrices for which the column labels are not
specified (e.g. clusterings). mcxload will autoincrement the columns.
* Fixed some documentation errors; inserted -abc-tf, --abc-log and
--abc-neg-log where -stream-tf, --stream-log and --stream-neg-log were
erroneously used.
* Added rand(<pbb-keep>) transformation (the -tf and -abc-tf options).
Selects each matrix entry with probability <pbb-keep>.
* mcl now prints a helpful reminder to cite the appropriate reference.
* Added configure-time check for
void* val = (void*) unsigned_number
idiom used by the stream interface.
Thu 17 Nov 2005
* mcl-05-321 released.
* Focus: uniform transformation syntax accross programs, improved
documentation, especially mcxio. Previous 'ascii' format is now called
interchange format throughout the documentation.
* mcl accepts the -abc-tf option to transform the input stream
and the -tf option to transform the input matrix (either constructed
from a stream with --abc or directly read from a stream).
-abc-tf 'pow(2), ceil(200), gt(20)'
This squares everything in the input stream, then truncates everything
larger than 200 to 200, and removes anything less than or equal to 20.
There are two special transform cases that appear as separate options.
--abc-log
--abc-neg-log
indicate that as the first thing to do the log or negative logarirthm
should be taken. The reason is that probability scores can get quite low
and are best represented as doubles (64 bit values); however mcl's
internal floating point representation is by default float (32 bit
values).
This means that blast clustering can be done from columnar format
like this:
grep -v '^#' hsfsp.cblast |\
cut -f 1,2,11 |\
mcl - --abc --abc-neg-log -tf 'ceil(460), gt(10)' -o -
This will make a few people very happy, and bewilder the rest.
For sake of completeness, ceil(460) because 1e-200 (standard
BLAST p-value cut-off) corresponds to 1/e/-460.517019 where
/e/ is the REAL e, namely 2.718281828.
* All of
- mcxsubs 'val(<spec>)'
- mcl -tf <spec>, -abc-tf <spec>
- mcxload -tf <spec>, -stream-tf <spec>
- mcxassemble -raw-tf <spec> -prm-tf <spec> -sym-tf <spec>
now accept the same syntax, documented in mcxio(5).
* The mcxio manual has gained two sections, one on transformation
syntax, one on label input.
* mcl -cache-graph saves the graph after any transformations have
been applied to it.
* Throughout the documentation, environment variables, and
logging statements, replaced 'ascii' by 'interchange'.
MCLXIOASCIIDIGITS is now MCLXIOINTERCHANGEDIGITS. bliss.
There is still plenty-o-ascii in the ChangeLog below.
Fri, 11 Nov 2005
* mcl-05-314 released - major new features.
* GRATUITOUS. Bumped the gratuitous version tag to 1.006 - because of
mcl's new label input munging abilities.
* mcl can read label input.
mcl <fname> --abc [options]
will read a line based white-space separated label format:
label1 label2 [value]
The current default is to resolve repeated entries by taking the maximum
of the values.
--abc or --expect-abc
input is expected to be in label format.
--abc or --yield-abc
cluster output will be done with labels.
-cache-tab <fname> (assumes label input)
the name of the file mcl writes the tab file too.
-cache-graph <fname> (assumes label input)
the name of the file mcl writes the input matrix.
-strict-tab <fname> (assumes label input)
makes MCL use the named tab file and die if labels
are not found.
-restrict-tab <fname> (assumes label input)
makes MCL use the named tab file and warn if labels
are not found.
-extend-tab <fname> (assumes label input)
makes MCL use the named tab file and extend it if labels
are not found.
* new utility mcxload with many custom options for reading in
label data and transforming the associated numerical values,
storing mappings in tab files and saving a graph in native mcl
input format.
* mcxdeblast acquired --abc-out to stream label input into mcl.
Thu 27 Oct 2005
* mcl-05-300 released.
* Added Q+A in FAQ on how to get application data into MCL format.
* Changed mcxassemble to pick the maximum between repeated entries
by default.
* clmmate was changed to do something reasonable when presented with
overlapping clusterings.
* Changed mcxdeblast to put the tab file in occurrence order by default.
* Fixed mcxsubs bug, introduced in last release, where selections never
materialize unless one mysteriously specifies --rand-merge.
* mcxsubs acquired the ext(dist(k)) spec option, where k is a number.
It applies to graphs and tells to extend the graph on the current
specification by including neighbours reachable in at most k steps.
ext(cdisc(k)) and ext(rdisc(k)) exist as well.
For example, the spec
'dom(cr, i(0-5)), ext(disc(2)), out(-)'
first takes the nodes 0-5 and then adds all nodes reachable
in at most 2 steps.
* mcxsubs can now also read a domain from a tab file.
use -tab <fname> with t() in the dom spec, e.g. dom(cr, i(0-5), t()).
mcxsubs -imx small.mci -dfac 0.8 'out(-)'
will now randomly select about 80 percent of the domains.
* mcxdump acquired the -sep-lead option to change the col-rowlist
separator. The -sep option was renamed to -sep-field.
* mcxdump can now also be used to restrict tab files.
mcxdump -imx matrix-file -tab tab-file --dump-tabc
mcxdump -imx matrix-file -tab tab-file --dump-tabr
The first will output the restriction of the input tab file
to the matrix column domain.
The second will do the same for the row domain.
Thu, 29 Sep 2005
* mcl-05-272 released
* sanitized clmimac, its analysis mode for detecting DAG structure in
iterands is now functional.
* mcl now accepts '-dump lines' to dump simple line-based pairs format.
With '-dump cat' it will dump all items to the same stream. The name for
the stream is then taken as the argument to the -o option, rather than
derived from '-ds dump-stem' option.
The -dump option now will simply look for substring occurrences
of its known targets in the argument string. An example is the
incarnation below.
-dump ite,lines,cat -o - -di all
will dump all iterands and the result clustering to stdout
in a line based format.
* fixed bug in mcxassemble/impala; mclsMap{Cols,Rows} would
not work due to wrongly set mclpAR->n_ivps.
* moved dump code from mcxdump to IO library.
* In clmdist and its manual page, replaced erroneous mention of Jacquard
index by Mirkin metric or edge hamming distance.
* mcl would not correctly read vectors specified in multiple places,
now fixed.
* mclblastline has changed.
By default it now only creates a line-based tab-separated dump file.
This means that by default it is not necessary to have zoem installed.
zoem *will* be invoked when the --fmt-fancy option is supplied.
* mcxdeblast can read from STDIN by setting the filename to '-'.
* mcxdeblasts now acts on --score=r as the documentation promises.
* clmformat now accepts the --fancy option on top of the
-dump <fname> option: it will do fancy output as well as dump output.
* clmformat will no longer by default output performance measures in dump
mode. Use --dump-measures to obtain them.
* added grok option to clxdo, to obtain clmformat's node stickiness
and cluster cohesion matrices.
* mcl accepts the --unchecked option, after which it will omit
consistency checks on the input matrix. See below.
* Setting the environment variable
MCLXIOUNCHECKED
causes consistency checks to be skipped during matrix input read.
This will speed up applications, but they will likely crash
when confronted with nonconforming input. Only use with very
large matrices in binary format and when in a hurry.
* added scripts/perllib/mcl/matrix.pm for reading/writing/manipulating
matrices from perl. It's simple and will not expand into something grand.
Thu, 28 Apr 2005
* mcl-05-118 released
* fixed matrix read speed problem. Reading a matrix went from
O(N^2) to O(E) where E is the number of edges (and N the number
of nodes).
* mcxassemble accepts --write-binary option to force binary format.
* mcxdump now accepts --no-loops and --force-loops options.
* Tweaked binary matrix read routine a bit - optimized full reads.
* GRATUITOUS. Bumped the gratuitous version tag to 1.005 - because of the
input read speed up.
Wed, 6 Apr 2005
* mcl-05-096 released
* [Joost] added clmorder.azm
* Updated mclfamily and mclindex documentation to mention
clmclose and clmorder.
Thu, 31 Mar 2005
* mcl-05-090 released.
* Added options to MCL for dumping submatrices during
iteration. Submatrices are, for now, extended principals, that
is, all matrix entries for which either the row or the column
index hits the specified domain.
-dump-subi <spec> Specify simple index list
-dump-subd <spec> Specify index list via union of domains
-dump-dom <mx> Domain matrix file
* Added --abc option to mcxdeblast for per-line ID1 ID2 SCORE format.
* Significant clean-up of the matrix IO library.
* Large rewrite of mcxsubs. It now takes a sane(r) and more
extendible language for submatrix specifications. Its implementation
is far less hideous than it used to be.
* mcxsubs has --block and --blockc options for taking respectively
a block diagonal matrix or its complement. Also, --skin for doing
manipulations on domains only, and --extend for computing extended
submatrices.
* Added -ax option to MCL, which prints the suffix MCL uses to construct
the output file name. This is useful in scripts that depend
on MCL to create unique (and convenient) filenames. Such as clxcoarse.
* Added util scripts clxcoarse and clxdo.
clxcoarse will currently do 2-level and 3-level clusterings. clxdo is
meant to automate simple tasks. It currently is able to
- give a granularity count of (presumably) a cluster file.
- test whether a graph/matrix is undirected/symmetric.
Both accept the -h option.
Not yet installed, copy them if needed.
* Replaced setenv in src/impala/io.c by putenv. The latter is POSIX,
the former is not. This caused compilation errors on (some)
Solaris systems.
* Added clmorder which, given a set of input clusterings, computes
an ordering that tries to put nodes that share many clusters over the
different clusters nearby, and puts nodes in larger clusters earlier in
the ordering. It is presumed that the clusterings are successive
subclusterings, but it need not be strictly the case - clmorder will
convert the input clusterings to a strictly nested sequence.
Not yet installed, copy them if needed.
Not yet documented.
* mcxmap has new
--mapi
--cmapi
--rmapi
options to facilitate use of inverted maps.
* mcxmap can map tab files with the -tab <tab-file> option.
* Added -my-scheme option to mcl for subtly better default output
naming capacities. Read the manual for what that means.
* Added --lazy-tab to clmformat.
Tue, 9 Nov 2004
* mcl-04-314 released, minor fixes.
* Some documentation fixes for blast scripts.
* Added automatic naming of dumped files.