16 May 2014 mcxassemble 14-137
mcxassemble — transform raw cooccurrence data to mcl matrix format.
mcxassemble -b base (base name) [-o fname (write to file fname)] [--write-binary (write output in binary format)] [--map (apply base.map)] [-raw-tf (apply transform spec to input)] [-rv MODE (repeated vectors)] [-re MODE (repeated entries)] [-ri MODE (adding mirror image)] [-r MODE (repeated entries/vectors/images)] [-prm-tf (apply transform spec to primary matrix)] [-sym-tf (apply transform spec to symmetrified matrix)] [-q (quiet mode)]
The options above embody the default setup when using mcxassemble. There are many more options which mostly provide subtly different ways of doing input/output, set warning levels, or regulate how repeated entries and vectors should be treated. The full list of options is shown below. Read DESCRIPTION for learning about mcxassemble input/output and the functionality it provides.
As of release 05-314 mcl is able to cluster label-type input on the fly. In most cases, this will be sufficient. Alternatively, mcxload can be used to map label-type input onto mcl matrices. Consequently, there are likely fewer scenarios nowadays where mcxassemble is the best solution. Consider first whether mcl in label mode or mcxload can do the job as well.
mcxassemble [-b base (base name)] [-hdr fname (read header file)] [-raw fname (read raw file)] [--map (apply base.map)] [--cmap (apply base.cmap)] [--rmap (apply base.rmap)] [-map fname (apply fname)] [-rmap fname (apply fname)] [-cmap fname (apply fname)] [-tag tag (apply base.tag)] [-rtag tag (apply base.tag)] [-ctag tag (apply base.tag)] [-skw fname (write skew matrix)] [-prm fname (write primary result matrix)] [--skw (write base.skw)] [--prm (write base.prm)] [-xo suf (write base.suf)] [-o fname (write to file fname)] [-n (do not write default symmetrized result)] [-i (read from single data file)] [-digits int (digits width)] [-s (check for symmetry)] [-raw-tf (apply transform spec to input)] [-rv <mode> (action for repeated vectors)] [-re <mode> (action for repeated entries)] [-ri <mode> (adding mirror image)] [-r <mode> (same for entries and vectors)] [-prm-tf (apply transform spec to primary matrix)] [-sym-tf (apply transform spec to symmetrified matrix)] [--quiet-re (quiet for repeated entries)] [--quiet-rv (quiet for repeated vectors)] [-q (the two above combined)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]
mcxassemble enables easy matrix creation from an intermediate raw matrix format that can easily be constructed from a one-pass-parse of cooccurrence data. The basic setup is as follows.
Parse cooccurrence data from some external format.
Transform cooccurrence data to raw mcl data as you parse.
When done, write out required header and domain information to a separate file. The domain information can be built during the parsing stage.
Use mcxassemble to construct a valid matrix from the raw data and the header information.
Nodes can optionally be relabeled by writing a separate map file to be read by mcxassemble, which takes the form of a very thin matrix file.
The easiest thing to do is to group all input/output files under the same base name, say base. A standard way of proceeding, which will lead to a concise mcxassemble command line, is by creating the input files base.raw and base.hdr, and optionally the file base.map. The default behaviour of mcxassemble is then to create base.sym as the resulting matrix file, containing the symmetrized matrix constructed from the raw input.
Suppose blastresult is a file containing blast results. The following two commands construct an mcl matrix file from the file.
mcxdeblast will generate the files blastresult.hdr, blastresult.raw, and blastresult.map. The --sort=a option will create a map file corresponding with alphabetic ordering. These files are processed by mcxassemble and it will generate the file blastresult.sym. The -r option tells mcxassemble that repeated entries should be maxed; each time the largest entry seen thus far will be taken.
This file contains a header as usually found in generic mcl matrix files, i.e. the required header part, and optionally the domain part(s) if not all domains are canonical. Refer to mcxio for more information. The domain information in the header file will be used to pre-construct a skeleton matrix and to validate the entries in the raw data file as they fill the skeleton matrix.
Raw input format
The file from which raw input is read should have the raw format as described in mcxio. Simply put; no header specification, no domain specification, and no matrix introduction syntax is used. The file just contains a listing of vectors. An example fragment is the following:
The listing of vectors need not be sorted, and neither does a vector itself need to be sorted - the mcl generic matrix format is actually not different in this respect. Furthermore, duplicate entries and duplicate vectors are allowed. This is in fact again allowed in the generic format, except that where applications expect generic format warnings will be issued and duplicate entries will be disregarded. mcxassemble allows customizable behaviour dictating how to merge repeated entries. Refer to the -re, -rv, -r options below.
The vectors read by mcxassemble do have to match the domains specified in the header file. The leading index that specifies the column index has to be present in the column domain; all subsequent indices that specify column entries have to be present in the row domain.
If one concatenates the contents of the header file and the data file, the result is almost but not quite a file containing a matrix in syntactically correct mcl generic matrix format. The parts missing are the (mclmatrix introduction token, (followed by) the begin token, and the closing ) token.
This file must contain a map matrix, which is a matrix with the following properties:
The column domain and row domain are of the same cardinality.
Each column has exactly one entry.
Each row domain index occurs in exactly one column.
Such a matrix is used to relabel the nodes as found in the raw data. A situation that might occur when parsing some external format (and producing raw matrix format), is that ID's (indices) are handed out on the fly during the parse. Afterwards, one may want to relabel the IDs such that they correspond with an alphabetic listing of the quantity that is represented by the node domain, or by some other sort criterion. A map file is then typically generated by the parser, as that is the utility in charge of the IDs. A small example of a map file for a graph containing five nodes is the following:
This corresponds to a relabeling such that the associated strings will be ordered alphabetically. Note that comments can be used to link string identifiers with indices. This map file says e.g. that the string identifier "mno" is represented by index 0 in the raw data, and by index 4 in the matrix output by mcxassemble.
Base name of files to be processed and output. Refer to DESCRIPTION above and the entries of other options below.
Explicitly specify the header file and the data file (rather than constructing the file names from a base name and suffixes).
Map options. --cmap combines with the -b option, and says that the map file in base.cmap (where base was specified with -b base) should be applied to the column domain only. --rmap works the same for the row domain, and --map can be used to apply the same map to both the column and row domains.
-cmap and its siblings are used to explicitly specify the map file to be used, rather than combining a base name with a fixed suffix. -tag and its siblings work in conjuction with the -b option, and require that a tag be specified from which to construct the map file (by appending it to the base name).
Options for writing matrices other than the default symmetrized result. The primary result matrix is the matrix constructed from reading in the raw data and adding entries to the skeleton matrix as specified with the -r, -re, and -rv options. This matrix can be written using one of the prm options. Calling the primary matrix A, the skew matrix (as defined here) is the matrix A - A^T, i.e. A minus its transposed matrix. It can be written using one of the skw options.
If for some reason the symmetrized result is not needed, its output can be prevented using the -n option.
The -xo option is used in conjunction with the -b option in order to change the suffix for the file in which the symmetrized result matrix is written. Use e.g. -xo mci to change the suffix from the default value sym to mci. Use -o to explicitly specify the filename in full. Use -digits to set the number of digits written for matrix entries (c.q. edge weights).
The -i option is special. It causes mcxassemble to read both the header information and the raw data from the same file, where the syntax should be fully conforming to generic mcl matrix format.
This will check whether the primary result matrix was symmetric. It reports the number of failing (or skew) edges.
The first applies its transformation spec to the values as found in the raw data. The second applies its transformation spec to the primary matrix. The third applies its transformation step to the symmetrified matrix. Refer to mcxio for documentation on the transformation spec syntax.
Merge options, dictating the behaviour when repeated entries are found. A distinction is made between entries that are repeated within the same column listing, and entries that are repeated between different column listings. An entry can be a repeat of both kinds simultaneously as well. Additionally, the final result is by default symmetrized by combining with the mirror image (in matrix terminology, the transposed matrix). This symmetrization can be done in the same variety of ways.
The re option, for repeats within the same column, is carried out first. It is applied after the column has its entries sorted, so the left and right options are not garantueed to follow the order found in the raw input. The rv option, for repeats over different columns, is carried out second.
The option -ri min can assist in implementing a (top-list) best reciprocal hit criterion.
is encountered in the input, listing entries for the vector labeled with index 0. If -re add or -r add is used, it will transform to the vector
If -re max or -r add is used instead, it will transform to the vector
Suppose add mode is used, and that later on another vector specification for the index 0 is found, leading to this transformed vector:
If -rv max was specified, this new vector is combined with the previous vector by taking the entry wise maximum:
Finally, suppose that somewhere one or more vector listings were specified for index 3, which eventually led to an entry 0:50. The final symmetrization step will take the [0,3] entry of weight 20 and combine it with the [3,0] entry of weight 50. The resulting matrix will then have the [0,3] and the [3,0] entry both equal to either the maximum, the sum, or the product of the two quantities 50 and 20.
Warning options. Turn these on if you expect the raw data to be free of repeats.
mcxio, mcl, mcxload and mclfamily for an overview of all the documentation and the utilities in the mcl family.