mcxconvert(1) [debian man page]
mcx convert(1) USER COMMANDS mcx convert(1) NAME mcx convert - convert between mcx storage types SYNOPSIS mcx convert <matrix-file-in> <matrix-file-out> mcx convert [--write-binary] --cone-to-stack <cat-file-in> <cat-file-out> mcx convert [--write-binary] --stack-to-cone <cat-file-in> <cat-file-out> mcxconvert is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode convert. The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the mcx manual page. mcx convert [--cone-to-stack (transform cone file to stack file)] [--stack-to-cone (transform stack file to cone file)] [--write-binary (output native binary format)] [--cat (read and write cat format)] [-cat-max <num> (limit the stack conversion to <num> matrices)] In the two-argument invocation without additional arguments, mcx convert converts from the format found in the first file to the other for- mat, i.e. from native interchange to native binary format or the other way around. When querying with the -q option, mcx{convert} will out- put a one-line synopsis describing the matrix in the argument. The --cone-to-stack and --stack-to-cone options convert between the two types of concatenated output provided by mclcm. DESCRIPTION The mcl libraries make extensive use of matrices. Matrices are used to encode graphs, matrices and clusterings. They can be stored either in interchange or in binary format. The latter is somewhat more efficient in storage and much faster in both reading and writing, but the default is interchange format. The mcl input routines recognize the type of storage they are dealing with. If you want to convert a matrix to the other storage type, sim- ply specify the file name of the matrix you want to convert. mcx convert will recognize its type, and write the other type to the file specified as the second argument. OPTIONS --cone-to-stack (transform cone file to stack file) This option requires two trailing options, the names of respectively the source cone file and the target stack file. --stack-to-cone (transform stack file to cone file) This option requires two trailing options, the names of respectively the source stack file and the target cone file. --cat (read and write cat format) -cat-max <num> (limit the stack conversion to <num> matrices) --write-binary (output native binary format) This option is only useful with either of the options --cone-to-stack, --stack-to-cone, or --cat. AUTHOR Stijn van Dongen. SEE ALSO mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family. mcx convert 12-068 8 Mar 2012 mcx convert(1)
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mcx clcf(1) USER COMMANDS mcx clcf(1) NAME mcx clcf - compute the clustering coefficient of a graph SYNOPSIS mcx clcf [options] [matrix-file] mcxclcf is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode clcf. The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the mcx manual page. mcx clcf [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-tab <fname> (use tab file)] [-o <fname> (write to this file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs are used)] [-j <intj> (this job has index <intj>)] [--summary (return mean clustering coefficient)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)] DESCRIPTION mcx clcf computes the clustering coefficient of a graph. The input graph/matrix, if specified with the -imx option, has to be in mcl matrix/graph format. You can use label input instead by using the -abc option. Refer to mcxio(5) for a description of these two input formats. By default mcx diameter reads from STDIN and expects matrix format. To specify label input from STDIN use -abc -. OPTIONS -abc <fname> (label input) The file name for input that is in label format. -imx <fname> (input matrix) The file name for input. STDIN is assumed if not specified. -o <fname> (output file) The file name for output. STDOUT is the default output stream. -tab <fname> (use tab file) This option causes the output to be printed with the labels found in the tab file. With -abc this option will, additionally, construct a graph only on the labels found in the tab file. If this option is used in conjunction with -imx the tab domain and the matrix domain are required to be identical. --summary (return mean clustering coefficient) By the default a 1-column table (with row names included) is output, one row for each node. This option causes the output of the average clustering coefficient only. -t <int> (use <int> threads) -J <intJ> (a total of <intJ> jobs are used) -j <intj> (this job has index <intj>) Computing clustering coefficients is time-intensive for large graphs. If you have multiple CPUs available consider using as many threads. Additionally it is possible to spread the computation over multiple jobs/machines. Conceptually, each job takes a number of threads from the total thread pool. If job control is used (the -J option is used) then the number of jobs should not exceed the number of threads. The total number of threads divided by the total number of jobs defines the number of threads that will be used by the current job. Addi- tionally, the number of threads specified signifies the total added amount of all threads across all machines and must be the same for all jobs. This number is used by each job to infer its own set of tasks. The following set of options, if given to as many commands, defines three jobs, each running four threads. -t 12 -G 3 -g 0 -t 12 -G 3 -g 1 -t 12 -G 3 -g 2 SEE ALSO mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family. mcx clcf 12-068 8 Mar 2012 mcx clcf(1)