Synopsis
- grcollect [options] <input> [...] [-o <output>|-b <basename>]
Description
- The main purpose of the program `grcollect` is twofold. First, it is intended to do data transposition on the input data, i.e. the input (which is read from files or standard input) is sorted and splitted to separate files where the splitting is based on a respective key. These keys are taken from the input data. In such a case where the input is from more files and each key is unique in a given file, this process is called data transposition (since it is similar when a 2 dimensional data matrix is stored in the form as each row is in a separate file, and one intends to transpose the matrix, i.e. store each column in a separate file). The other feature of `grcollect` is to do some sort of statistics on data associated to different keys. These statistics include average (mean, median, mode) and scatter (standard deviation or median deviance) estimations with the optional deselection of outlier points, summation, count statistics and so on.
Options:
General options:
- -h, --help
- Give general summary about the command line options.
- --long-help
- Give a detailed list of command line options.
- --version
- Give some version information about the program.
- <input> [,<input>, ...]
- Name of the input file. At least, one file should be specified. Reading from standard input can be forced using a single dash - as input file name. More dashes are silently ignored.
- -c, --col-base <key column index>
- Column index for the key.
Data transposition specific options:
- -b, --basename <base-%b-name>
- Base name of the output files. The base name string should conatain at least one %b tag, which is replaced by the respective key string on the creation of the file.
- -x, --extension <extension>, -p, --prefix <prefix>
- Equivalent to -b|--basename <prefix>%b.<extension>. Note that in practice, <prefix> might be some sort of directory name and extension is a regular file extension, but the above substitution is done literally. Therefore, the dot between the key and the <extension> is always inserted in the final name of the output files but a trailing slash is required at the end of <prefix> if the files are to be created in that particular directory. Note also that this case, the target directory must exist before the invocation of `grcollect`, otherwise the output files cannot be created.
- -C, --comment
- Insert a commented line (starting with #) containing information about the version and command line invocation syntax of `grcollect` to the beginning of the transposed files.
- -S, --additional-comment <...>
- Insert an additional commented lines (starting with #) to the beginning of the transposed files.
Options for cumulative statistics:
- -d, --col-stat <>[,...]
- Comma-separated list of column indices on which the statistics are to be calculated. Columns with non-numerical contents are ignored.Note that this option imply the cumulative statistics mode of `grcollect`.
- -o, --output <filename>
- The name of the output file to which the output statistics are written. The total number of columns in this file will be 1+C*N, where C is the number of columns (see -d|--col-stat) on which the statistics are calculated and N is the number of statistic quantities (see --stat). The first column in the output file is the key, which is followed by the per-column list of statistics, in the same order as the user defined after -d|--col-stat and --stat.
- -s, --stat <list of statistics>
- Comma-separated list of statistics to be estimated on the input data. These can be one or more of the following:
- count
- Total number of records, for the given key.
- rcount
- The number of records after rejecting outliers (i.e. it is always the same as the count value if no --rejection was used).
- mean, median, mode
- Mean, median or mode statistics of the data.
- rmean, rmedian, rmode
- Mean, median or mode, after rejecting outliers.
- {mean|median|mode}stddev, {mean|median|mode}meddev, stddev
- Scatter of the data around the mean, median or mode. The scatter can either be standard deviation (stddev) or median deviance (meddev). The literal stddev is the classic standard deviation, equivalent to meanstddev.
- r{mean|median|mode}stddev, r{mean|median|mode}meddev, rstddev
- The same scatters as above but after rejecting outliers.
- sum, rsum
- Sum of the data, esp. total sum and sum after rejecting outliers.
- sum2, rsum2
- Sum of the squares, total and after rejecting outliers.
- min, max
- Minimal and maximal data values.
- rmin, rmax
- Minimal and maximal data values after the rejection of outliers.
- -r, --rejection column=<index>,<rejection parameters>
- Comma-separated directives for outlier rejection for the specified column. The rejection parameters are:
- iterations=<n>
- Maximum number of iterations to reject outliers.
- mean, median, mode
- Use the mean, median or mode for the center of the rejection.
- stddev, meddev, absolute=<limit>
- Use the standard deviation or median deviance for rejection limit units or define an absolute limit for rejection level.
- Note that each column can have different kind of rejection method, thus more than one "--rejection ..." command line option can be used at the invocation of `grcollect`.
Other options:
- -m, --max-memory <memory>[kmg]
- Maximum amount of memory available for `grcollect`. The prefixes k, m or g can be used for kilobytes, megabytes and gigabytes, respectively. On 32bit systems, the maximum memory is limited to 3gigabytes. Note that `grcollect` does not use any kind of operating system specific methods to determine the maximum amount of memory, it always should be set by the user. The default value of 8 megabytes is somewhat small, so upon massive data transposition (tens or hundreds of gigabytes), this limit is worth to be set accordingly to the physical memory available.
- -t, --tmpdir <directory>
- Directory for temporary file storage. Note that the default temporary directory is always the current one (which is is equivalent to define --tmpdir ./), since in a usual configuration the /tmp directory is small, moreover, it can be some sort of tmpfs, temporary file system mount on the physical memory itself.