NAME

       kmc_tools-complex - complex operations with a number of input databases

SYNOPSIS

       kmc_tools complex <operations_definition_file>

DESCRIPTION

       This command executes a combination of operations as defined by
       <operations_definition_file>. It is text file with following syntax:

            __________________________________________________________________
           |INPUT:                                                            |
           |<input1>=<input1_db_path> [params]                                |
           |<input2>=<input2_db_path> [params]                                |
           |... |
           |<inputN>=<inputN_db_path> [params]                                |
           |OUTPUT:                                                           |
           |<out_db_path>=<ref_input><oper><ref_input>[<oper><ref_input>[...] |
           |[OUTPUT_PARAMS:                                                 __|
           |<output_params>]                                               |  /
           |                                                               | /
           |_______________________________________________________________|/

PARAMETERS

       input1, input2, ..., inputN
           names of inputs used to define equation

       input1_db_path, input2_db_path, ..., inputN_db_path
           paths to k-mers sets

       For each input there are additional parameters which can be set:

       -ci<value>
           exclude k-mers occurring less than <value> times

       cx<value>
           exclude k-mers occurring more of than <value> times

       out_db_path
           path to output database

       ref_input
           one of input1, input2, ..., inputN

       oper
           one of {*,-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract,
           union}

       Operator '*' has the highest priority. Other operators have equal priorities. The order of
       operations can be changed with parentheses.

       Output parameters:

       -ci<value>
           exclude k-mers occurring less than <value> times

       -cx<value>
           exclude k-mers occurring more of than <value> times

       -cs<value>
           maximal value of a counter

EXAMPLE

            __________________________________________________________________
           |INPUT:                                                            |
           |set1 = kmc_o1 -ci5                                                |
           |set2 = kmc_o2                                                     |
           |set3 = kmc_o3 -ci10 -cx100                                      __|
           |OUTPUT:                                                        |  /
           |result = (set3+set1)*set2                                      | /
           |_______________________________________________________________|/

AUTHOR

       KMC was originally written by:

       •   Sebastian Deorowicz (sebastian.deorowicz@polsl.pl)

       •   Marek Kokot

       •   Szymon Grabowski

       •   Agnieszka Debudaj-Grabysz

COPYING

       KMC is a free software distributed under GNU GPL3 licence for academic, research, and
       commercial use.

                                                                             KMC_TOOLS-COMPLEX(1)