Scroll to navigation

KMC_TOOLS-COMPLEX(1)   KMC_TOOLS-COMPLEX(1)

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.