KMC_TOOLS-COMPLEX

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.