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This is the command kmc_tools-complex that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 | /
|_______________________________________________________________|/

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