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= 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.
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