KMC_TOOLS-COMPLEX(1)

💖 KMC_TOOLS-COMPLEX 💖

okay bestie, welcome to the KMC_TOOLS-COMPLEX(1) page — yes that's the manual name, that's literally what you typed to get here, and no you're not lost, this is exactly where you're supposed to be 💅

✨ NAME ✨

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

like, not one database, not two... a whole friend group of databases, doing math together. iconic behaviour fr fr.

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🌸 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>]                                               |  /
           |                                                               | /
           |_______________________________________________________________|/

so you write one lil text file, you tell it all your inputs, you give it a whole equation, and it just... runs it. no cap. that diagram is giving "I drew this in a text editor and I stand by it" and honestly? respect. 👑

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💅 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 😭

bestie. look closely. the first one has a dash and the second one does not. that is not me being sloppy, that is literally what the page says, so type it exactly like that. do not "fix" it. I am begging. 🫶

• 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.

iykyk — that's just PEMDAS energy, but make it k-mers. the parentheses are your best friend, use them. 💜

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 🍓

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🧚 EXAMPLE 🧚

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

see how set1, set2, set3 are the lil nicknames, kmc_o1, kmc_o2, kmc_o3 are the actual database paths, and then result gets the whole (set3+set1)*set2 equation? main character energy. go off. 🎀

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👑 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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and that's the whole page bestie, we ate and left no crumbs 💖 thanks for reading all the way to the bottom, where the footer just says KMC_TOOLS-COMPLEX(1) one more time like a little goodbye kiss — mwah, go run your complex operations, you've got this 🫶✨