This is a collection of unix bash scripts solving my regular BioInformatic problems. Most of these scripts have been run is bash (ZSH shell). You need to adjust to your shell if different. Hope this collection is helpful saving you time.
I am a strong believer in UNIX philosopy. Unix command tools are there in the abosolute perfection state to be utilised on files as large as your mounted storage can handle. They do very simple tasks but with such speed and efficiency that no interpreped/modular language can compete with (on the same number of cores). I use R, SQL and Python regularly in order to deal with complex statistical or data wrangling issues; however, I am yet to see the effciency and simplicity of awk, sed and grep challagned in the slighest way.
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If ever wanted to know why I do things the way I do, have a read HERE:
http://homepage.cs.uri.edu/~thenry/resources/unix_art/ch01s06.html
or as an abstract:
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Rule of Modularity: Write simple parts connected by clean interfaces.
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Rule of Clarity: Clarity is better than cleverness.
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Rule of Composition: Design programs to be connected to other programs.
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Rule of Separation: Separate policy from mechanism; separate interfaces from engines.
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Rule of Simplicity: Design for simplicity; add complexity only where you must.
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Rule of Parsimony: Write a big program only when it is clear by demonstration that nothing else will do.
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Rule of Transparency: Design for visibility to make inspection and debuggingeasier.
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Rule of Robustness: Robustness is the child of transparency and simplicity.
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Rule of Representation: Fold knowledge into data so program logic can be stupid and robust.
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Rule of Least Surprise: In interface design, always do the least surprising thing.
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Rule of Silence: When a program has nothing surprising to say, it should say nothing.
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Rule of Repair: When you must fail, fail noisily and as soon as possible.
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Rule of Economy: Programmer time is expensive; conserve it in preference to machine time.
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Rule of Generation: Avoid hand-hacking; write programs to write programs when you can.
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Rule of Optimization: Prototype before polishing. Get it working before you optimize it.
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Rule of Diversity: Distrust all claims for “one true way”.
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Rule of Extensibility: Design for the future, because it will be here sooner than you think.
##+++++++++++++++++++++ Where there is AWK there is a way +++++++++++++++++++++##