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lecture-10 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 5, Lecture 10 István Albert Bioinformatics Consulting Center Penn State
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Some Programming Required Existing software tools can rarely do all steps Source data in different files may be formatted differently We need to bridge the differences with simple transformations Some programming ability is usually necessary for every project
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Files for this presentation: lecture-10.zip SGD_features.tab obtained from SGD
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The first scripting language: awk appeared in 1977, strong UNIX (1972) roots it is the precursor of languages such as Perl (1987) and Python (1989) Has fallen into disuse for a while; the large text have datasets lead to a resurgence of the language
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The structure of an awk program line oriented acts on each line of a stream and produces another line if there is a match do something with each line default match = match everything awk ‘ pattern { action } ‘
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Special variables Awk automatically splits the input by
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