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Top Forums Shell Programming and Scripting Parse two patterns and print next few characters following the pattern Post 302594567 by pirates.genome on Tuesday 31st of January 2012 04:42:50 PM
Old 01-31-2012
Question Parse two patterns and print next few characters following the pattern

Hi all,

I have many large files with data like following in each line:
Code:
1    822381    rs116091741    C    T    .    PASS    ASP;G5;G5A;GMAF=0.014308426073132;KGPilot123;RSPOS=822381;SAO=0;

I want output like this:
rs116091741 0.014308426073132

I tried some of the commands unsuccessfully, for example:

Code:
sed -n 's/.*rs//p' dbsnp_132.b37.vcf

I am very much new to linux and learning basics so please forgive me if it seems to be simple question....but I am not able to understand how to parse both the pattern and print characters following 'rs' including 'rs' itself and print values followed by 'GMAF=' excluding GMAF= itself.
 

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case(n) 						       Tcl Built-In Commands							   case(n)

__________________________________________________________________________________________________________________________________________________

NAME
case - Evaluate one of several scripts, depending on a given value SYNOPSIS
case string ?in? patList body ?patList body ...? case string ?in? {patList body ?patList body ...?} _________________________________________________________________ DESCRIPTION
Note: the case command is obsolete and is supported only for backward compatibility. At some point in the future it may be removed entirely. You should use the switch command instead. The case command matches string against each of the patList arguments in order. Each patList argument is a list of one or more patterns. If any of these patterns matches string then case evaluates the following body argument by passing it recursively to the Tcl interpreter and returns the result of that evaluation. Each patList argument consists of a single pattern or list of patterns. Each pattern may con- tain any of the wild-cards described under string match. If a patList argument is default, the corresponding body will be evaluated if no patList matches string. If no patList argument matches string and no default is given, then the case command returns an empty string. Two syntaxes are provided for the patList and body arguments. The first uses a separate argument for each of the patterns and commands; this form is convenient if substitutions are desired on some of the patterns or commands. The second form places all of the patterns and commands together into a single argument; the argument must have proper list structure, with the elements of the list being the patterns and commands. The second form makes it easy to construct multi-line case commands, since the braces around the whole list make it unneces- sary to include a backslash at the end of each line. Since the patList arguments are in braces in the second form, no command or variable substitutions are performed on them; this makes the behavior of the second form different than the first form in some cases. SEE ALSO
switch(n) KEYWORDS
case, match, regular expression Tcl 7.0 case(n)
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