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Top Forums UNIX for Dummies Questions & Answers Reporting characters after string Post 302970782 by Xterra on Monday 11th of April 2016 10:26:37 PM
Old 04-11-2016
Your script with the latest mods:
Code:
 real 9m13.651s
 user 9m13.210s
 sys 0m0.436s

my sed script:
Code:
 sed -n '0,/AATTCCGG/s/^[ATCG]*AATTCCGG\(.\)\(.\)\(.\)\(.\)[ATCG]*$/\1\2\3\4/p; 0,/CCGGAATT/y/ATCG/TAGC/; s/^[ATCG]*\(.\)\(.\)\(.\)\(.\)GGCCTTAA[ATCG]*$/\4\3\2\1/p'

This is what I got:
Code:
 real 1m10.950s
 user 1m10.715s
 sys 0m0.234s

I was wondering if there is any way I can limit the extent of either script to let say the first 10 occurrences only? That will significantly reduce the running time, and still allow me to 'sample' the data sufficiently to identify the consensus string for each file
Thanks a TON!
 

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Graphics::Primitive::Component(3pm)			User Contributed Perl Documentation		       Graphics::Primitive::Component(3pm)

NAME
Graphics::Primitive::Component - Base graphical unit DESCRIPTION
A Component is an entity with a graphical representation. SYNOPSIS
my $c = Graphics::Primitive::Component->new({ origin => Geometry::Primitive::Point->new({ x => $x, y => $y }), width => 500, height => 350 }); LIFECYCLE
prepare Most components do the majority of their setup in the prepare. The goal of prepare is to establish it's minimum height and width so that it can be properly positioned by a layout manager. $driver->prepare($comp); layout This is not a method of Component, but a phase introduced by the use of Layout::Manager. If the component is a container then each of it's child components (even the containers) will be positioned according to the minimum height and width determined during prepare. Different layout manager implementations have different rules, so consult the documentation for each for details. After this phase has completed the origin, height and width should be set for all components. $lm->do_layout($comp); finalize This final phase provides and opportunity for the component to do any final changes to it's internals before being passed to a driver for drawing. An example might be a component that draws a fleuron at it's extremities. Since the final height and width isn't known until this phase, it was impossible for it to position these internal components until now. It may even defer creation of this components until now. It is not ok to defer all action to the finalize phase. If you do not establish a minimum hieght and width during prepare then the layout manager may not provide you with enough space to draw. $driver->finalize($comp); draw Handled by Graphics::Primitive::Driver. $driver->draw($comp); METHODS
Constructor new Creates a new Component. Instance Methods background_color Set this component's background color. border Set this component's border, which should be an instance of Border. callback Optional callback that is fired at the beginning of the "finalize" phase. This allows you to add some sort of custom code that can modify the component just before it is rendered. The only argument is the component itself. Note that changing the position or the dimensions of the component will not re-layout the scene. You may have weird results of you manipulate the component's dimensions here. class Set/Get this component's class, which is an abitrary string. Graphics::Primitive has no internal use for this attribute but provides it for outside use. color Set this component's foreground color. fire_callback Method to execute this component's "callback". get_tree Get a tree for this component. Since components are -- by definiton -- leaf nodes, this tree will only have the one member at it's root. has_callback Predicate that tells if this component has a "callback". height Set this component's height. inside_bounding_box Returns a Rectangle that defines the edges of the 'inside' box for this component. This box is relative to the origin of the component. inside_height Get the height available in this container after taking away space for padding, margin and borders. inside_width Get the width available in this container after taking away space for padding, margin and borders. margins Set this component's margins, which should be an instance of Insets. Margins are the space outside the component's bounding box, as in CSS. The margins should be outside the border. maximum_height Set/Get this component's maximum height. Used to inform a layout manager. maximum_width Set/Get this component's maximum width. Used to inform a layout manager. minimum_height Set/Get this component's minimum height. Used to inform a layout manager. minimum_inside_height Get the minimum height available in this container after taking away space for padding, margin and borders. minimum_inside_width Get the minimum width available in this container after taking away space for padding, margin and borders. minimum_width Set/Get this component's minimum width. Used to inform a layout manager. name Set this component's name. This is not required, but may inform consumers of a component. Pay attention to that library's documentation. origin Set/Get the origin point for this component. outside_height Get the height consumed by padding, margin and borders. outside_width Get the width consumed by padding, margin and borders. finalize Method provided to give component one last opportunity to put it's contents into the provided space. Called after prepare. padding Set this component's padding, which should be an instance of Insets. Padding is the space inside the component's bounding box, as in CSS. This padding should be between the border and the component's content. page If true then this component represents stand-alone page. This informs the driver that this component (and any children) are to be renderered on a single surface. This only really makes sense in formats that have pages such as PDF of PostScript. prepare Method to prepare this component for drawing. This is an empty sub and is meant to be overridden by a specific implementation. preferred_height Set/Get this component's preferred height. Used to inform a layout manager. preferred_width Set/Get this component's preferred width. Used to inform a layout manager. to_string Get a string representation of this component in the form of: $name $x,$y ($widthx$height) visible Set/Get this component's visible flag. width Set/Get this component's width. AUTHOR
Cory Watson, "<gphat@cpan.org>" BUGS
Please report any bugs or feature requests to "bug-geometry-primitive at rt.cpan.org", or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Geometry-Primitive <http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Geometry-Primitive>. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. COPYRIGHT &; LICENSE Copyright 2008-2009 by Cory G Watson. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.12.3 2011-06-02 Graphics::Primitive::Component(3pm)
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