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Top Forums UNIX for Advanced & Expert Users Map snps into a ref gene file Post 302989932 by Don Cragun on Thursday 19th of January 2017 10:24:56 PM
Old 01-19-2017
No you have not. None of the data shown in the columns of the output you said you wanted in post #5 and in post #7 (even if the asterisks are removed) in this thread:
Code:
genename   SNPID   chrom   position   txstart   txend

show up anywhere in either of the sample input files shown in post #1 except for the chrom field.

This thread is closed!

Please consider opening a new thread where you show us two small sample input files and show us the exact output that you want your script to produce from those sample input files. Make sure that the data given in those files includes data that tests all of your corner cases and be sure that your description clearly specifies what should happen if multiple values match, what should happen if no values match, what should happen if one value matches, and any special cases that haven't been identified so far by this list.
This User Gave Thanks to Don Cragun For This Post:
 

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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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