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Full Discussion: Awk OFS issues
Top Forums Shell Programming and Scripting Awk OFS issues Post 302719149 by elixir_sinari on Monday 22nd of October 2012 07:20:42 AM
Old 10-22-2012
Quote:
Originally Posted by 02JayJay02
Hi, thankyou for the help but Im still getting the below error message after trying your suggestion

Code:
awk: can't open BEGIN {OFS="\t";} {print $1,$2,$3,$4,$5,$6,$7,$8,$9;}

Please post (exactly) what you typed in.
 

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LEARN ABOUT DEBIAN

bio::treeio::svggraph

Bio::TreeIO::svggraph(3pm)				User Contributed Perl Documentation				Bio::TreeIO::svggraph(3pm)

NAME

       Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output

SYNOPSIS

	 use Bio::TreeIO;
	 my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick');
	 my $out = Bio::TreeIO->new(-file => '>output', -format => 'svggraph');

	 while( my $tree = $in->next_tree ) {
	     my $svg_xml = $out->write_tree($tree);
	 }

DESCRIPTION

       This outputs a tree as an SVG graphic using the SVG::Graph API

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Brian OConnor
       Email brian.oconnor-at-excite.com

CONTRIBUTORS

       Allen Day Guillaume Rousse, Guillaume-dot-Rousse-at-inria-dot-fr

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::TreeIO::svggraph->new();
	Function: Builds a new Bio::TreeIO::svggraph object
	Returns : Bio::TreeIO::svggraph
	Args	:-width    => image width (default 1600)
		 -height   => image height (default 1000)
		 -margin   => margin (default 30)
		 -stroke   => stroke color (default 'black')
		 -stroke_width=> stroke width (default 2)
		 -font_size=> font size (default '10px')
		 -nomalize => undef or 'log' (default is undef)

   write_tree
	Title	: write_tree
	Usage	: $treeio->write_tree($tree);
	Function: Write a tree out to data stream in newick/phylip format
	Returns : none
	Args	: Bio::Tree::TreeI object

   decorateRoot
	Title	: _decorateRoot
	Usage	: internal methods
	Function:
	Example :
	Returns :
	Args	:

   next_tree
	Title	: next_tree
	Usage	:
	Function: Sorry not possible with this format
	Returns : none
	Args	: none

perl v5.14.2							    2012-03-02						Bio::TreeIO::svggraph(3pm)
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