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Full Discussion: Iterating over a list using awk, when variable
Top Forums Shell Programming and Scripting Iterating over a list using awk, when variable Post 302582765 by radoulov on Sunday 18th of December 2011 05:18:57 AM
Old 12-18-2011
In addition, this will calculate the average per DNA sequence for all the entries:

Code:
awk 'END {
  for (d in dna)
    print d, dna[d]/count[d]
  }
{
  dna[$1]   += $3
  count[$1] ++
  }' infile

This User Gave Thanks to radoulov For This Post:
cavanac2
 

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LEARN ABOUT DEBIAN

bio::graphics::glyph::phylo_align

Bio::Graphics::Glyph::phylo_align(3pm)			User Contributed Perl Documentation		    Bio::Graphics::Glyph::phylo_align(3pm)

NAME

       Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph

SYNOPSIS

	 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

       This glyph draws a cladogram for any set of species along with their alignment data in relation to the reference species.  At high
       magnification, base pair alignements will be displayed.	At lower magnification, a conservation score plot will be drawn.  Gaps as
       specified by CIGAR are supported.  Currently the scores are drawn to a log plot with the restriction that the score will be the same across
       all base pairs within an alignment.  It is hoped that this restriction can be addressed in the future.

       For this glyph to work, the feature must return a DNA sequence string in response to the dna() method.  Also, a valid tree file must be
       available in a format readable by the Bio::Tree library.

   OPTIONS
       The following options are standard among all Glyphs.  See Bio::Graphics::Glyph for a full explanation.

	 Option      Description		      Default
	 ------      -----------		      -------

	 -fgcolor      Foreground color 	      black

	 -outlinecolor Synonym for -fgcolor

	 -bgcolor      Background color 	      turquoise

	 -fillcolor    Synonym for -bgcolor

	 -linewidth    Line width		      1

	 -height       Height of glyph		      10

	 -font	       Glyph font		      gdSmallFont

	 -connector    Connector type		      0 (false)

	 -connector_color
		       Connector color		      black

	 -label        Whether to draw a label	      0 (false)

	 -description  Whether to draw a description  0 (false)

	 -hilite       Highlight color		      undef (no color)

       In addition to the common options, the following glyph-specific options are recognized:

	 Option      Description	       Default
	 ------      -----------	       -------

	 -draw_clado_left
		     Draws the Cladogram on left 0

	 -species_spacing
		     Spacing of species in DNA	 1
		     mode in units of font height

	 -species_spacing_score
		     Spacing of spcies in	 5
		     conservation view in units
		     of font height

	 -hide_label Whether to label spcies	 0

	 -tree_file  Path of file containing	 undef
		     cladogram tree information
	 -tree_format Format of tree file	  newick

	 -axis_color Color of the vertical axes  fgcolor
		     in the GC content graph

	 -errcolor   Color of all misalignment	 fgcolor
		     indicators

	 -mid_axis_color
		     Color of the middle axis of
		     the conservation score graph axis_color

	 -clado_bg  Color of the clado bg	bgcolor
		     indicators

	 -ref_color  Color of base pair bg for	 bgcolor
		     the reference sequence

	 -targ_color Color of base pair bg for	 bgcolor
		     all base pairs that match
		     reference

BUGS

       Please report them.

SEE ALSO

       Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
       Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
       Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
       Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
       Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
       Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
       Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

AUTHORS

       Hisanaga Mark Okada Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2001 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

perl v5.14.2							    2012-02-20				    Bio::Graphics::Glyph::phylo_align(3pm)
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