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Full Discussion: Need to increment number in data file
Top Forums Shell Programming and Scripting Need to increment number in data file Post 302727003 by deneuve01 on Monday 5th of November 2012 04:10:57 PM
Old 11-05-2012
Here is the data with pipe delimiters so you can clearly identify the fields I am referencing:

Code:
 
|Refntns3_1 |char         |30 |Ref H77 nt codon 1      |Reference H77 Nucleotide Codon 1                                |             |--
|Codns3_1   |char         |30 |Obs Nucleotides codon 1 |Observed Nucleotides Codon 1                                    |             |--
|Refaans3_1 |char         |30 |Ref  H77 aa codon 1     |Reference H77 Amino Acid Codon 1                                |             |--
|Ns3_1      |char         |30 |Obs Amino acid codon 1  |Observed Amino Acid Codon 1                                     |             |--
|Mutns3_1   |char         |30 |Ref/Obs aa 1 (b_codes)  |Reference and Observed Amino Acid Codon 1 (see mut in b_codes)  |             |--
|Synns3_1   |int/value    | 3 |Syn codon 1 (b_codes)   |Synonymity Code Codon 1 (see syn in b_codes)                    |-2:4         |--
|Aamixns3_1 |int/value    | 3 |Mix codon 1 (b_codes)   |Mixture/Mutation Code Codon 1 (see aamix in b_codes)            |-2:4         |--

---------- Post updated at 04:10 PM ---------- Previous update was at 01:11 PM ----------

I figured the solution out myself and wrote a simple shell script to create the interation I needed.

Code:
#!/bin/csh
rm -f test1.txt
touch test1.txt
foreach X (`cat num`)
echo "| |refntns3_"$X" |Ref H77 nt codon "$X"      |Reference H77 Nucleotide Codon "$X"                                |6 |30 |0 |0 |  |">>test1.txt
echo "| |codns3_"$X"   |Obs Nucleotides codon "$X" |Observed Nucleotides Codon "$X"                                    |6 |30 |0 |0 |  |">>test1.txt
echo "| |refaans3_"$X" |Ref  H77 aa codon "$X"     |Reference H77 Amino Acid Codon "$X"                                |6 |30 |0 |0 |  |">>test1.txt
echo "| |ns3_"$X"      |Obs Amino acid codon "$X"  |Observed Amino Acid Codon "$X"                                     |6 |30 |0 |0 |  |">>test1.txt
echo "| |mutns3_"$X"   |Ref/Obs aa "$X" (b_codes)  |Reference and Observed Amino Acid Codon "$X" (see mut in b_codes)  |6 |30 |0 |0 |  |">>test1.txt
echo "| |synns3_"$X"   |Syn codon "$X" (b_codes)   |Synonymity Code Codon "$X" (see syn in b_codes)                    |2 |3  |0 |0 |-2:4 |">>test1.txt
echo "| |aamixns3_"$X" |Mix codon "$X" (b_codes)   |Mixture/Mutation Code Codon "$X" (see aamix in b_codes)            |2 |3 |0 |0 |-2:4  |">>test1.txt
end
exit

** the num file contains a simple list of numbers, 1-100

Thank you!
 

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LEARN ABOUT DEBIAN

bio::graphics::glyph::translation

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

NAME

       Bio::Graphics::Glyph::translation - The "6-frame translation" glyph

SYNOPSIS

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

DESCRIPTION

       This glyph draws the conceptual translation of DNA sequences.  At high magnifications, it simply draws lines indicating open reading
       frames.	At low magnifications, it draws a conceptual protein translation.  Options can be used to set 1-frame, 3-frame or 6-frame
       translations.

   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
	 ------        -----------		   -------

	 -translation  Type of translation to	   1frame
		       perform.  One of "1frame",
		       "3frame", or "6frame"

	 -strand       Forward (+1) or reverse (-1) +1
		       translation.

	 -frame0       Color for the first frame    fgcolor

	 -frame1       Color for the second frame   fgcolor

	 -frame2       Color for the third frame    fgcolor

	 -gridcolor    Color for the horizontal     lightgrey
		       lines of the reading frames

	 -start_codons Draw little arrowheads	    0 (false)
		       indicating start codons

	 -stop_codons  Draw little vertical ticks   1 (true)
		       indicating stop codons

	 -arrow_height Height of the start codon    1
		       arrowheads

	 -show_sequence Show the amino acid sequence 1 (true)
		       if there's room.

	 -triletter_code Show the 3-letter amino acid 0 (false)
		       code if there's room

	 -codontable   Codon table to use	    1 (see Bio::Tools::CodonTable)

SUGGESTED STANZA FOR GENOME BROWSER

       This produces a nice gbrowse display in which the DNA/GC Content glyph is sandwiched between the forward and reverse three-frame
       translations.  The frames are color-coordinated with the example configuration for the "cds" glyph.

	[TranslationF]
	glyph	     = translation
	global feature = 1
	frame0	     = cadetblue
	frame1	     = blue
	frame2	     = darkblue
	height	     = 20
	fgcolor      = purple
	strand	     = +1
	translation  = 3frame
	key	     = 3-frame translation (forward)

	[DNA/GC Content]
	glyph	     = dna
	global feature = 1
	height	     = 40
	do_gc	     = 1
	fgcolor      = red
	axis_color   = blue

	[TranslationR]
	glyph	     = translation
	global feature = 1
	frame0	     = darkred
	frame1	     = red
	frame2	     = crimson
	height	     = 20
	fgcolor      = blue
	strand	     = -1
	translation  = 3frame
	key	     = 3-frame translation (reverse)

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

AUTHOR

       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::translation(3pm)
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