Fasta2SVG - Creates a svg-graphic from a fasta file

I wrote this software for the PhD-thesis of my girlfriend to print the various fasta-files of her work in nice fashion. The script uses perl and the SVG-module to convert a fasta-graphic into a svg-vector-graphic. The result can easily be reformated by using Skencil or Sodipodi. Under Windows you have to use a commercial software as Corel Draw or Adobe Illustrator (or boot from a Knoppix-CD).

For running the program you need perl and some modules from the cpan. If you are running linux, perl is contained in your distribution. A Windows-version is available at ActiveState.

If the software is installed, you have to get the following modules from CPAN (www.cpan.org):

SVG
Getopt::Long

Under Windows you have to use the following commands:

ppm
ppm> install SVG
ppm> install Getopt-Long

If you use the program, please give me some feedback.

Download

Date	Description	Download
07. 07. 2005	Version 0.01: Initial version.	Download

Examples

For the sake of illustration I added some examples to this page. If you look up the parameters in the lower part of this page the examples are self-explanatory. Just in case you don't have a svg-viewer installed I alos included a pdf-version of each example.

perl fasta2svg example.fas > example1.svg

SVG Graphic Graphic as PDF-file

perl fasta2svg example.fas --align --nonumber --color="0:#ffe57d" --color="1:#ffaa00" --color="2:#ff5b01" --color="3:#ff0101" > example2.svg

SVG Graphic Graphic as PDF-file

perl fasta2svg example.fas --color="A:#ff0000" --color="T:#ff0000" --color="C:#0000ff" --color="G:#0000ff" > example3.svg

SVG Graphic Graphic as PDF-file

perl fasta2svg example.fas --color="A:#ffff00" --offset=-55 --stroke=0 --space=3 --lineheight=15 --itemwidth=15 --maxwidth=10 > example4.svg

SVG Graphic Graphic as PDF-file

NAME

faste2svg - Creates a svg-graphic from a fasta file

SYNOPSIS

fasta2svp [options] file

 Options:
   --help       get help

OPTIONS

--help: Prints this manual page in text format.
--maxwidth=i: Sets the numbers of bases / nucleotides in a line to i. The default is 75.
--space=f: Sets the space beween two lines to f; the default is 1.5.
--lineheight=f: Sets the height of a line to f. Default is 8.
--itemwidth=f: Sets the with of one item to f. Default is 6.
--scale=f: Scales the image by factor f. Default is 1.
--leftspace=i: Sets the space between sequence name and sequence to i. Default is 100.
--stroke=i: Sets the stroke of the rectangles surrounding the bases. Default is 1.
--nonumbers: Switches off the numbering (default is on).
--offset=i: Sets a offset for the numbering.
--align!: Switches to alignment-mode.
--color=s: Sets the color. If the mode is align the form is 0:#ff0000. This sets the color for no difference at this site to red. If the mode is not align, the form is A:#0000ff; this sets the base A to red.

DESCRIPTION

fasta2svg reads a fasta file and converts it to a svg-graphic that can be processed with sketch, sodipodi or other vector graphic programs.

LICENCE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.