Bio-Graphics
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configuration section to get a reasonable image. However, to tune the
appearance of the image, you will probably want to tweak the
configuration. Here is an excerpt from the configuration section:
# example file
[general]
bases = -1000..21000
height = 12
[EST]
glyph = segments
bgcolor= yellow
connector = solid
height = 5
[FGENES]
glyph = transcript2
bgcolor = green
description = 1
The configuration section is divided into a set of sections, each one
labeled with a [section title]. The [general] section specifies global
options for the entire image. Other sections apply to particular
feature types. In the example above, the configuration in the [EST]
section applies to features labeled as ESTs, while the configuration
in the [FGENES] section applies to features labeled as predictions
from the FGENES gene prediction program.
Inside each section is a series of name=value pairs, where the name is
the name of an option to set. You can put whitespace around the = sign
to make it more readable, or even use a colon (:) if you prefer. The
following option names are recognized:
Option Value Example
------ ----- -------
bases Min & max of the sequence range (bp) 1200..60000
width width of the image (pixels) 600
height Height of each graphical element (pixels) 10
glyph Style of each graphical element (see below) transcript
fgcolor Foreground color of each element yellow
bgcolor Background color of each element blue
linewidth Width of lines 3
label Print the feature's name 1
description Whether to print the feature's description 0
bump Elements are not allowed to collide 1
ticks Print tick marks on arrows 1
connector Type of group connector (dashed, hat or solid) dashed
The "bases" and "width" options are only relevant in the [general]
section. They are overridden by the like-named command-line options.
The remainder of the options can be located in any section, but if
present in the [general] section will set defaults for the others.
Colors are English-language color names or Web-style #RRGGBB colors
(see a book on HTML for an explanation). True/false values are 1 for
true, and 0 for false. Numeric ranges can be expressed in start..end
fashion with two dots, or as start-end with a hyphen.
The "glyph" option controls how the features are rendered. The
following glyphs are implemented:
Name Description
---- -----------
box A filled rectangle, nondirectional.
ellipse An oval.
arrow An arrow; can be unidirectional or
bidirectional. It is also capable of displaying
a scale with major and minor tickmarks, and can
be oriented horizontally or vertically.
segments A set of filled rectangles connected by solid
lines. Used for interrupted features, such as
gapped alignments and exon groups.
transcript Similar to segments, but the connecting line is
a "hat" shape, and the direction of
transcription is indicated by a small arrow.
transcript2 Similar to transcript, but the direction of
transcription is indicated by a terminal segment
in the shape of an arrow.
primers Two inward pointing arrows connected by a line. Used for STSs.
The bump option is the most important option for controlling the look
of the image. If set to false (the number 0), then the features are
allowed to overlap. If set to true (the number 1), then the features
will move vertically to avoid colliding. If not specified, bump is
turned on if the number of any given type of sequence feature is
greater than 50.
=head2 Data Section
The data section can follow or proceed the configuration section. The
two sections can also be intermixed. The data section is a tab or
whitespace-delimited file which you can export from a spreadsheet
application or word processor file (be sure to save as text only!)
Here is an example data section:
Cosmid B0511 . 516-619
Cosmid B0511 . 3185-3294
Cosmid B0511 . 10946-11208
Cosmid B0511 . 13126-13511
Cosmid B0511 . 66-208
Cosmid B0511 . 6354-6499
Cosmid B0511 . 13955-14115
EST yk595e6.5 + 3187-3294
EST yk846e07.3 - 11015-11208
EST yk53c10
yk53c10.5 + 18892-19154
yk53c10.3 - 15000-15500,15700-15800
EST yk53c10.5 + 16032-16105
SwissProt PECANEX + 13153-13656 Swedish fish
FGENESH "Gene 1" - 1-205,518-616,661-735,3187-3365,3436-3846 Transmembrane domain
FGENESH "Gene 2" - 16626-17396,17451-17597 Kinase and sushi domains
Each line of the file contains five columns. The columns are:
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