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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 = dashed
 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: