Options

 --width=800
 --width 800
 -width 800
 -w 800

--width

This sets the width of the image, in pixels. The default is 800 pixels.

--range

This sets the range of the region displayed, in base pairs from start to stop. Any of the following formats are accepted:

  --range 1..1000
  --range 1,1000
  --range 1-1000
    

Negative ranges are allowed.

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.

Data Section

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:

 Column #   Description
 --------   -----------

 1          feature type
 2          feature name
 3          strand
 4          coordinates
 5          description

Feature type

The feature type should correspond to one of the [feature type] headings in the configuration section. If it doesn't, the [general] options will be applied to the feature when rendering it. The feature name is a name for the feature. Use a "." or "-" if this is not relevant. If the name contains whitespace, put single or double quotes ("") around the name.

Strand

The strand indicates which strand the feature is on. It is one of "+" for the forward strand, "-" for the reverse strand, or "." for features that are not stranded.

Coordinates

The coordinates column is a set of one or more ranges that the feature occupies. Ranges are written using ".." as in start..stop, or with hyphens, as in start-stop. For features that are composed of multiple ranges &em; for example transcripts that have multiple exons &em; you can either put the ranges on the same line separated by commas or spaces, or put the ranges on individual lines and just use the same feature name and type to group them. In the example above, the Cosmid B0511 features use the individual line style, while the FGENESH features use the all-ranges-on-one-line style.

Description

The last column contains some descriptive text. If the description option is set to true, this text will be printed underneath the feature in the rendering.

Finally, it is possible to group related features together. An example is the ESTs yk53c10.5 and yk53c10.3, which are related by being reads from the two ends of the clone yk53c10. To indicate this relationship, generate a section that looks like this:

 EST        yk53c10
            yk53c10.5    +       18892-19154
            yk53c10.3    -       15000-15500,15700-15800

The group is indicated by a line that contains just two columns containing the feature type and a unique name for the group. Follow this line with all the features that form the group, but leave the first column (the feature type) blank. The group will be rendered by drawing a dashed line between all the members of the group. You can change this by specifying a different connector option in the configuration section for this feature type.