feature_draw.pl [options] file.txt [file2.txt...] > rendering.png feature_draw.pl [options] file.txt [file2.txt...] | display -
--width=800 --width 800 -width 800 -w 800
The feature file format has a configuration section and a data section. The configuration section sets up the size and overall properties of the image, and the data section gives the feature data itself.
# 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.
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
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.