Provided by: libbio-graphics-perl_2.40-3_all bug

NAME -- Render a Bio::Graphics Feature File

SYNOPSIS [options] file.txt [file2.txt...] > rendering.png [options] file.txt [file2.txt...] | display -


       The script is a thin front end around the Bio::Graphics module.  It
       accepts a list of files containing sequence (protein, nucleotide) feature coordinates from
       the file(s) listed on the command line or on standard input, renders them, and produces a
       PNG file on standard output.

       This script uses GNU-style long options.  This allows you to specify the image width
       option, for example, with any of the following alternative forms:

        --width 800
        -width 800
        -w 800

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

           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.

Feature Files Format

       This script accepts and processes sequence annotations in a simple tab-delimited format or
       in GFF format.

       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.

   Configuration Section
       If not provided, this scripts generates a reasonable default configuration section for
       you, so you do not need to provide a 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
        bases = -1000..21000
        height = 12

        glyph = segments
        bgcolor= yellow
        connector = dashed
        height = 5

        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

         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
       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

       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.

           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.

           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

           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


       Please report them to the author.




       Lincoln Stein,