FREND(1) User Contributed Perl Documentation FREND(1)NAMEfrend.pl-- Render a Bio::Graphics Feature File on the web
SYNOPSIS
http://your.host.com/cgi-bin/frend.pl
DESCRIPTION
The frend.pl 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.
INSTALLATION
Copy this script into your web site's cgi-bin directory. Name it
whatever you want.
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
[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.
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:
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.
BUGS
Please report them to the author.
SEE ALSO
Bio::Graphics, feature_draw.pl
AUTHOR
Lincoln Stein, lstein@cshl.org
perl v5.14.1 2011-07-22 FREND(1)
