1FEATURE_DRAW(1) User Contributed Perl Documentation FEATURE_DRAW(1)
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6 feature_draw.pl -- Render a Bio::Graphics Feature File
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9 feature_draw.pl [options] file.txt [file2.txt...] > rendering.png
10 feature_draw.pl [options] file.txt [file2.txt...] | display -
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13 The feature_draw.pl script is a thin front end around the Bio::Graphics
14 module. It accepts a list of files containing sequence (protein,
15 nucleotide) feature coordinates from the file(s) listed on the command
16 line or on standard input, renders them, and produces a PNG file on
17 standard output.
18 Options
20 This script uses GNU-style long options. This allows you to specify
21 the image width option, for example, with any of the following
22 alternative forms:
23 --width=800
25 --width 800
26 -width 800
27 -w 800
28 --width
30 This sets the width of the image, in pixels. The default is 800
31 pixels.
32 --range
34 This sets the range of the region displayed, in base pairs from
35 start to stop. Any of the following formats are accepted:
36 --range 1..1000
38 --range 1,1000
39 --range 1-1000
40 Negative ranges are allowed.
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44 This script accepts and processes sequence annotations in a simple tab-
45 delimited format or in GFF format.
46 The feature file format has a configuration section and a data section.
48 The configuration section sets up the size and overall properties of
49 the image, and the data section gives the feature data itself.
50 Configuration Section
52 If not provided, this scripts generates a reasonable default
53 configuration section for you, so you do not need to provide a
54 configuration section to get a reasonable image. However, to tune the
55 appearance of the image, you will probably want to tweak the
56 configuration. Here is an excerpt from the configuration section:
57 # example file
59 [general]
60 bases = -1000..21000
61 height = 12
62 [EST]
64 glyph = segments
65 bgcolor= yellow
66 connector = dashed
67 height = 5
68 [FGENES]
70 glyph = transcript2
71 bgcolor = green
72 description = 1
73 The configuration section is divided into a set of sections, each one
75 labeled with a [section title]. The [general] section specifies global
76 options for the entire image. Other sections apply to particular
77 feature types. In the example above, the configuration in the [EST]
78 section applies to features labeled as ESTs, while the configuration in
79 the [FGENES] section applies to features labeled as predictions from
80 the FGENES gene prediction program.
81 Inside each section is a series of name=value pairs, where the name is
83 the name of an option to set. You can put whitespace around the = sign
84 to make it more readable, or even use a colon (:) if you prefer. The
85 following option names are recognized:
86 Option Value Example
88 ------ ----- -------
89 bases Min & max of the sequence range (bp) 1200..60000
91 width width of the image (pixels) 600
92 height Height of each graphical element (pixels) 10
93 glyph Style of each graphical element (see below) transcript
94 fgcolor Foreground color of each element yellow
95 bgcolor Background color of each element blue
96 linewidth Width of lines 3
97 label Print the feature's name 1
98 description Whether to print the feature's description 0
99 bump Elements are not allowed to collide 1
100 ticks Print tick marks on arrows 1
101 connector Type of group connector (dashed, hat or solid) dashed
102 The "bases" and "width" options are only relevant in the [general]
104 section. They are overridden by the like-named command-line options.
105 The remainder of the options can be located in any section, but if
107 present in the [general] section will set defaults for the others.
108 Colors are English-language color names or Web-style #RRGGBB colors
110 (see a book on HTML for an explanation). True/false values are 1 for
111 true, and 0 for false. Numeric ranges can be expressed in start..end
112 fashion with two dots, or as start-end with a hyphen.
113 The "glyph" option controls how the features are rendered. The
115 following glyphs are implemented:
116 Name Description
118 ---- -----------
119 box A filled rectangle, nondirectional.
121 ellipse An oval.
122 arrow An arrow; can be unidirectional or
123 bidirectional. It is also capable of displaying
124 a scale with major and minor tickmarks, and can
125 be oriented horizontally or vertically.
126 segments A set of filled rectangles connected by solid
127 lines. Used for interrupted features, such as
128 gapped alignments and exon groups.
129 transcript Similar to segments, but the connecting line is
130 a "hat" shape, and the direction of
131 transcription is indicated by a small arrow.
132 transcript2 Similar to transcript, but the direction of
133 transcription is indicated by a terminal segment
134 in the shape of an arrow.
135 primers Two inward pointing arrows connected by a line. Used for STSs.
136 The bump option is the most important option for controlling the look
138 of the image. If set to false (the number 0), then the features are
139 allowed to overlap. If set to true (the number 1), then the features
140 will move vertically to avoid colliding. If not specified, bump is
141 turned on if the number of any given type of sequence feature is
142 greater than 50.
143 Data Section
145 The data section can follow or proceed the configuration section. The
146 two sections can also be intermixed. The data section is a tab or
147 whitespace-delimited file which you can export from a spreadsheet
148 application or word processor file (be sure to save as text only!)
149 Here is an example data section:
151 Cosmid B0511 . 516-619 Cosmid B0511 .
153 3185-3294 Cosmid B0511 . 10946-11208 Cosmid B0511
154 . 13126-13511 Cosmid B0511 . 66-208 Cosmid
155 B0511 . 6354-6499 Cosmid B0511 .
156 13955-14115 EST yk595e6.5 + 3187-3294 EST
157 yk846e07.3 - 11015-11208 EST yk53c10
158 yk53c10.5 + 18892-19154
159 yk53c10.3 - 15000-15500,15700-15800 EST
160 yk53c10.5 + 16032-16105 SwissProt PECANEX +
161 13153-13656 Swedish fish FGENESH "Gene 1" -
162 1-205,518-616,661-735,3187-3365,3436-3846 Transmembrane domain
163 FGENESH "Gene 2" - 16626-17396,17451-17597 Kinase and
164 sushi domains
165 Each line of the file contains five columns. The columns are:
167 Column # Description
169 -------- -----------
170 1 feature type
172 2 feature name
173 3 strand
174 4 coordinates
175 5 description
176 Feature type
178 The feature type should correspond to one of the [feature type]
179 headings in the configuration section. If it doesn't, the [general]
180 options will be applied to the feature when rendering it. The
181 feature name is a name for the feature. Use a "." or "-" if this is
182 not relevant. If the name contains whitespace, put single or double
183 quotes ("") around the name.
184 Strand
186 The strand indicates which strand the feature is on. It is one of
187 "+" for the forward strand, "-" for the reverse strand, or "." for
188 features that are not stranded.
189 Coordinates
191 The coordinates column is a set of one or more ranges that the
192 feature occupies. Ranges are written using ".." as in start..stop,
193 or with hyphens, as in start-stop. For features that are composed
194 of multiple ranges &em; for example transcripts that have multiple
195 exons &em; you can either put the ranges on the same line separated
196 by commas or spaces, or put the ranges on individual lines and just
197 use the same feature name and type to group them. In the example
198 above, the Cosmid B0511 features use the individual line style,
199 while the FGENESH features use the all-ranges-on-one-line style.
200 Description
202 The last column contains some descriptive text. If the description
203 option is set to true, this text will be printed underneath the
204 feature in the rendering.
205 Finally, it is possible to group related features together. An example
207 is the ESTs yk53c10.5 and yk53c10.3, which are related by being reads
208 from the two ends of the clone yk53c10. To indicate this relationship,
209 generate a section that looks like this:
210 EST yk53c10
212 yk53c10.5 + 18892-19154
213 yk53c10.3 - 15000-15500,15700-15800
214 The group is indicated by a line that contains just two columns
216 containing the feature type and a unique name for the group. Follow
217 this line with all the features that form the group, but leave the
218 first column (the feature type) blank. The group will be rendered by
219 drawing a dashed line between all the members of the group. You can
220 change this by specifying a different connector option in the
221 configuration section for this feature type.
222
224 Please report them to the author.
225
227 Bio::Graphics
228
230 Lincoln Stein, lstein@cshl.org
231perl v5.12.0 2010-04-29 FEATURE_DRAW(1)