/ 
Bio-Graphics-1.00
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Graphics::FeatureFile

NAME

Bio::Graphics::FeatureFile - Parse a simple feature file format into a form suitable for rendering

SYNOPSIS

This package parses and renders a simple tab-delimited format for features. It is simpler than GFF, but still has a lot of expressive power.

Documentation is pending, but see the file format here, and eg/feature_draw.pl for an example of usage.

# file begins
[general]
pixels = 1024
bases = 1-20000
height = 12

[Cosmid]
glyph = segments
fgcolor = blue
key = C. elegans conserved regions

[EST]
glyph = segments
bgcolor= yellow
connector = dashed
height = 5;

[FGENESH]
glyph = transcript2
bgcolor = green
description = 1

Cosmid	B0511	+	516-619
Cosmid	B0511	+	3185-3294
Cosmid	B0511	+	10946-11208
Cosmid	B0511	+	13126-13511
Cosmid	B0511	+	11394-11539
Cosmid	B0511	+	14383-14490
Cosmid	B0511	+	15569-15755
Cosmid	B0511	+	18879-19178
Cosmid	B0511	+	15850-16110
Cosmid	B0511	+	66-208
Cosmid	B0511	+	6354-6499
Cosmid	B0511	+	13955-14115
Cosmid	B0511	+	7985-8042
Cosmid	B0511	+	11916-12046
EST	yk260e10.5	+	15569-15724
EST	yk672a12.5	+	537-618,3187-3294
EST	yk595e6.5	+	552-618
EST	yk595e6.5	+	3187-3294
EST	yk846e07.3	+	11015-11208
EST	yk53c10
	yk53c10.3	+	15000-15500,15700-15800
	yk53c10.5	+	18892-19154
EST	yk53c10.5	+	16032-16105
SwissProt	PECANEX	+	13153-13656	Swedish fish
FGENESH	Predicted gene 1	-	1-205,518-616,661-735,3187-3365,3436-3846	Pfam domain
FGENESH	Predicted gene 2	+	5513-6497,7968-8136,8278-8383,8651-8839,9462-9515,10032-10705,10949-11340,11387-11524,11765-12067,12876-13577,13882-14121,14169-14535,15006-15209,15259-15462,15513-15753,15853-16219	Mysterious
FGENESH	Predicted gene 3	-	16626-17396,17451-17597
FGENESH	Predicted gene 4	+	18459-18722,18882-19176,19221-19513,19572-19835	Transmembrane protein
# file ends

SEE ALSO

Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Feature, Bio::Graphics::FeatureFile

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.