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.