Bio::Graphics::FeatureFile - Parse a simple feature file format into a form suitable for rendering
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
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Feature, Bio::Graphics::FeatureFile
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.
To install Bio::Graphics::Panel, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Graphics::Panel
CPAN shell
perl -MCPAN -e shell install Bio::Graphics::Panel
For more information on module installation, please visit the detailed CPAN module installation guide.