The following tutorial was presented as part of the 2011 GMOD Spring Training.
SOBA is a command line tool and web application for analyzing GFF3 annotations. GFF3 is a standard file format for genomic annotation data. SOBA gathers statistics from GFF3 files and renders them as tables and graphs.
The web version of SOBA will produce the following:
In addition, the command line tool (SOBAcl) flexibly produces a much wider variety of tables, figures and graphs based on the data in a GFF3 file as well as the the ability to produce complex and extensible custom reports via a robust template system.
SOBA is intended is a tool for those dealing with genomic sequence annotation who want to view genome wide summaries their annotation files. For example: SOBA would be a useful tool at an annotation jamboree for a newly sequenced organism and when preparing a the resulting genome paper; SOBA would help those developing annotation tools to quickly evaluate updates to their tool; SOBA assists comparative genomics analyses by providing a high-level overview of the genome of multiple organisms. SOBA complements genome browsers by providing a summary of all the features annotated in the genome.
SOBA is built with Perl (and JavaScript for the web interface). The web interface uses CGI::Application as a Perl webapp framework and the JQuery JavaScript library for Web 2.0 effects and AJAX. Both versions of SOBA use the Template Tooklit (TT) to generate html/txt reports, graphviz for the ontology graphs, and GD for charts. Template Toolkit makes extensibility very easy, at least for someone who’s willing to learn the fairly simple template language of TT (you don’t need to know Perl or any other programming to use TT).
Documentation for the web interface to SOBA is available on the Sequence Ontology Wiki as well as via tool-tips on the site itself.
Navigate to the SOBA Web Application with any modern browser that has JavaScript enabled.
| Figure:8 SOBA feature lengths by chromosome |
We can constrain the features reported in other ways as well.
SOBAcl --columns seqid --rows type --data length --data_type mean --layout table --format text --select 'start => [">=", "1000"], end => ["<=", "1000000"]' hsap_hg18_demo.gff3
SOBAcl has support for more complex reports.
SOBAcl --report attributes --format html_page hsap_hg18_demo.gff3
These reports can be generated by custom templates.
SOBAcl --columns file --rows type --data length --data_type mean --layout table --format tab --template soba_custom_template_text.tt hsap_hg18_demo.gff3
count length (mean)
CDS 11944 165.853064300067
contig 3 229900897.333333
exon 12918 288.366697631212
five_prime_UTR 1381 597.052136133237
gene 1157 67319.117545376
mRNA 1085 70187.8202764977
ncRNA 72 24089.3611111111
three_prime_UTR 1385 569.969675090253