Validate GFF/BED/WIG/FASTA input, give helpful feedback
Reported by Ian Holmes | July 8th, 2009 @ 12:56 PM
JBrowse server scripts currently give little or no (or cryptic) feedback about invalid input data. This problem gets much worse for the TWiki plugin (where interactive inspection of the command-line error logs, output files, etc., is impossible). Even Lincoln accidentally uploaded an invalid GFF3 file & was then perplexed by the lack of input; if the maintainer of the GFF3 spec does that, we can reasonably expect others to make the same mistake.
Things to validate (as well as standard format glitches): do the sequence names match up between GFF and FASTA files? Any blank or malformed lines? Any empty (unannotated) chromosomes? Any zero-length sequences in the FASTA? etc.
Feedback should be in the form of a generated HTML page (or snippet), so that it can be displayed in an embedding CMS application, such as TWiki.
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AJAX Genome Browser
Ian Holmes
Mitch