GMOD/jbrowse — Issue #56: Validate GFF/BED/WIG/FASTA input, give helpful feedback
Author: jbrowsetix
Created: 2012-01-25 19:48:11+00:00
State: open
Labels: @Mitch, from-lighthouse, |S| new

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.

[original LH ticket](http://jbrowse.lighthouseapp.com/projects/23792/tickets/28)

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