Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-08-26

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Time Nick Message
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14:05 Topic for #bioperl is now Be patient!  Sometimes it takes a few minutes for people to notice your question! | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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19:58 pyrimidine um, wow, 466 pages of GFF3 validation errors from NCBI-generated GFF3 files.  ick
19:58 pyrimidine (that was from one file of 18, btw)
20:00 pyrimidine ftp://ftp.ncbi.nlm.nih.gov/genomes/​Apis_mellifera/special_requests/gff​/ame_ref_Amel_4.5_unplaced.gff3.gz
20:07 pyrimidine apparently, they thinks that mRNA ddoesn't exist and that tabs are allowed in the last column.  I'm actually wondering if they bothered reading the specification.
20:38 rbuels pyrimidine:  you actually got a gff3 validator to run to completion on a non-trivially-sized file??
20:39 rbuels :-O
20:39 pyrimidine strangely, it seemed to go just fine :)
20:39 rbuels which validator?
20:39 pyrimidine modencode
20:40 pyrimidine http://modencode.oicr.on.ca/​cgi-bin/validate_gff3_online
20:40 pyrimidine you know, the one we can never find the source for
20:41 rbuels ah
20:44 * pyrimidine finds it hugely ironic that there is a *validator* for GFF3 that is essentially closed-source
20:48 rbuels erm, i think they put it on github in /gmod
20:48 * rbuels looks
20:48 rbuels yeah, i think that's it
20:48 rbuels https://github.com/GMOD/gff3_validator
20:49 rbuels after we prodded them at the evo hackathon
20:59 pyrimidine ah, cool, will have a look at that, then
21:00 * pyrimidine -> home
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