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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 |
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pyrimidine |
um, wow, 466 pages of GFF3 validation errors from NCBI-generated GFF3 files. ick |
| 19:58 |
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pyrimidine |
(that was from one file of 18, btw) |
| 20:00 |
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pyrimidine |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/special_requests/gff/ame_ref_Amel_4.5_unplaced.gff3.gz |
| 20:07 |
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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 |
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rbuels |
pyrimidine: you actually got a gff3 validator to run to completion on a non-trivially-sized file?? |
| 20:39 |
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rbuels |
:-O |
| 20:39 |
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pyrimidine |
strangely, it seemed to go just fine :) |
| 20:39 |
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rbuels |
which validator? |
| 20:39 |
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pyrimidine |
modencode |
| 20:40 |
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pyrimidine |
http://modencode.oicr.on.ca/cg[…]idate_gff3_online |
| 20:40 |
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pyrimidine |
you know, the one we can never find the source for |
| 20:41 |
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rbuels |
ah |
| 20:44 |
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* pyrimidine |
finds it hugely ironic that there is a *validator* for GFF3 that is essentially closed-source |
| 20:48 |
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rbuels |
erm, i think they put it on github in /gmod |
| 20:48 |
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* rbuels |
looks |
| 20:48 |
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rbuels |
yeah, i think that's it |
| 20:48 |
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rbuels |
https://github.com/GMOD/gff3_validator |
| 20:49 |
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rbuels |
after we prodded them at the evo hackathon |
| 20:59 |
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pyrimidine |
ah, cool, will have a look at that, then |
| 21:00 |
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* pyrimidine |
-> home |
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