[ensembl-dev] BED file format on custom track

Liam Thompson dejmail at gmail.com
Mon Oct 10 14:44:00 BST 2016


Hi Anne

Thank you for looking at that. I can't confirm that it has been fixed as 
my bed file still doesn't validate. I am still getting "There was a 
problem uploading your data: File did not validate as format BED.
Please try again."

The file seems to work fine on Genoverse, although UCSC is now giving me 
hassles.

I have left a modified version at http://textuploader.com/d5ry1

It would be really helpful if the validation logic could output what it 
is about the validation that has failed, because as it stands I am just 
fiddling around in the dark. However I don't know how easy that is to do 
on your system.

Many thanks
Liam






On 2016-10-10 14:54, Anne Lyle wrote:
> Hi Liam
>
> As I suspected, there was a logic error in the validation code. I’m just pushing the fix out to our servers this afternoon.
>
> Regards
>
> Anne
>
>
>
> Anne Lyle
> Senior Ensembl Web Developer
> EMBL-EBI, Wellcome Trust Genome Campus
> Cambridge CB10 1SD, UK
> Tel: +44-(0)1223-494178
>
>
>
>> On 6 Oct 2016, at 14:29, Liam Thompson <dejmail at gmail.com> wrote:
>>
>> Hi Anne
>>
>> I retried the GFF file on the Genoverse browser, and it loads fine and displays correctly (albeit in need of some tweaking), but still no luck on Ensembl.
>>
>> I have uploaded the file in case you want to see what is different with it, compared to the validator does.
>>
>> http://textuploader.com/dabl6
>>
>> Kind regards
>> Liam
>>
>> On 2016-10-06 11:36, Anne Lyle wrote:
>>> Hi Liam
>>>
>>> BED should be fine - I’ll have a look at your file and see if there’s some reason it’s breaking our validator. The validation is quite new code, so there may be an error in its logic.
>>>
>>> Cheers
>>>
>>> Anne
>>>
>>>
>>>> On 5 Oct 2016, at 19:01, Liam Thompson <dejmail at gmail.com> wrote:
>>>>
>>>> Hi Anne
>>>>
>>>> Thanks for the reply. I'm working from a Linux system, but not sure that
>>>> makes any difference.
>>>>
>>>> I have just tried it on Firefox v. 49, and the uploader just doesn't
>>>> seem to go anywhere, so I can confirm that behaviour. It also happens in
>>>> Private mode, so it's not a plugin.
>>>>
>>>> I tried in Google Chrome (53.0.2785.143 (64-bit)) normal and
>>>> Private/Incognito mode and the same thing happens.
>>>>
>>>> Is there another file format you would recommend that I can use to
>>>> display short sequences of interest in a track in the genome browser ?
>>>>
>>>> Kind regards
>>>> Liam
>>>>
>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 2
>>>>> Date: Wed, 5 Oct 2016 17:14:57 +0100
>>>>> From: Anne Lyle <annelyle at ebi.ac.uk>
>>>>> Subject: Re: [ensembl-dev] BED file format on custom track
>>>>> To: Ensembl developers list <dev at ensembl.org>
>>>>> Message-ID: <3FBA2DBE-8EB3-4317-9785-A1FD61902772 at ebi.ac.uk>
>>>>> Content-Type: text/plain; charset=utf-8
>>>>>
>>>>> Hi Liam
>>>>>
>>>>> Are you using Firefox (version 49) by any chance? We?ve seen some upload issues in this browser, so it could be related. If not, I?ll have a look at your file and see if there?s any reason why our parser isn?t reading it correctly.
>>>>>
>>>>> Cheers
>>>>>
>>>>> Anne
>>>>
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