[ensembl-dev] BED file format on custom track

[Anne Lyle]

Hi Liam



> On 10 Oct 2016, at 14:44, Liam Thompson <dejmail at gmail.com> wrote:
> 
> 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 <http://textuploader.com/d5ry1>

Sorry about that - I got called into a meeting and didn’t have a chance to reboot the servers to pick up the code fix. You should find that your files work now.

> 
> 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.

That’s a great suggestion, and one we’d like to implement, but at the moment we don’t have full validation across all formats so it would be of limited functionality. I will however put it into a development ticket, to be addressed in due course.


Cheers

Anne

> 
> 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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>> 
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