[ensembl-dev] BED file format on custom track

Mon Oct 10 19:36:09 BST 2016

Hi Anne

Thanks for rebooting. It still doesn't work, so there is probably 
something rather wrong with my files formatting. I will wait to see if 
the ticket you created throws me some hints.

Thanks for assisting

Regards
Liam

On 2016-10-10 16:40, Anne Lyle wrote:
> Hi Liam
>
>
>
>> On 10 Oct 2016, at 14:44, Liam Thompson <dejmail at gmail.com
>> <mailto: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
>
> 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
>>>> <mailto: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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