[Gmod-ajax] Fwd: JBrowse 1.11.1 Labels and Search

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[Gmod-ajax] Fwd: JBrowse 1.11.1 Labels and Search

Masa Roller
Dear all,

I am having two issues with the newest installation of JBrowse 1.11.1.

1. The tracks which I configured to show labels (which was working fine
in JBrowse 1.10.x we had before) are no longer showing their labels in
the browser. The example Volvox date shows labels just fine, and I
copied over the configuration for my data from our old 1.10.x JBrowse.

2. I set up the search function to search the names of my genes and
transcripts. The names are all predicted with homology to known
databases so they all start with "PREDICTED". E.g. "PREDICTED similar to
gi|148700221|gb|EDL32168.1| cadherin 23 (otocadherin)". When searching
these names through the search box, PREDICTED will give a selection of
all the names, but I cannot search for a word in the middle, for example
"cadherin". That gives no matches.
Is JBrowse only looking from exact matches from the beginning of the
name? Can I somehow set up wildcard search?
I vaguely remember from an old GBrowse we had that the searching worked
better.

Thank you in advance,
Masa Roller



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Re: Fwd: JBrowse 1.11.1 Labels and Search

Robert Buels-2
On 02/13/2014 05:09 AM, Masa Roller wrote:
> 1. The tracks which I configured to show labels (which was working
> fine in JBrowse 1.10.x we had before) are no longer showing their
> labels in the browser. The example Volvox date shows labels just
> fine, and I copied over the configuration for my data from our old
> 1.10.x JBrowse.

Try clearing your browser's cache, does that help?  Otherwise, could you
send me a URL that demonstrates the problem, if it's public?

> 2. I set up the search function to search the names of my genes and
> transcripts. The names are all predicted with homology to known
> databases so they all start with "PREDICTED". E.g. "PREDICTED similar
> to gi|148700221|gb|EDL32168.1| cadherin 23 (otocadherin)". When
> searching these names through the search box, PREDICTED will give a
> selection of all the names, but I cannot search for a word in the
> middle, for example "cadherin". That gives no matches. Is JBrowse
> only looking from exact matches from the beginning of the name? Can I
> somehow set up wildcard search? I vaguely remember from an old
> GBrowse we had that the searching worked better.

JBrowse's static-file name indexing backend only searches for partial
names from the beginning of words, it doesn't support wildcard searches
from the middle (like *cadherin*).  It has a REST backend for name
searching, though, so if you have the inclination you might consider
using that to hook JBrowse up to your own name index and see how that goes.



Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

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Re: Fwd: JBrowse 1.11.1 Labels and Search

Masa Roller


On 13.2.2014. 13:57, Robert Buels wrote:

> On 02/13/2014 05:09 AM, Masa Roller wrote:
>> 1. The tracks which I configured to show labels (which was working
>> fine in JBrowse 1.10.x we had before) are no longer showing their
>> labels in the browser. The example Volvox date shows labels just
>> fine, and I copied over the configuration for my data from our old
>> 1.10.x JBrowse.
>
> Try clearing your browser's cache, does that help?  Otherwise, could you
> send me a URL that demonstrates the problem, if it's public?
>

I always clear the cache. It's not that. Unfortunately I cannot share
this yet, but this is not that big an issue.

>> 2. I set up the search function to search the names of my genes and
>> transcripts. The names are all predicted with homology to known
>> databases so they all start with "PREDICTED". E.g. "PREDICTED similar
>> to gi|148700221|gb|EDL32168.1| cadherin 23 (otocadherin)". When
>> searching these names through the search box, PREDICTED will give a
>> selection of all the names, but I cannot search for a word in the
>> middle, for example "cadherin". That gives no matches. Is JBrowse
>> only looking from exact matches from the beginning of the name? Can I
>> somehow set up wildcard search? I vaguely remember from an old
>> GBrowse we had that the searching worked better.
>
> JBrowse's static-file name indexing backend only searches for partial
> names from the beginning of words, it doesn't support wildcard searches
> from the middle (like *cadherin*).  It has a REST backend for name
> searching, though, so if you have the inclination you might consider
> using that to hook JBrowse up to your own name index and see how that goes.
>

This is a bigger issue. I've looked into the REST backend with JBrowse
and the documentation is not that detailed. I am afraid that it would be
a lot of work.
Given that I really do not have that many names I need a wildcard search
for (~40,000 total), do you think I could do a simpler workaround in
this manner: edit the .json files in the names directory to include all
possible partials?
i.e. in the above example add to the index ""PREDICTED similar
to gi|148700221|gb|EDL32168.1| cadherin 23 (otocadherin)" and
"gi|148700221|gb|EDL32168.1| cadherin 23 (otocadherin)" and "cadherin 23
(otocadherin)"?
I don't know how much this would slow things down...

Thanks for the help!
Masa

>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org

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