[Gmod-ajax] JBrowse view on locus

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[Gmod-ajax] JBrowse view on locus

pparsons
Hi,

Please forgive the simple question. I think it is probably a conceptual rather than technical problem. 

I'm trying to figure out how to convert a locus such as 1p21.1 into a location that JBrowse will recognize. I am doing a query to the NCBI nucleotide database and getting loci as a result. I specifically would like to change the view of JBrowse using a URL query string (as explained here: http://gmod.org/wiki/JBrowse_Configuration_Guide#Controlling_JBrowse_with_the_URL_Query_String), and my "location" is in the locus form that I mentioned above.

Thanks,
Paul

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Re: JBrowse view on locus

Robert Buels-2
If you have your loci loaded in JBrowse, and their names indexed, you
can just put the locus name in the "loc" variable in the JBrowse URL and
JBrowse will go to it on load, like "loc=1p21.1".  If you can search for
it in the location box, you can use it in the "loc" part of the URL.

Does that do what you need?


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


On 11/18/2013 06:49 PM, Paul Parsons wrote:

> Hi,
>
> Please forgive the simple question. I think it is probably a conceptual
> rather than technical problem.
>
> I'm trying to figure out how to convert a locus such as 1p21.1 into a
> location that JBrowse will recognize. I am doing a query to the NCBI
> nucleotide database and getting loci as a result. I specifically would
> like to change the view of JBrowse using a URL query string (as
> explained here:
> http://gmod.org/wiki/JBrowse_Configuration_Guide#Controlling_JBrowse_with_the_URL_Query_String),
> and my "location" is in the locus form that I mentioned above.
>
> Thanks,
> Paul
>
>
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Re: JBrowse view on locus

pparsons
I don't think it can work that way. The setup I have is the following: a user goes to a website and enters a query (e.g., brca1). The website queries the NCBI nucleotide database using entrez eutils. Some data is returned, which is then parsed to extract gene names, descriptions, and locations. So one result might be: gene--RRM1, desc--ribonucleotide reductase M1, locus--11p15.5. The user should be able to click on that and go to that location in JBrowse. Right now I have the reference genome loaded in JBrowse, so there is no problem displaying chromosome 11. I just don't know how to point it to the specific location on that chromosome. And I don't think I can have loci loaded in JBrowse as you suggest, because I don't know ahead of time what the user will search for.

If there is a better way to do what I'm trying to do just let me know. I'm new to this stuff, and I'm modelling my code after some old code that was supposedly working with GBrowse using the same approach but is not working anymore.

Thanks for your help.


On Tue, Nov 19, 2013 at 8:38 AM, Robert Buels <[hidden email]> wrote:
If you have your loci loaded in JBrowse, and their names indexed, you can just put the locus name in the "loc" variable in the JBrowse URL and JBrowse will go to it on load, like "loc=1p21.1".  If you can search for it in the location box, you can use it in the "loc" part of the URL.

Does that do what you need?


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



On 11/18/2013 06:49 PM, Paul Parsons wrote:
Hi,

Please forgive the simple question. I think it is probably a conceptual
rather than technical problem.

I'm trying to figure out how to convert a locus such as 1p21.1 into a
location that JBrowse will recognize. I am doing a query to the NCBI
nucleotide database and getting loci as a result. I specifically would
like to change the view of JBrowse using a URL query string (as
explained here:
http://gmod.org/wiki/JBrowse_Configuration_Guide#Controlling_JBrowse_with_the_URL_Query_String),
and my "location" is in the locus form that I mentioned above.

Thanks,
Paul


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Re: JBrowse view on locus

Robert Buels-2
If you know the location of the locus, from eutils or however, you can
put that in the loc in the URL like loc=chr1:1234..5678 and JBrowse will
come up at that location.

But of course, in that location, it will display what you have
configured it to display.


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

On 11/19/2013 01:58 PM, Paul Parsons wrote:

> I don't think it can work that way. The setup I have is the following: a
> user goes to a website and enters a query (e.g., brca1). The website
> queries the NCBI nucleotide database using entrez eutils. Some data is
> returned, which is then parsed to extract gene names, descriptions, and
> locations. So one result might be: gene--RRM1, desc--ribonucleotide
> reductase M1, locus--11p15.5. The user should be able to click on that
> and go to that location in JBrowse. Right now I have the reference
> genome loaded in JBrowse, so there is no problem displaying chromosome
> 11. I just don't know how to point it to the specific location on that
> chromosome. And I don't think I can have loci loaded in JBrowse as you
> suggest, because I don't know ahead of time what the user will search for.
>
> If there is a better way to do what I'm trying to do just let me know.
> I'm new to this stuff, and I'm modelling my code after some old code
> that was supposedly working with GBrowse using the same approach but is
> not working anymore.
>
> Thanks for your help.
>
>
> On Tue, Nov 19, 2013 at 8:38 AM, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     If you have your loci loaded in JBrowse, and their names indexed,
>     you can just put the locus name in the "loc" variable in the JBrowse
>     URL and JBrowse will go to it on load, like "loc=1p21.1".  If you
>     can search for it in the location box, you can use it in the "loc"
>     part of the URL.
>
>     Does that do what you need?
>
>
>     Robert Buels
>     Lead Developer
>     JBrowse - http://jbrowse.org
>
>
>
>     On 11/18/2013 06:49 PM, Paul Parsons wrote:
>
>         Hi,
>
>         Please forgive the simple question. I think it is probably a
>         conceptual
>         rather than technical problem.
>
>         I'm trying to figure out how to convert a locus such as 1p21.1
>         into a
>         location that JBrowse will recognize. I am doing a query to the NCBI
>         nucleotide database and getting loci as a result. I specifically
>         would
>         like to change the view of JBrowse using a URL query string (as
>         explained here:
>         http://gmod.org/wiki/JBrowse___Configuration_Guide#__Controlling_JBrowse_with_the___URL_Query_String
>         <http://gmod.org/wiki/JBrowse_Configuration_Guide#Controlling_JBrowse_with_the_URL_Query_String>),
>         and my "location" is in the locus form that I mentioned above.
>
>         Thanks,
>         Paul
>
>
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>
>
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Re: JBrowse view on locus

pparsons
Thanks again. For anyone who is interested, here is the solution I discovered to this particular problem. An additional query to the NCBI Gene database using entrez eutils is needed. The input to the query is the gene name that the user wants to see. The result of the query can be parsed to get the sequence start and end, and then plug that into the url for JBrowse as loc="[seqstart..end]".


On Tue, Nov 19, 2013 at 2:09 PM, Robert Buels <[hidden email]> wrote:
If you know the location of the locus, from eutils or however, you can put that in the loc in the URL like loc=chr1:1234..5678 and JBrowse will come up at that location.

But of course, in that location, it will display what you have configured it to display.



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

On 11/19/2013 01:58 PM, Paul Parsons wrote:
I don't think it can work that way. The setup I have is the following: a
user goes to a website and enters a query (e.g., brca1). The website
queries the NCBI nucleotide database using entrez eutils. Some data is
returned, which is then parsed to extract gene names, descriptions, and
locations. So one result might be: gene--RRM1, desc--ribonucleotide
reductase M1, locus--11p15.5. The user should be able to click on that
and go to that location in JBrowse. Right now I have the reference
genome loaded in JBrowse, so there is no problem displaying chromosome
11. I just don't know how to point it to the specific location on that
chromosome. And I don't think I can have loci loaded in JBrowse as you
suggest, because I don't know ahead of time what the user will search for.

If there is a better way to do what I'm trying to do just let me know.
I'm new to this stuff, and I'm modelling my code after some old code
that was supposedly working with GBrowse using the same approach but is
not working anymore.

Thanks for your help.


On Tue, Nov 19, 2013 at 8:38 AM, Robert Buels <[hidden email]
<mailto:[hidden email]>> wrote:

    If you have your loci loaded in JBrowse, and their names indexed,
    you can just put the locus name in the "loc" variable in the JBrowse
    URL and JBrowse will go to it on load, like "loc=1p21.1".  If you
    can search for it in the location box, you can use it in the "loc"
    part of the URL.

    Does that do what you need?


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



    On 11/18/2013 06:49 PM, Paul Parsons wrote:

        Hi,

        Please forgive the simple question. I think it is probably a
        conceptual
        rather than technical problem.

        I'm trying to figure out how to convert a locus such as 1p21.1
        into a
        location that JBrowse will recognize. I am doing a query to the NCBI
        nucleotide database and getting loci as a result. I specifically
        would
        like to change the view of JBrowse using a URL query string (as
        explained here:
        http://gmod.org/wiki/JBrowse___Configuration_Guide#__Controlling_JBrowse_with_the___URL_Query_String
        <http://gmod.org/wiki/JBrowse_Configuration_Guide#Controlling_JBrowse_with_the_URL_Query_String>),

        and my "location" is in the locus form that I mentioned above.

        Thanks,
        Paul


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        Shape the Mobile Experience: Free Subscription
        Software experts and developers: Be at the forefront of tech
        innovation.
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        conversations that shape the rapidly evolving mobile landscape.
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