Thread: [Gmod-ajax] filter_by_location in Bio::DB::SeqFeature::Store::memory

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gmod-ajax

[Gmod-ajax] filter_by_location in Bio::DB::SeqFeature::Store::memory

From: Mitch S. <mit...@be...> - 2010-01-14 22:26:25

Attachments: casbon.gff3 bdsfsm-filter_by_location.patch

Hi,

Some people haven't been getting all of the features in their GFF3 into 
JBrowse, and a nice test case that James Casbon posted to the list 
helped me track it down.

Here's an example of the behavior I was seeing with BioPerl 1.6.1 (using 
Devel::REPL):

==============
$ use Bio::DB::SeqFeature::Store

$ my $db = Bio::DB::SeqFeature::Store->new(-adaptor=>"memory", 
-dsn=>"casbon.gff3")
$Bio_DB_SeqFeature_Store_memory1 = 
Bio::DB::SeqFeature::Store::memory=HASH(0xa27ceec);

$ $db->features(-seq_id=>"CYP2C8")
$ARRAY1 = [
             Feature:src(41),
             region(CYP2C8),
             Feature:src(37),
             Feature:src(39),
             Feature:src(42),
             Feature:src(40),
             Feature:src(38)
           ];
==============

I expected to also see the features with IDs 43 and 44 (the gff3 file is 
attached).

I think there's a problem in the filter_by_location method.  If start 
and end parameters aren't passed to the method, it sets default start 
and end values that lead it to examine all of the bins in its index.  
But the end value that it creates is at the beginning of the last bin, 
and I think it should be at the end of the last bin instead.  The 
attached patch changes it to be at the end of the last bin.

Regards,
Mitch

Re: [Gmod-ajax] [Bioperl-l] filter_by_location in Bio::DB::SeqFeature::Store::memory

From: Christopher F. <cjf...@gm...> - 2010-01-15 06:36:11

<html><body class="ApplePlainTextBody" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Mitch,<br><br>I went ahead and committed that fix (r16695), seems to pass all SeqFeature::Store tests using mem, BDB, mysql. &nbsp;thanks for the patch!<br><br>chris<br><br>On Jan 14, 2010, at 4:10 PM, Mitch Skinner wrote:<br><br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Some people haven't been getting all of the features in their GFF3 into JBrowse, and a nice test case that James Casbon posted to the list helped me track it down.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Here's an example of the behavior I was seeing with BioPerl 1.6.1 (using Devel::REPL):<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">==============<br></blockquote><blockquote type="cite">$ use Bio::DB::SeqFeature::Store<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">$ my $db = Bio::DB::SeqFeature::Store-&gt;new(-adaptor=&gt;"memory", -dsn=&gt;"casbon.gff3")<br></blockquote><blockquote type="cite">$Bio_DB_SeqFeature_Store_memory1 = Bio::DB::SeqFeature::Store::memory=HASH(0xa27ceec);<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">$ $db-&gt;features(-seq_id=&gt;"CYP2C8")<br></blockquote><blockquote type="cite">$ARRAY1 = [<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;Feature:src(41),<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;region(CYP2C8),<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;Feature:src(37),<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;Feature:src(39),<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;Feature:src(42),<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;Feature:src(40),<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;Feature:src(38)<br></blockquote><blockquote type="cite">&nbsp;&nbsp; &nbsp; &nbsp;];<br></blockquote><blockquote type="cite">==============<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I expected to also see the features with IDs 43 and 44 (the gff3 file is attached).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I think there's a problem in the filter_by_location method. &nbsp;If start and end parameters aren't passed to the method, it sets default start and end values that lead it to examine all of the bins in its index. &nbsp;But the end value that&nbsp;it creates is at the beginning of the last bin, and I think it should be at the end of the last bin instead. &nbsp;The attached patch changes it to be at the end of the last bin.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Regards,<br></blockquote><blockquote type="cite">Mitch<br></blockquote><blockquote type="cite">&lt;casbon.gff3&gt;&lt;bdsfsm-filter_by_location.patch&gt;_______________________________________________<br></blockquote><blockquote type="cite">Bioperl-l mailing list<br></blockquote><blockquote type="cite">Bio...@li...<br></blockquote><blockquote type="cite">http://lists.open-bio.org/mailman/listinfo/bioperl-l<br></blockquote><br></body></html>

[Gmod-ajax] installing multiple browsers on a single server

From: Brenton G. <brg...@gm...> - 2010-03-01 20:37:08

Hi Mitch, 

I have a question about how you recommend installing browsers for multiple organisms on a  single server?  I am currently doing this by installing JBrowse in separate folders on the server, but this seems inefficient since I have multiple copies of the source code that each browser is using.  What is the best way of doing this?

Thanks,

Brent

Re: [Gmod-ajax] installing multiple browsers on a single server

From: James C. <ca...@gm...> - 2010-03-02 09:11:17

On 1 March 2010 20:36, Brenton Graveley <brg...@gm...> wrote:
> Hi Mitch,
>
> I have a question about how you recommend installing browsers for multiple organisms on a  single server?  I am currently doing this by installing JBrowse in separate folders on the server, but this seems inefficient since I have multiple copies of the source code that each browser is using.  What is the best way of doing this?

Have two index.htmls, in the browser construction point to different
locations for dataRoot but one location for browserRoot:

eg:
           var b = new Browser({
                                   containerID: "GenomeBrowser",
                                   refSeqs: refSeqs,
                                   trackData: trackInfo,
                                   defaultTracks: "DNA,gene,mRNA,noncodingRNA",
                                   location: queryParams.loc,
                                   tracks: queryParams.tracks,
                                   bookmark: bookmarkCallback,
                                   browserRoot: CODE_PATH,
                                   dataRoot: DATA_PATH
                               });

James