Ideograms are drawn incorrectly after upgrading to GBrowse 1.70

[Bill Pulec]

Hi All,
    I recently upgraded to gbrowse 1.70. The upgrade seems to have worked except now the ideogram tracks that displayed correctly before no longer display correctly. It seems as if gbrowse is drawing each region of the chromosome as a separate chromosome. The border cuts between regions making it hard to tell where the region boundries are.(This is a little hard to explain so I included an attached Image) I noticed there is a new version of ideogram.pm dated 2009/05/20 the one I was previously using was 2008/04/17. To see if this was the issue I checked to see if the old ideogram.pm would work, but the same issue still arises. I have also include my configuration settings and an example from the gff below.

Thanks,
Bill


[CYT:overview]
feature       = chromosome_band centromere
glyph         = ideogram
fgcolor       = black
bgcolor       = gneg:white gpos25:silver gpos50:gray gpos:gray  gpos75:darkgray gpos100:black acen:cen gvar:var
arcradius     = 5
height        = 15
bump          = 0

chr11    UCSC    chromosome_band    1    1000000    .    .    .    Parent=11;label=tip;Alias tip;stain tip
chr11    UCSC    centromere    1000001    3000000    .    .    .    Parent=11;label=11_cent;Alias 11_cent
chr11    UCSC    chromosome_band    3000000    9289765    .    .    .    Parent=11;label=A1;Alias A1;stain gpos100


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looking to deploy the next generation of Solaris that includes the latest
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[Lincoln Stein]

If you are using the Bio::DB::GFF adaptor, could you try instead using Bio::DB::SeqFeature::Store? This will help track down the problem.

Lincoln

On Fri, Jun 5, 2009 at 3:21 PM, Bill Pulec <wpulec@...> wrote:

Hi All,
    I recently upgraded to gbrowse 1.70. The upgrade seems to have worked except now the ideogram tracks that displayed correctly before no longer display correctly. It seems as if gbrowse is drawing each region of the chromosome as a separate chromosome. The border cuts between regions making it hard to tell where the region boundries are.(This is a little hard to explain so I included an attached Image) I noticed there is a new version of ideogram.pm dated 2009/05/20 the one I was previously using was 2008/04/17. To see if this was the issue I checked to see if the old ideogram.pm would work, but the same issue still arises. I have also include my configuration settings and an example from the gff below.

Thanks,
Bill


[CYT:overview]
feature       = chromosome_band centromere
glyph         = ideogram
fgcolor       = black
bgcolor       = gneg:white gpos25:silver gpos50:gray gpos:gray  gpos75:darkgray gpos100:black acen:cen gvar:var
arcradius     = 5
height        = 15
bump          = 0

chr11    UCSC    chromosome_band    1    1000000    .    .    .    Parent=11;label=tip;Alias tip;stain tip
chr11    UCSC    centromere    1000001    3000000    .    .    .    Parent=11;label=11_cent;Alias 11_cent
chr11    UCSC    chromosome_band    3000000    9289765    .    .    .    Parent=11;label=A1;Alias A1;stain gpos100

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
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Gmod-gbrowse mailing list
Gmod-gbrowse@...
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
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