|

Bio-Informatics

»

Generic Model Organism System Database

»

URL links in gbrowse 2, cont

View: New views

3 Messages — Rating Filter: Alert me

	URL links in gbrowse 2, cont by Maureen J. Donlin :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message I've continued to play with the code trying to get this simple URL link to work. I tried putting the link within the subroutine that pulls out the GeneID, but now all it does is take me to the gbrowse_details page, but still does NOT link to the Gene database. [GENE] feature = gene glyph = arrow fgcolor = red linewidth = 2 height = 6 description = sub { my $feature = shift; return $feature->attributes('geneid'); link = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term="$feature } key = Annotated Genes Can anyone tell me why this link doesn't work and how I can fix it? I've attached the conf file in case that helps. Thanks, Maureen -- Maureen J. Donlin, Ph.D. Research Associate Professor Dept. of Biochemistry & Molecular Biology Dept. of Molecular Microbiology & Immunology Saint Louis University School of Medicine 507 Doisy Research Center 314-977-8858 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse drad2.conf (5K) Download Attachment
	Re: URL links in gbrowse 2, cont by Lincoln Stein-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Maureen, I think you are misunderstanding how the callback works. You want to do this instead: [GENE] feature = gene glyph = arrow fgcolor = red linewidth = 2 height = 6 description = sub { my $feature = shift; return $feature->attributes('geneid') } link = sub { my $feature = shift; my ($geneid) = $feature->attributes('geneid'); return "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$geneid"; } key = Annotated Genes Lincoln On Fri, Sep 4, 2009 at 4:05 PM, Maureen Donlin <donlinmj@...> wrote: I've continued to play with the code trying to get this simple URL link to work. I tried putting the link within the subroutine that pulls out the GeneID, but now all it does is take me to the gbrowse_details page, but still does NOT link to the Gene database. [GENE] feature = gene glyph = arrow fgcolor = red linewidth = 2 height = 6 description = sub { my $feature = shift; return $feature->attributes('geneid'); link = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term="$feature } key = Annotated Genes Can anyone tell me why this link doesn't work and how I can fix it? I've attached the conf file in case that helps. Thanks, Maureen -- Maureen J. Donlin, Ph.D. Research Associate Professor Dept. of Biochemistry & Molecular Biology Dept. of Molecular Microbiology & Immunology Saint Louis University School of Medicine 507 Doisy Research Center 314-977-8858 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- 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@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: URL links in gbrowse 2, cont by Maureen J. Donlin :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Lincoln, Thanks so very much. Yes, that took care of the problem. Regards and have a nice weekend. Maureen On Fri, Sep 4, 2009 at 3:10 PM, Lincoln Stein<lincoln.stein@...> wrote: > Hi Maureen, > > I think you are misunderstanding how the callback works. You want to do this > instead: > > [GENE] > feature = gene > glyph = arrow > fgcolor = red > linewidth = 2 > height = 6 > description = sub { > my $feature = shift; > return $feature->attributes('geneid') > } > link = sub { > my $feature = shift; > my ($geneid) = $feature->attributes('geneid'); > return > "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$geneid"; > } > key = Annotated Genes > > Lincoln > > On Fri, Sep 4, 2009 at 4:05 PM, Maureen Donlin <donlinmj@...> wrote: >> >> I've continued to play with the code trying to get this simple URL >> link to work. >> I tried putting the link within the subroutine that pulls out the >> GeneID, but now all it does is take me to the gbrowse_details page, >> but still does NOT link to the Gene database. >> >> [GENE] >> feature = gene >> glyph = arrow >> fgcolor = red >> linewidth = 2 >> height = 6 >> description = sub { >> my $feature = shift; >> return $feature->attributes('geneid'); >> link = >> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term="$feature >> } >> key = Annotated Genes >> >> >> Can anyone tell me why this link doesn't work and how I can fix it? >> I've attached the conf file in case that helps. >> >> >> Thanks, >> Maureen >> >> -- >> Maureen J. Donlin, Ph.D. >> >> Research Associate Professor >> Dept. of Biochemistry & Molecular Biology >> Dept. of Molecular Microbiology & Immunology >> Saint Louis University School of Medicine >> 507 Doisy Research Center >> 314-977-8858 >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> 30-Day >> trial. Simplify your report design, integration and deployment - and focus >> on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > > -- > 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@...> > -- Maureen J. Donlin, Ph.D. Research Associate Professor Dept. of Biochemistry & Molecular Biology Dept. of Molecular Microbiology & Immunology Saint Louis University School of Medicine 507 Doisy Research Center 314-977-8858 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse