URL links in gbrowse 2
|
View:
New views
4 Messages
—
Rating Filter:
Alert me
|
 |
URL links in gbrowse 2
by Maureen J. Donlin
::
Rate this Message:
I have a Gbrowse2 installation; Bioperl 1.6
Located at: http://hagrid.slu.edu/cgi-bin/gbrowse/drad2/ Edited the Genbank file so the "db_xref=GeneID:" are now "geneid=" Generated GFF3 and imported into mysql. Now geneid is one of the key:value pairs in the fattributes table. Trying to create a link to the Gene database from the main Gbrowse page. Why does this link for GENE feature not work when a similar link for [ORIGIN] does? [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 All I see in the link is $feature rather than the ID number of the Gene db record. Here is the code for the [ORIGIN] track: [ORIGIN] feature = region glyph = anchored_arrow fgcolor = orange font2color = red linewidth = 2 height = 10 description = 1 link = http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=1&field=Sequence+ID&term=$name key = Definition line Thanks in advance for any suggestions. Regards, 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 |
|
|
Re: URL links in gbrowse 2
by Lincoln Stein-3
::
Rate this Message:
Hi Maureen,
I think it will work if you use "$name" instead of "$feature". Lincoln On Fri, Sep 4, 2009 at 2:50 PM, Maureen Donlin <donlinmj@...> wrote: I have a Gbrowse2 installation; Bioperl 1.6 -- 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
by Maureen J. Donlin
::
Rate this Message:
Lincoln,
No, that didn't help. Whether I use $name or $ f it still opens the gbrowse_details page and there is not link to the Gene db on that either. If I remove the link = AUTO line, then it no longer calls the gbrowse_details script, but still no link to Genbank. I'll have to revisit it next week. Regards, Maureen On Fri, Sep 4, 2009 at 3:06 PM, Lincoln Stein<lincoln.stein@...> wrote: > Hi Maureen, > > I think it will work if you use "$name" instead of "$feature". > > Lincoln > > On Fri, Sep 4, 2009 at 2:50 PM, Maureen Donlin <donlinmj@...> wrote: >> >> I have a Gbrowse2 installation; Bioperl 1.6 >> >> Located at: http://hagrid.slu.edu/cgi-bin/gbrowse/drad2/ >> >> Edited the Genbank file so the "db_xref=GeneID:" are now "geneid=" >> >> Generated GFF3 and imported into mysql. Now geneid is one of the >> key:value pairs in the fattributes table. >> >> Trying to create a link to the Gene database from the main Gbrowse page. >> >> Why does this link for GENE feature not work when a similar link for >> [ORIGIN] does? >> >> [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 >> >> All I see in the link is $feature rather than the ID number of the >> Gene db record. >> >> Here is the code for the [ORIGIN] track: >> [ORIGIN] >> feature = region >> glyph = anchored_arrow >> fgcolor = orange >> font2color = red >> linewidth = 2 >> height = 10 >> description = 1 >> link = >> >> http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=1&field=Sequence+ID&term=$name >> key = Definition line >> >> Thanks in advance for any suggestions. >> >> Regards, >> 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 |
|
|
Re: URL links in gbrowse 2
by Scott Cain-4
::
Rate this Message:
Hi Maureen,
I haven't seen the GFF, nor do I actually know what you want to appear in the url, but I suspect that you want the value of what geneid is set to. To do that, you need a callback, like this: 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 "; } Scott On Sep 4, 2009, at 4:25 PM, Maureen Donlin wrote: > Lincoln, > > No, that didn't help. Whether I use $name or $ f it still opens the > gbrowse_details page and there is not link to the Gene db on that > either. > > If I remove the link = AUTO line, then it no longer calls the > gbrowse_details script, but still no link to Genbank. > > I'll have to revisit it next week. > > Regards, > Maureen > > On Fri, Sep 4, 2009 at 3:06 PM, Lincoln > Stein<lincoln.stein@...> wrote: >> Hi Maureen, >> >> I think it will work if you use "$name" instead of "$feature". >> >> Lincoln >> >> On Fri, Sep 4, 2009 at 2:50 PM, Maureen Donlin <donlinmj@...> >> wrote: >>> >>> I have a Gbrowse2 installation; Bioperl 1.6 >>> >>> Located at: http://hagrid.slu.edu/cgi-bin/gbrowse/drad2/ >>> >>> Edited the Genbank file so the "db_xref=GeneID:" are now "geneid=" >>> >>> Generated GFF3 and imported into mysql. Now geneid is one of the >>> key:value pairs in the fattributes table. >>> >>> Trying to create a link to the Gene database from the main Gbrowse >>> page. >>> >>> Why does this link for GENE feature not work when a similar link for >>> [ORIGIN] does? >>> >>> [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 >>> >>> All I see in the link is $feature rather than the ID number of the >>> Gene db record. >>> >>> Here is the code for the [ORIGIN] track: >>> [ORIGIN] >>> feature = region >>> glyph = anchored_arrow >>> fgcolor = orange >>> font2color = red >>> linewidth = 2 >>> height = 10 >>> description = 1 >>> link = >>> >>> http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=1&field=Sequence+ID&term=$name >>> key = Definition line >>> >>> Thanks in advance for any suggestions. >>> >>> Regards, >>> 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 ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ 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 |
| Free embeddable forum powered by Nabble | Forum Help |
