Selecting the correct SOFA term
|
View:
New views
6 Messages
—
Rating Filter:
Alert me
|
 |
Selecting the correct SOFA term
by Wes Barris
::
Rate this Message:
Hi,
I am creating a .gff3 file containing 5kb bins of reads. Here is an example: ##gff-version 3 BTA1 read SOFA 1 5000 267 . . Name=BTA1 BTA1 read SOFA 5001 10000 114 . . Name=BTA1 BTA1 read SOFA 10001 15000 115 . . Name=BTA1 BTA1 read SOFA 15001 20000 123 . . Name=BTA1 However, I am not sure what to use for the type in the 3rd column. I've browsed through http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12 but nothing seems appropriate. Any suggestions? -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Selecting the correct SOFA term
by Nicole Washington
::
Rate this Message:
No need to be limited to SOFA for gff3. You can use any term from the
whole of SO: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo for individual reads, i'd choose "read". to mark a region on the genome where some transcribed sequences occur, then perhaps "transcribed_cluster" is appropriate http://www.sequenceontology.org/miso/current_cvs/term/SO:0001457 nicole On Oct 29, 2009, at 8:36 PM, Wes Barris wrote: > Hi, > > I am creating a .gff3 file containing 5kb bins of reads. Here is > an example: > > ##gff-version 3 > BTA1 read SOFA 1 5000 267 . . > Name=BTA1 > BTA1 read SOFA 5001 10000 114 . . > Name=BTA1 > BTA1 read SOFA 10001 15000 115 . . > Name=BTA1 > BTA1 read SOFA 15001 20000 123 . . > Name=BTA1 > > However, I am not sure what to use for the type in the 3rd column. > I've browsed through > > http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12 > > but nothing seems appropriate. Any suggestions? > -- > Wes Barris <wes.barris@...> > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: Selecting the correct SOFA term
by Nicole Washington
::
Rate this Message:
There's also "overlapping_feature_set", which is pretty generic:
http://www.sequenceontology.org/miso/current_cvs/term/SO:0001261 nicole On Oct 29, 2009, at 9:59 PM, Nicole Washington wrote: > No need to be limited to SOFA for gff3. You can use any term from the > whole of SO: > > http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo > > for individual reads, i'd choose "read". to mark a region on the > genome where some transcribed sequences occur, then perhaps > "transcribed_cluster" is appropriate http://www.sequenceontology.org/miso/current_cvs/term/SO:0001457 > > nicole > > On Oct 29, 2009, at 8:36 PM, Wes Barris wrote: > >> Hi, >> >> I am creating a .gff3 file containing 5kb bins of reads. Here is >> an example: >> >> ##gff-version 3 >> BTA1 read SOFA 1 5000 267 . . >> Name=BTA1 >> BTA1 read SOFA 5001 10000 114 . . >> Name=BTA1 >> BTA1 read SOFA 10001 15000 115 . . >> Name=BTA1 >> BTA1 read SOFA 15001 20000 123 . . >> Name=BTA1 >> >> However, I am not sure what to use for the type in the 3rd column. >> I've browsed through >> >> http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12 >> >> but nothing seems appropriate. Any suggestions? >> -- >> Wes Barris <wes.barris@...> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart >> your >> developing skills, take BlackBerry mobile applications to market and >> stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
centralized restrict option for tracks
by Jan-Ole Christian
::
Rate this Message:
Hi,
I want to hide some tracks using the restrict option, e.g.: [myTrack] restrict= Order deny,allow deny from all allow from localhost which is perfectly working. I wrote an subroutine: init_code = sub inhouse{ return 'Order deny,allow deny from all allow from localhost'; } and for the track: [myTrack] restrict = \&inhouse But the restriction has no effect! I tested my subfunction successfully with [myTrack] restrict = \&inhouse description = \&inhouse How can I cetralize the restrict option for all tracks? Any idea what went wrong? Regards, Jan-Ole ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: centralized restrict option for tracks
by Dave Clements, GMOD Help Desk-2
::
Rate this Message:
Hi Ole,
The rules for what a callout returns are different from if you specify the restrict directly. According to http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Authentication_.26_Authorization: As with other gbrowse options, restrict can be a code subroutine. The subroutine will be called with three arguments consisting of the host, ip address and authenticated user. It should return a true value to allow access to the track, or a false value to forbid it. You could try init_code = sub inhouse{ my $host = shift; return $host eq 'localhost'; } Dave C On Fri, Oct 30, 2009 at 8:43 AM, Jan-Ole Christian <jan-ole.christian@...> wrote: > Hi, > I want to hide some tracks using the restrict option, e.g.: > > [myTrack] > restrict= Order deny,allow deny from all allow from localhost > > which is perfectly working. > I wrote an subroutine: > > init_code = sub inhouse{ > > return 'Order deny,allow deny from all allow from localhost'; > > } > > and for the track: > > [myTrack] > restrict = \&inhouse > > > But the restriction has no effect! > I tested my subfunction successfully with > > [myTrack] > restrict = \&inhouse > description = \&inhouse > > > How can I cetralize the restrict option for all tracks? Any idea what > went wrong? > > Regards, > Jan-Ole > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- Please keep responses on the list! http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback ------------------------------------------------------------------------------ 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: centralized restrict option for tracks
by Jan-Ole Christian
::
Rate this Message:
Thank you!
That's it. I overlooked it in the documentation. Regards, Ole. Dave Clements, GMOD Help Desk schrieb: > Hi Ole, > > The rules for what a callout returns are different from if you specify > the restrict directly. According to > http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Authentication_.26_Authorization: > > As with other gbrowse options, restrict can be a code subroutine. The > subroutine will be called with three arguments consisting of the host, > ip address and authenticated user. It should return a true value to > allow access to the track, or a false value to forbid it. > > You could try > > init_code = sub inhouse{ > my $host = shift; > return $host eq 'localhost'; > } > > Dave C > > On Fri, Oct 30, 2009 at 8:43 AM, Jan-Ole Christian > <jan-ole.christian@...> wrote: > >> Hi, >> I want to hide some tracks using the restrict option, e.g.: >> >> [myTrack] >> restrict= Order deny,allow deny from all allow from localhost >> >> which is perfectly working. >> I wrote an subroutine: >> >> init_code = sub inhouse{ >> >> return 'Order deny,allow deny from all allow from localhost'; >> >> } >> >> and for the track: >> >> [myTrack] >> restrict = \&inhouse >> >> >> But the restriction has no effect! >> I tested my subfunction successfully with >> >> [myTrack] >> restrict = \&inhouse >> description = \&inhouse >> >> >> How can I cetralize the restrict option for all tracks? Any idea what >> went wrong? >> >> Regards, >> Jan-Ole >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > > > ------------------------------------------------------------------------------ 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 |
