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GFF3 validation
by Wes Barris
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Hi,
The GFF3 validation link to wormbase on this page: http://gmod.org/wiki/GFF3#GFF3_Validation results in an error. I don't know whether or not wormbase is still providing a gff3 validator. Also, the gff3 validation perl code from the same page: http://www.pathogenportal.org/resources/gff3Valid.pl has errors in it: perl -c gff3Valid.pl Number found where operator expected at gff3Valid.pl line 8, near "GFF3 1.01" (Do you need to predeclare GFF3?) Bareword found where operator expected at gff3Valid.pl line 8, near "1.01 spec" (Missing operator before spec?) Bareword found where operator expected at gff3Valid.pl line 10, near "//www" (Missing operator before www?) Number found where operator expected at gff3Valid.pl line 22, near "over 4" (Do you need to predeclare over?) syntax error at gff3Valid.pl line 8, near "GFF3 1.01" Unmatched right curly bracket at gff3Valid.pl line 190, at end of line syntax error at gff3Valid.pl line 190, near "}" gff3Valid.pl had compilation errors. -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: GFF3 validation
by Dave Clements, GMOD Help Desk
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Hi Wes,
Thanks for the heads up on the GFF3 validator at WormBase. I don't know what happened to it, but I'll investigate, and drop the link. For the validator from pathogenportal, try dropping everything between line 2 and the line that says =cut. Thanks, Dave C On Mon, Sep 14, 2009 at 8:47 PM, Wes Barris <wes.barris@...> wrote: > Hi, > > The GFF3 validation link to wormbase on this page: > > http://gmod.org/wiki/GFF3#GFF3_Validation > > results in an error. I don't know whether or not wormbase is still > providing a gff3 validator. > > Also, the gff3 validation perl code from the same page: > > http://www.pathogenportal.org/resources/gff3Valid.pl > > has errors in it: > > perl -c gff3Valid.pl > Number found where operator expected at gff3Valid.pl line 8, near "GFF3 1.01" > (Do you need to predeclare GFF3?) > Bareword found where operator expected at gff3Valid.pl line 8, near "1.01 spec" > (Missing operator before spec?) > Bareword found where operator expected at gff3Valid.pl line 10, near "//www" > (Missing operator before www?) > Number found where operator expected at gff3Valid.pl line 22, near "over 4" > (Do you need to predeclare over?) > syntax error at gff3Valid.pl line 8, near "GFF3 1.01" > Unmatched right curly bracket at gff3Valid.pl line 190, at end of line > syntax error at gff3Valid.pl line 190, near "}" > gff3Valid.pl had compilation errors. > > -- > Wes Barris <wes.barris@...> > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® 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/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: GFF3 validation
by Jim Hu
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The Wormbase gff validator has been down for a long time. The pathogen portal one is not very good. The one that should be at Wormbase should be available somewhere in the (formerly cvs) svn repository.
I should try to put a copy up on one of our public servers. Jim On Sep 14, 2009, at 11:41 PM, Dave Clements, GMOD Help Desk wrote:
===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: GFF3 validation
by Todd Harris-3
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Hi Jim, Wes -
I've used our very own GFF3 validator on-and-off over the past two years. Although we have had some downtime with the validator due to migrating services to a new hosting facility and new hardware, it is functioning now. Still, I think it makes sense for this service to be subsumed by GMOD, with interested users assuming maintenance of the code. The original developer of the validator left WormBase years ago. At that time, there was some discussion of handover to GMOD but that clearly never got very far. Zheng Zha has made some changes (principally updating the version of the sequence ontology file; the WormBase validator uses a very old version). This represents the most logical branch of code for import to the GMOD repository. I'm happy to check it in and help set up an instance on GMOD.org if I can get shell access to the machine. Todd On Sun, Sep 20, 2009 at 4:25 PM, Jim Hu <jimhu@...> wrote: > The Wormbase gff validator has been down for a long time. The pathogen > portal one is not very good. The one that should be at Wormbase should be > available somewhere in the (formerly cvs) svn repository. > I should try to put a copy up on one of our public servers. > > Jim > On Sep 14, 2009, at 11:41 PM, Dave Clements, GMOD Help Desk wrote: > > Hi Wes, > > Thanks for the heads up on the GFF3 validator at WormBase. I don't > know what happened to it, but I'll investigate, and drop the link. > > For the validator from pathogenportal, try dropping everything between > line 2 and the line that says =cut. > > Thanks, > > Dave C > > On Mon, Sep 14, 2009 at 8:47 PM, Wes Barris <wes.barris@...> wrote: > > Hi, > > The GFF3 validation link to wormbase on this page: > > http://gmod.org/wiki/GFF3#GFF3_Validation > > results in an error. I don't know whether or not wormbase is still > > providing a gff3 validator. > > Also, the gff3 validation perl code from the same page: > > http://www.pathogenportal.org/resources/gff3Valid.pl > > has errors in it: > > perl -c gff3Valid.pl > > Number found where operator expected at gff3Valid.pl line 8, near "GFF3 > 1.01" > > (Do you need to predeclare GFF3?) > > Bareword found where operator expected at gff3Valid.pl line 8, near "1.01 > spec" > > (Missing operator before spec?) > > Bareword found where operator expected at gff3Valid.pl line 10, near "//www" > > (Missing operator before www?) > > Number found where operator expected at gff3Valid.pl line 22, near "over 4" > > (Do you need to predeclare over?) > > syntax error at gff3Valid.pl line 8, near "GFF3 1.01" > > Unmatched right curly bracket at gff3Valid.pl line 190, at end of line > > syntax error at gff3Valid.pl line 190, near "}" > > gff3Valid.pl had compilation errors. > > -- > > Wes Barris <wes.barris@...> > > ------------------------------------------------------------------------------ > > Come build with us! The BlackBerry® 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/devconf > > _______________________________________________ > > Gmod-gbrowse mailing list > > Gmod-gbrowse@... > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > > -- > * Please keep responses on the list! > * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® 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/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® 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/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: GFF3 validation
by Chris Fields-5
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What is the validator written in? Just curious, but we have discussed
rewriting hunks of the bioperl GFF-related code, and I'm wondering if this would fit in somehow or could be delegated to. chris On Sep 20, 2009, at 6:11 PM, Todd Harris wrote: > Hi Jim, Wes - > > I've used our very own GFF3 validator on-and-off over the past two > years. Although we have had some downtime with the validator due to > migrating services to a new hosting facility and new hardware, it is > functioning now. > > Still, I think it makes sense for this service to be subsumed by GMOD, > with interested users assuming maintenance of the code. The original > developer of the validator left WormBase years ago. At that time, > there was some discussion of handover to GMOD but that clearly never > got very far. > > Zheng Zha has made some changes (principally updating the version of > the sequence ontology file; the WormBase validator uses a very old > version). This represents the most logical branch of code for import > to the GMOD repository. > > I'm happy to check it in and help set up an instance on GMOD.org if I > can get shell access to the machine. > > Todd > > > > > On Sun, Sep 20, 2009 at 4:25 PM, Jim Hu <jimhu@...> wrote: >> The Wormbase gff validator has been down for a long time. The >> pathogen >> portal one is not very good. The one that should be at Wormbase >> should be >> available somewhere in the (formerly cvs) svn repository. >> I should try to put a copy up on one of our public servers. >> >> Jim >> On Sep 14, 2009, at 11:41 PM, Dave Clements, GMOD Help Desk wrote: >> >> Hi Wes, >> >> Thanks for the heads up on the GFF3 validator at WormBase. I don't >> know what happened to it, but I'll investigate, and drop the link. >> >> For the validator from pathogenportal, try dropping everything >> between >> line 2 and the line that says =cut. >> >> Thanks, >> >> Dave C >> >> On Mon, Sep 14, 2009 at 8:47 PM, Wes Barris <wes.barris@...> >> wrote: >> >> Hi, >> >> The GFF3 validation link to wormbase on this page: >> >> http://gmod.org/wiki/GFF3#GFF3_Validation >> >> results in an error. I don't know whether or not wormbase is still >> >> providing a gff3 validator. >> >> Also, the gff3 validation perl code from the same page: >> >> http://www.pathogenportal.org/resources/gff3Valid.pl >> >> has errors in it: >> >> perl -c gff3Valid.pl >> >> Number found where operator expected at gff3Valid.pl line 8, near >> "GFF3 >> 1.01" >> >> (Do you need to predeclare GFF3?) >> >> Bareword found where operator expected at gff3Valid.pl line 8, near >> "1.01 >> spec" >> >> (Missing operator before spec?) >> >> Bareword found where operator expected at gff3Valid.pl line 10, >> near "//www" >> >> (Missing operator before www?) >> >> Number found where operator expected at gff3Valid.pl line 22, near >> "over 4" >> >> (Do you need to predeclare over?) >> >> syntax error at gff3Valid.pl line 8, near "GFF3 1.01" >> >> Unmatched right curly bracket at gff3Valid.pl line 190, at end of >> line >> >> syntax error at gff3Valid.pl line 190, near "}" >> >> gff3Valid.pl had compilation errors. >> >> -- >> >> Wes Barris <wes.barris@...> >> >> ------------------------------------------------------------------------------ >> >> Come build with us! The BlackBerry® 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/devconf >> >> _______________________________________________ >> >> Gmod-gbrowse mailing list >> >> Gmod-gbrowse@... >> >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> >> >> >> -- >> * Please keep responses on the list! >> * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® 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/devconf >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> ===================================== >> >> Jim Hu >> >> Associate Professor >> >> Dept. of Biochemistry and Biophysics >> >> 2128 TAMU >> >> Texas A&M Univ. >> >> College Station, TX 77843-2128 >> >> 979-862-4054 >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® 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/devconf >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® 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/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: GFF3 validation
by Todd Harris-3
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Hi Chris -
It's in Perl and is quite clean OO. t On Sun, Sep 20, 2009 at 5:21 PM, Chris Fields <cjfields@...> wrote: > What is the validator written in? Just curious, but we have discussed > rewriting hunks of the bioperl GFF-related code, and I'm wondering if this > would fit in somehow or could be delegated to. > > chris > > On Sep 20, 2009, at 6:11 PM, Todd Harris wrote: > >> Hi Jim, Wes - >> >> I've used our very own GFF3 validator on-and-off over the past two >> years. Although we have had some downtime with the validator due to >> migrating services to a new hosting facility and new hardware, it is >> functioning now. >> >> Still, I think it makes sense for this service to be subsumed by GMOD, >> with interested users assuming maintenance of the code. The original >> developer of the validator left WormBase years ago. At that time, >> there was some discussion of handover to GMOD but that clearly never >> got very far. >> >> Zheng Zha has made some changes (principally updating the version of >> the sequence ontology file; the WormBase validator uses a very old >> version). This represents the most logical branch of code for import >> to the GMOD repository. >> >> I'm happy to check it in and help set up an instance on GMOD.org if I >> can get shell access to the machine. >> >> Todd >> >> >> >> >> On Sun, Sep 20, 2009 at 4:25 PM, Jim Hu <jimhu@...> wrote: >>> >>> The Wormbase gff validator has been down for a long time. The pathogen >>> portal one is not very good. The one that should be at Wormbase should >>> be >>> available somewhere in the (formerly cvs) svn repository. >>> I should try to put a copy up on one of our public servers. >>> >>> Jim >>> On Sep 14, 2009, at 11:41 PM, Dave Clements, GMOD Help Desk wrote: >>> >>> Hi Wes, >>> >>> Thanks for the heads up on the GFF3 validator at WormBase. I don't >>> know what happened to it, but I'll investigate, and drop the link. >>> >>> For the validator from pathogenportal, try dropping everything between >>> line 2 and the line that says =cut. >>> >>> Thanks, >>> >>> Dave C >>> >>> On Mon, Sep 14, 2009 at 8:47 PM, Wes Barris <wes.barris@...> wrote: >>> >>> Hi, >>> >>> The GFF3 validation link to wormbase on this page: >>> >>> http://gmod.org/wiki/GFF3#GFF3_Validation >>> >>> results in an error. I don't know whether or not wormbase is still >>> >>> providing a gff3 validator. >>> >>> Also, the gff3 validation perl code from the same page: >>> >>> http://www.pathogenportal.org/resources/gff3Valid.pl >>> >>> has errors in it: >>> >>> perl -c gff3Valid.pl >>> >>> Number found where operator expected at gff3Valid.pl line 8, near "GFF3 >>> 1.01" >>> >>> (Do you need to predeclare GFF3?) >>> >>> Bareword found where operator expected at gff3Valid.pl line 8, near "1.01 >>> spec" >>> >>> (Missing operator before spec?) >>> >>> Bareword found where operator expected at gff3Valid.pl line 10, near >>> "//www" >>> >>> (Missing operator before www?) >>> >>> Number found where operator expected at gff3Valid.pl line 22, near "over >>> 4" >>> >>> (Do you need to predeclare over?) >>> >>> syntax error at gff3Valid.pl line 8, near "GFF3 1.01" >>> >>> Unmatched right curly bracket at gff3Valid.pl line 190, at end of line >>> >>> syntax error at gff3Valid.pl line 190, near "}" >>> >>> gff3Valid.pl had compilation errors. >>> >>> -- >>> >>> Wes Barris <wes.barris@...> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> Come build with us! The BlackBerry® 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/devconf >>> >>> _______________________________________________ >>> >>> Gmod-gbrowse mailing list >>> >>> Gmod-gbrowse@... >>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>> >>> >>> >>> -- >>> * Please keep responses on the list! >>> * Was this helpful? Let us know at >>> http://gmod.org/wiki/Help_Desk_Feedback >>> >>> >>> ------------------------------------------------------------------------------ >>> Come build with us! The BlackBerry® 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/devconf >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Come build with us! The BlackBerry® 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/devconf >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>> >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® 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/devconf >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: GFF3 validation
by Jim Hu
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Hi Todd,
Sorry! I should have confirmed that it was still down before replying to Wes. Glad it's back up. It trances for me with the default selection for the SO file, but works if I pick SOFA latest. Subsuming into gmod.org or into the SO project (that's where the top Google hit for GFF3 spec is) would make a lot of sense. I downloaded the trunk version from sourceforge and it was pretty easy to get it working on our server: It looks like the one at Wormbase may still be Payan's. The one from trunk looks like Zheng's. At least it has a different version number. It was pretty easy to set up, but I did have to make one change that may be a Mac Perl dialect thing. In GFF::Online.pm I had to change my $file_length = `wc -l $report_file` =~ /^(\d+)/; in sub _store_report_file_info to two lines my $file_length = `wc -l $report_file`; $file_length =~ /^(\d+)/; There may be a few other things to tweak. I'm trying to figure out how it decides what the latest SO.obo file is. Jim On Sep 20, 2009, at 6:11 PM, Todd Harris wrote:
===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: GFF3 validation
by Wes Barris
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Jim Hu wrote:
> The Wormbase gff validator has been down for a long time. The pathogen > portal one is not very good. The one that should be at Wormbase should > be available somewhere in the (formerly cvs) svn repository. Yes, the pathogen one has some problems. I found another working validator here: http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online > I should try to put a copy up on one of our public servers. > > Jim > > On Sep 14, 2009, at 11:41 PM, Dave Clements, GMOD Help Desk wrote: > >> Hi Wes, >> >> Thanks for the heads up on the GFF3 validator at WormBase. I don't >> know what happened to it, but I'll investigate, and drop the link. >> >> For the validator from pathogenportal, try dropping everything between >> line 2 and the line that says =cut. >> >> Thanks, >> >> Dave C >> >> On Mon, Sep 14, 2009 at 8:47 PM, Wes Barris <wes.barris@... >> <mailto:wes.barris@...>> wrote: >>> Hi, >>> >>> The GFF3 validation link to wormbase on this page: >>> >>> http://gmod.org/wiki/GFF3#GFF3_Validation >>> >>> results in an error. I don't know whether or not wormbase is still >>> providing a gff3 validator. >>> >>> Also, the gff3 validation perl code from the same page: >>> >>> http://www.pathogenportal.org/resources/gff3Valid.pl >>> >>> has errors in it: >>> >>> perl -c gff3Valid.pl >>> Number found where operator expected at gff3Valid.pl line 8, near >>> "GFF3 1.01" >>> (Do you need to predeclare GFF3?) >>> Bareword found where operator expected at gff3Valid.pl line 8, near >>> "1.01 spec" >>> (Missing operator before spec?) >>> Bareword found where operator expected at gff3Valid.pl line 10, near >>> "//www" >>> (Missing operator before www?) >>> Number found where operator expected at gff3Valid.pl line 22, near >>> "over 4" >>> (Do you need to predeclare over?) >>> syntax error at gff3Valid.pl line 8, near "GFF3 1.01" >>> Unmatched right curly bracket at gff3Valid.pl line 190, at end of line >>> syntax error at gff3Valid.pl line 190, near "}" >>> gff3Valid.pl had compilation errors. >>> >>> -- >>> Wes Barris <wes.barris@... <mailto:wes.barris@...>> >>> >>> ------------------------------------------------------------------------------ >>> Come build with us! The BlackBerry® 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/devconf >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> <mailto:Gmod-gbrowse@...> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> >> -- >> * Please keep responses on the list! >> * Was this helpful? Let us know at >> http://gmod.org/wiki/Help_Desk_Feedback >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® 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/devconf >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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