GFF2 vs GFF3
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GFF2 vs GFF3
by Ryan Golhar
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Hi,
I have a GFF file that is being generated with the header line stating its a GFF version 2 file. However, it is actually a GFF 3 file based on the number of columns in the file. I see in my apache error log: Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF2Loader.pm line 410, <F> line 2611781., referer: http://localhost/cgi-bin/gbrowse/arabidopsis/ If I change the version number in the file from 2 or 3, the errors go away. Unfortunately the software generating the GFF file is not under my control so I can't fix that. Is it possible to have Gbrowse check the file for version regardless of what the file says? Sort of to correct for user mistake? Ryan ------------------------------------------------------------------------------ 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 |
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Re: GFF2 vs GFF3
by Scott Cain-4
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Hi Ryan,
Both GFF2 and GFF3 have 9 columns, so the number of columns in the file is not informative. Nevertheless, I don't think it is reasonable for GBrowse/BioPerl to disregard the version information it is given and to instead second guess what the file says it is. If it is really wrong, I suggest you write a simple perl tool to fix the GFF file before it is put in place or uploaded or whatever its ultimate destiny is. Scott On Nov 4, 2009, at 12:33 PM, Ryan Golhar wrote: > Hi, > > I have a GFF file that is being generated with the header line stating > its a GFF version 2 file. However, it is actually a GFF 3 file > based on > the number of columns in the file. > > I see in my apache error log: > > Use of uninitialized value in pattern match (m//) at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF2Loader.pm > line 410, <F> line 2611781., referer: > http://localhost/cgi-bin/gbrowse/arabidopsis/ > > > If I change the version number in the file from 2 or 3, the errors go > away. Unfortunately the software generating the GFF file is not under > my control so I can't fix that. Is it possible to have Gbrowse check > the file for version regardless of what the file says? Sort of to > correct for user mistake? > > Ryan > > ------------------------------------------------------------------------------ > 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 |
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Re: GFF2 vs GFF3
by Ryan Golhar
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According to this,
http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml, GFF 2 has 10 columns: <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments] It attributes and comments are optional. GFF v3, http://www.sequenceontology.org/gff3.shtml, has 9 columns...comments is now part of attributes. Is it possible for Gbrowse/bioperl to output to the user that something is wrong with their file that they uploaded? Right now, users have no way of knowing w/o asking me to look at the apache error log... Ryan Scott Cain wrote: > Hi Ryan, > > Both GFF2 and GFF3 have 9 columns, so the number of columns in the file > is not informative. Nevertheless, I don't think it is reasonable for > GBrowse/BioPerl to disregard the version information it is given and to > instead second guess what the file says it is. If it is really wrong, I > suggest you write a simple perl tool to fix the GFF file before it is > put in place or uploaded or whatever its ultimate destiny is. > > Scott > > > On Nov 4, 2009, at 12:33 PM, Ryan Golhar wrote: > >> Hi, >> >> I have a GFF file that is being generated with the header line stating >> its a GFF version 2 file. However, it is actually a GFF 3 file based on >> the number of columns in the file. >> >> I see in my apache error log: >> >> Use of uninitialized value in pattern match (m//) at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF2Loader.pm >> line 410, <F> line 2611781., referer: >> http://localhost/cgi-bin/gbrowse/arabidopsis/ >> >> >> If I change the version number in the file from 2 or 3, the errors go >> away. Unfortunately the software generating the GFF file is not under >> my control so I can't fix that. Is it possible to have Gbrowse check >> the file for version regardless of what the file says? Sort of to >> correct for user mistake? >> >> Ryan >> >> ------------------------------------------------------------------------------ >> >> 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 |
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Re: GFF2 vs GFF3
by Scott Cain-4
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Hi Ryan,
The GFF2 spec is not particularly good as specifications go (which is part of the reason we needed GFF3), as it doesn't explicitly say how many tab delimited columns there are. While both attributes and comments are (sort of*) optional, the only way to include comments is with perl-style hash marks to set them off, and most parsers would miss comments at the end of a GFF line since they do a split on tabs into an array with 9 elements, so, GFF2 has 9 tab-delimited columns. *I wrote "sort of" with respect to attributes, since GBrowse won't function without at least a minimal attribute line indicating the feature's name/group. What this problem boils down to is that validating user input is hard; in fact, I'm still not sure that what you said is GFF3 really is, so trying to get a program to do it in a reasonable amount of time and with a reasonable user interface would be tough. There is a GFF3 validator at: http://dev.wormbase.org/db/validate_gff3/validate_gff3_online but it can be somewhat slow for large files. However, if you have more concrete suggestions for how to amend this situation, I would be willing to take a look. Scott On Nov 4, 2009, at 12:48 PM, Ryan Golhar wrote: > According to this, > http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml, GFF 2 has > 10 columns: > > <seqname> <source> <feature> <start> <end> <score> <strand> <frame> > [attributes] [comments] > > It attributes and comments are optional. > > GFF v3, http://www.sequenceontology.org/gff3.shtml, has 9 > columns...comments is now part of attributes. > > Is it possible for Gbrowse/bioperl to output to the user that > something > is wrong with their file that they uploaded? Right now, users have no > way of knowing w/o asking me to look at the apache error log... > > Ryan > > > Scott Cain wrote: >> Hi Ryan, >> >> Both GFF2 and GFF3 have 9 columns, so the number of columns in the >> file >> is not informative. Nevertheless, I don't think it is reasonable for >> GBrowse/BioPerl to disregard the version information it is given >> and to >> instead second guess what the file says it is. If it is really >> wrong, I >> suggest you write a simple perl tool to fix the GFF file before it is >> put in place or uploaded or whatever its ultimate destiny is. >> >> Scott >> >> >> On Nov 4, 2009, at 12:33 PM, Ryan Golhar wrote: >> >>> Hi, >>> >>> I have a GFF file that is being generated with the header line >>> stating >>> its a GFF version 2 file. However, it is actually a GFF 3 file >>> based on >>> the number of columns in the file. >>> >>> I see in my apache error log: >>> >>> Use of uninitialized value in pattern match (m//) at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF2Loader.pm >>> line 410, <F> line 2611781., referer: >>> http://localhost/cgi-bin/gbrowse/arabidopsis/ >>> >>> >>> If I change the version number in the file from 2 or 3, the errors >>> go >>> away. Unfortunately the software generating the GFF file is not >>> under >>> my control so I can't fix that. Is it possible to have Gbrowse >>> check >>> the file for version regardless of what the file says? Sort of to >>> correct for user mistake? >>> >>> Ryan >>> >>> ------------------------------------------------------------------------------ >>> >>> 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 ----------------------------------------------------------------------- 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 |
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Re: GFF2 vs GFF3
by Sheldon McKay-3
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I have never, ever seen GFF2 with more than nine columns, so a tenth
column is certainly not diagnostic. But a very easy way to tell if it is GFF3 or GFF2 is that the attribute/value pairs are in the ninth column are space-delimited (not tab-delimited) in GFF2 and '='-delimited in GFF3. GFF2: Name SpongeBob GFF3: Name=SpongeBob On Wed, Nov 4, 2009 at 2:10 PM, Scott Cain <scott@...> wrote: > Hi Ryan, > > The GFF2 spec is not particularly good as specifications go (which is > part of the reason we needed GFF3), as it doesn't explicitly say how > many tab delimited columns there are. While both attributes and > comments are (sort of*) optional, the only way to include comments is > with perl-style hash marks to set them off, and most parsers would > miss comments at the end of a GFF line since they do a split on tabs > into an array with 9 elements, so, GFF2 has 9 tab-delimited columns. > > *I wrote "sort of" with respect to attributes, since GBrowse won't > function without at least a minimal attribute line indicating the > feature's name/group. > > What this problem boils down to is that validating user input is hard; > in fact, I'm still not sure that what you said is GFF3 really is, so > trying to get a program to do it in a reasonable amount of time and > with a reasonable user interface would be tough. There is a GFF3 > validator at: > > http://dev.wormbase.org/db/validate_gff3/validate_gff3_online > > but it can be somewhat slow for large files. However, if you have > more concrete suggestions for how to amend this situation, I would be > willing to take a look. > > Scott > > > > On Nov 4, 2009, at 12:48 PM, Ryan Golhar wrote: > >> According to this, >> http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml, GFF 2 has >> 10 columns: >> >> <seqname> <source> <feature> <start> <end> <score> <strand> <frame> >> [attributes] [comments] >> >> It attributes and comments are optional. >> >> GFF v3, http://www.sequenceontology.org/gff3.shtml, has 9 >> columns...comments is now part of attributes. >> >> Is it possible for Gbrowse/bioperl to output to the user that >> something >> is wrong with their file that they uploaded? Right now, users have no >> way of knowing w/o asking me to look at the apache error log... >> >> Ryan >> >> >> Scott Cain wrote: >>> Hi Ryan, >>> >>> Both GFF2 and GFF3 have 9 columns, so the number of columns in the >>> file >>> is not informative. Nevertheless, I don't think it is reasonable for >>> GBrowse/BioPerl to disregard the version information it is given >>> and to >>> instead second guess what the file says it is. If it is really >>> wrong, I >>> suggest you write a simple perl tool to fix the GFF file before it is >>> put in place or uploaded or whatever its ultimate destiny is. >>> >>> Scott >>> >>> >>> On Nov 4, 2009, at 12:33 PM, Ryan Golhar wrote: >>> >>>> Hi, >>>> >>>> I have a GFF file that is being generated with the header line >>>> stating >>>> its a GFF version 2 file. However, it is actually a GFF 3 file >>>> based on >>>> the number of columns in the file. >>>> >>>> I see in my apache error log: >>>> >>>> Use of uninitialized value in pattern match (m//) at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF2Loader.pm >>>> line 410, <F> line 2611781., referer: >>>> http://localhost/cgi-bin/gbrowse/arabidopsis/ >>>> >>>> >>>> If I change the version number in the file from 2 or 3, the errors >>>> go >>>> away. Unfortunately the software generating the GFF file is not >>>> under >>>> my control so I can't fix that. Is it possible to have Gbrowse >>>> check >>>> the file for version regardless of what the file says? Sort of to >>>> correct for user mistake? >>>> >>>> Ryan >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> 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 > > ----------------------------------------------------------------------- > 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 > -- Sheldon McKay, PhD Cold Spring Harbor Laboratory New! Google Voice: (203) 701-9204 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ 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 |
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Re: GFF2 vs GFF3
by Ryan Golhar
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Here is an example from my questionable GFF file.
chr1 wtp read 3801 3842 42 + . bd=710_1348_1327_F3;rs=1;mm=0;g=T10223223101012112332220313011000323202020031123231;i=1; I am about to run the file through the GFF validator to see what happens... Sheldon McKay wrote: > I have never, ever seen GFF2 with more than nine columns, so a tenth > column is certainly not diagnostic. But a very easy way to tell if > it is GFF3 or GFF2 is that the attribute/value pairs are in the ninth > column are space-delimited (not tab-delimited) in GFF2 and > '='-delimited in GFF3. > > GFF2: Name SpongeBob > GFF3: Name=SpongeBob > > On Wed, Nov 4, 2009 at 2:10 PM, Scott Cain <scott@...> wrote: >> Hi Ryan, >> >> The GFF2 spec is not particularly good as specifications go (which is >> part of the reason we needed GFF3), as it doesn't explicitly say how >> many tab delimited columns there are. While both attributes and >> comments are (sort of*) optional, the only way to include comments is >> with perl-style hash marks to set them off, and most parsers would >> miss comments at the end of a GFF line since they do a split on tabs >> into an array with 9 elements, so, GFF2 has 9 tab-delimited columns. >> >> *I wrote "sort of" with respect to attributes, since GBrowse won't >> function without at least a minimal attribute line indicating the >> feature's name/group. >> >> What this problem boils down to is that validating user input is hard; >> in fact, I'm still not sure that what you said is GFF3 really is, so >> trying to get a program to do it in a reasonable amount of time and >> with a reasonable user interface would be tough. There is a GFF3 >> validator at: >> >> http://dev.wormbase.org/db/validate_gff3/validate_gff3_online >> >> but it can be somewhat slow for large files. However, if you have >> more concrete suggestions for how to amend this situation, I would be >> willing to take a look. >> >> Scott >> >> >> >> On Nov 4, 2009, at 12:48 PM, Ryan Golhar wrote: >> >>> According to this, >>> http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml, GFF 2 has >>> 10 columns: >>> >>> <seqname> <source> <feature> <start> <end> <score> <strand> <frame> >>> [attributes] [comments] >>> >>> It attributes and comments are optional. >>> >>> GFF v3, http://www.sequenceontology.org/gff3.shtml, has 9 >>> columns...comments is now part of attributes. >>> >>> Is it possible for Gbrowse/bioperl to output to the user that >>> something >>> is wrong with their file that they uploaded? Right now, users have no >>> way of knowing w/o asking me to look at the apache error log... >>> >>> Ryan >>> >>> >>> Scott Cain wrote: >>>> Hi Ryan, >>>> >>>> Both GFF2 and GFF3 have 9 columns, so the number of columns in the >>>> file >>>> is not informative. Nevertheless, I don't think it is reasonable for >>>> GBrowse/BioPerl to disregard the version information it is given >>>> and to >>>> instead second guess what the file says it is. If it is really >>>> wrong, I >>>> suggest you write a simple perl tool to fix the GFF file before it is >>>> put in place or uploaded or whatever its ultimate destiny is. >>>> >>>> Scott >>>> >>>> >>>> On Nov 4, 2009, at 12:33 PM, Ryan Golhar wrote: >>>> >>>>> Hi, >>>>> >>>>> I have a GFF file that is being generated with the header line >>>>> stating >>>>> its a GFF version 2 file. However, it is actually a GFF 3 file >>>>> based on >>>>> the number of columns in the file. >>>>> >>>>> I see in my apache error log: >>>>> >>>>> Use of uninitialized value in pattern match (m//) at >>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF2Loader.pm >>>>> line 410, <F> line 2611781., referer: >>>>> http://localhost/cgi-bin/gbrowse/arabidopsis/ >>>>> >>>>> >>>>> If I change the version number in the file from 2 or 3, the errors >>>>> go >>>>> away. Unfortunately the software generating the GFF file is not >>>>> under >>>>> my control so I can't fix that. Is it possible to have Gbrowse >>>>> check >>>>> the file for version regardless of what the file says? Sort of to >>>>> correct for user mistake? >>>>> >>>>> Ryan >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> 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 >> ----------------------------------------------------------------------- >> 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 >> > > > ------------------------------------------------------------------------------ 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 |
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