PrimerDesigner bug and fix
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PrimerDesigner bug and fix
by Joan Pontius-3
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Hi Gmod Mailing List
I am installing gbrowse on a new server, and found a problem and fix I want to share. The Bio::PrimerDesigner::primer3.pm that I installed has the sequence being saved as SEQUENCE. However, the new Primer3_core uses SEQUENCE_TEMPLATE for the sequence. So replacing SEQUENCE with SEQUENCE TEMPLATE in Bio::PrimerDesigner::primer3.pm seems to do the trick. Joan Pontius SAIC NCI Frederick ------------------------------------------------------------------------------ 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: PrimerDesigner bug and fix
by Taner Z. Sen
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Hi,
Is this bug fixed on CPAN? Or should I go ahead and make the changes Joan suggested? Taner At 12:58 PM 9/28/2009, Joan Pontius wrote: Hi Gmod Mailing List Computational Biologist, USDA-ARS, MaizeGDB Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology Iowa State University 1025 Crop Genome Informatics Lab Ames, IA 50011 Phone: (515) 294-5326 Fax: (515) 294-8280 taner@... taner@... http://www.public.iastate.edu/~taner/ ------------------------------------------------------------------------------ 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 |
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Re: PrimerDesigner bug and fix
by Sheldon McKay-3
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Hi Taner,
I maintain the CPAN module. I will have to add the fix in a way that maintains backward compatibility. I'll let you know. Sheldon On Tue, Oct 13, 2009 at 11:12 AM, Taner Z. Sen <taner@...> wrote: > Hi, > > Is this bug fixed on CPAN? Or should I go ahead and make the changes Joan > suggested? > > Taner > > At 12:58 PM 9/28/2009, Joan Pontius wrote: > > Hi Gmod Mailing List > > I am installing gbrowse on a new server, and found a problem and fix I > want to share. > > The Bio::PrimerDesigner::primer3.pm that I installed has the sequence > being saved as SEQUENCE. > However, the new Primer3_core uses SEQUENCE_TEMPLATE for the sequence. > > So replacing SEQUENCE with SEQUENCE TEMPLATE in > Bio::PrimerDesigner::primer3.pm seems to do the trick. > > > > Joan Pontius > SAIC NCI Frederick > > Taner Z. Sen, Ph.D. > Computational Biologist, USDA-ARS, MaizeGDB > Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology > Iowa State University > 1025 Crop Genome Informatics Lab > Ames, IA 50011 > Phone: (515) 294-5326 > Fax: (515) 294-8280 > taner@iastate. edu > http://www.public.iastate.edu/~taner/ > > ------------------------------------------------------------------------------ > 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 > > -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 203-893-1682 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ 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 |
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Re: PrimerDesigner bug and fix
by Taner Z. Sen
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Good idea. I installed primer3-1.1.4, and it works great!
Thanks Sheldon. On Nov 3, 2009, at 11:29 AM, Sheldon McKay wrote: > Hi Taner, > > This is not a GBrowse problem but a Bio::PrimerDesigner (and primer3) > problem. A short-term fix would be to downgrade to the stable release > (1.xx) of primer3, which works just fine. They introduced API changes > in the 2.0 alpha release that I am not done adjusting to in > Bio::PrimerDesigner. > > Sheldon > > On Tue, Nov 3, 2009 at 12:23 PM, Taner Zafer Sen <taner@...> > wrote: >> Hey Sheldon, >> >> Have you looked at this problem? My primer3 gives an error, and I >> don't know >> how to even start handling it. >> >> Gbrowse 1.70 >> RHEL 5.3 >> primer3-2.0.0-alpha >> >> The error is this: When I click "Design Primers", I get the >> following error: >> Some sort of primer3 error: >> PRIMER_PAIR_MAX_MISPRIMING=24.00 >> TARGET=9301,1 >> PRIMER_MAX_TM=63.0 >> PRIMER_OPT_TM=60.0 >> PRIMER_SELF_END=3.00 >> PRIMER_MAX_POLY_X=5 >> PRIMER_PRODUCT_SIZE_RANGE=50-350 >> PRIMER_OPT_SIZE=20 >> SEQUENCE=TCCATGTT ..DELETED... >> PRIMER_MIN_SIZE=18 >> PRIMER_MAX_GC=80.0 >> PRIMER_MIN_GC=20.0 >> PRIMER_MAX_END_STABILITY=9.0 >> PRIMER_MIN_TM=57.0 >> PRIMER_SELF_ANY=8.00 >> PRIMER_SEQUENCE_ID=Chr1 >> PRIMER_MAX_SIZE=27 >> PRIMER_NUM_RETURN=3 >> PRIMER_ERROR=Missing SEQUENCE tag >> I think it is related to the options to run primer3, but I am not >> sure. Any >> pointers to solve the problem? >> >> (BTW, if you'd like you can forward it to the gmod group; I didn't >> know what >> the right place to send) >> >> Thanks, >> Taner >> >> >> On Oct 13, 2009, at 4:02 PM, Sheldon McKay wrote: >> >>> Hi Taner, >>> >>> Not to worry. This has become a non-trivial problem, though, as the >>> primer3 devs have changed the API in other ways as well. Very >>> naughty >>> of them. >>> >>> Sheldon >>> >>> >>> On Tue, Oct 13, 2009 at 4:51 PM, Taner Z. Sen <taner@...> >>> wrote: >>>> >>>> BTW, I didn't mean to say that I will make the changes on the CPAN >>>> module, >>>> but I was planning to make changes in my local installation. I >>>> thought if >>>> the module was changed, I would just get it from CPAN. :) Now >>>> that I >>>> reread >>>> my e-mail, I realized I didn't explain that well :):) >>>> >>>> Taner >>>> >>>> At 11:41 AM 10/13/2009, you wrote: >>>> >>>> Hi Taner, >>>> >>>> I maintain the CPAN module. I will have to add the fix in a way >>>> that >>>> maintains backward compatibility. I'll let you know. >>>> >>>> Sheldon >>>> >>>> On Tue, Oct 13, 2009 at 11:12 AM, Taner Z. Sen >>>> <taner@...> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Is this bug fixed on CPAN? Or should I go ahead and make the >>>>> changes >>>>> Joan >>>>> suggested? >>>>> >>>>> Taner >>>>> >>>>> At 12:58 PM 9/28/2009, Joan Pontius wrote: >>>>> >>>>> Hi Gmod Mailing List >>>>> >>>>> I am installing gbrowse on a new server, and found a problem and >>>>> fix I >>>>> want to share. >>>>> >>>>> The Bio::PrimerDesigner::primer3.pm that I installed has the >>>>> sequence >>>>> being saved as SEQUENCE. >>>>> However, the new Primer3_core uses SEQUENCE_TEMPLATE for the >>>>> sequence. >>>>> >>>>> So replacing SEQUENCE with SEQUENCE TEMPLATE in >>>>> Bio::PrimerDesigner::primer3.pm seems to do the trick. >>>>> >>>>> >>>>> >>>>> Joan Pontius >>>>> SAIC NCI Frederick >>>>> >>>>> Taner Z. Sen, Ph.D. >>>>> Computational Biologist, USDA-ARS, MaizeGDB >>>>> Collab. Assist. Prof., Dept. of Genetics, Development and Cell >>>>> Biology >>>>> Iowa State University >>>>> 1025 Crop Genome Informatics Lab >>>>> Ames, IA 50011 >>>>> Phone: (515) 294-5326 >>>>> Fax: (515) 294-8280 >>>>> taner@iastate. edu >>>>> http://www.public.iastate.edu/~taner/ >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> 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 >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Sheldon McKay, PhD >>>> Cold Spring Harbor Laboratory >>>> Office/Mobile: 516-367-6998 / 203-893-1682 >>>> >>>> Sent from Milford, Connecticut, United States >>>> >>>> Taner Z. Sen, Ph.D. >>>> Computational Biologist, USDA-ARS, MaizeGDB >>>> Collab. Assist. Prof., Dept. of Genetics, Development and Cell >>>> Biology >>>> Iowa State University >>>> 1025 Crop Genome Informatics Lab >>>> Ames, IA 50011 >>>> Phone: (515) 294-5326 >>>> Fax: (515) 294-8280 >>>> taner@iastate. edu >>>> http://www.public.iastate.edu/~taner/ >>> >>> >>> >>> -- >>> Sheldon McKay, PhD >>> Cold Spring Harbor Laboratory >>> Office/Mobile: 516-367-6998 / 203-893-1682 >>> >>> Sent from Milford, Connecticut, United States >>> >> >> >> Taner Z. Sen, Ph.D. >> Computational Biologist, USDA-ARS, MaizeGDB >> Collab. Assist. Prof., Dept. of Genetics, Development and Cell >> Biology >> Iowa State University >> 1025 Crop Genome Informatics Lab >> Ames, IA 50011 >> Phone: (515) 294-5326 >> Fax: (515) 294-8280 >> taner@iastate. edu >> http://www.public.iastate.edu/~taner/ >> >> >> >> >> > > > > -- > Sheldon McKay, PhD > Cold Spring Harbor Laboratory > Office/Mobile: 516-367-6998 / 203-893-1682 > Taner Z. Sen, Ph.D. Computational Biologist, USDA-ARS, MaizeGDB Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology Iowa State University 1025 Crop Genome Informatics Lab Ames, IA 50011 Phone: (515) 294-5326 Fax: (515) 294-8280 taner@iastate. edu http://www.public.iastate.edu/~taner/ ------------------------------------------------------------------------------ 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 |
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Re: PrimerDesigner bug and fix
by Chris Fields-5
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Just to note, the bioperl primer tools have been updated to work with
primer3 2.0. chris On Nov 3, 2009, at 2:05 PM, Taner Zafer Sen wrote: > Good idea. I installed primer3-1.1.4, and it works great! > > Thanks Sheldon. > > On Nov 3, 2009, at 11:29 AM, Sheldon McKay wrote: > >> Hi Taner, >> >> This is not a GBrowse problem but a Bio::PrimerDesigner (and primer3) >> problem. A short-term fix would be to downgrade to the stable >> release >> (1.xx) of primer3, which works just fine. They introduced API >> changes >> in the 2.0 alpha release that I am not done adjusting to in >> Bio::PrimerDesigner. >> >> Sheldon >> >> On Tue, Nov 3, 2009 at 12:23 PM, Taner Zafer Sen <taner@...> >> wrote: >>> Hey Sheldon, >>> >>> Have you looked at this problem? My primer3 gives an error, and I >>> don't know >>> how to even start handling it. >>> >>> Gbrowse 1.70 >>> RHEL 5.3 >>> primer3-2.0.0-alpha >>> >>> The error is this: When I click "Design Primers", I get the >>> following error: >>> Some sort of primer3 error: >>> PRIMER_PAIR_MAX_MISPRIMING=24.00 >>> TARGET=9301,1 >>> PRIMER_MAX_TM=63.0 >>> PRIMER_OPT_TM=60.0 >>> PRIMER_SELF_END=3.00 >>> PRIMER_MAX_POLY_X=5 >>> PRIMER_PRODUCT_SIZE_RANGE=50-350 >>> PRIMER_OPT_SIZE=20 >>> SEQUENCE=TCCATGTT ..DELETED... >>> PRIMER_MIN_SIZE=18 >>> PRIMER_MAX_GC=80.0 >>> PRIMER_MIN_GC=20.0 >>> PRIMER_MAX_END_STABILITY=9.0 >>> PRIMER_MIN_TM=57.0 >>> PRIMER_SELF_ANY=8.00 >>> PRIMER_SEQUENCE_ID=Chr1 >>> PRIMER_MAX_SIZE=27 >>> PRIMER_NUM_RETURN=3 >>> PRIMER_ERROR=Missing SEQUENCE tag >>> I think it is related to the options to run primer3, but I am not >>> sure. Any >>> pointers to solve the problem? >>> >>> (BTW, if you'd like you can forward it to the gmod group; I didn't >>> know what >>> the right place to send) >>> >>> Thanks, >>> Taner >>> >>> >>> On Oct 13, 2009, at 4:02 PM, Sheldon McKay wrote: >>> >>>> Hi Taner, >>>> >>>> Not to worry. This has become a non-trivial problem, though, as >>>> the >>>> primer3 devs have changed the API in other ways as well. Very >>>> naughty >>>> of them. >>>> >>>> Sheldon >>>> >>>> >>>> On Tue, Oct 13, 2009 at 4:51 PM, Taner Z. Sen <taner@...> >>>> wrote: >>>>> >>>>> BTW, I didn't mean to say that I will make the changes on the CPAN >>>>> module, >>>>> but I was planning to make changes in my local installation. I >>>>> thought if >>>>> the module was changed, I would just get it from CPAN. :) Now >>>>> that I >>>>> reread >>>>> my e-mail, I realized I didn't explain that well :):) >>>>> >>>>> Taner >>>>> >>>>> At 11:41 AM 10/13/2009, you wrote: >>>>> >>>>> Hi Taner, >>>>> >>>>> I maintain the CPAN module. I will have to add the fix in a way >>>>> that >>>>> maintains backward compatibility. I'll let you know. >>>>> >>>>> Sheldon >>>>> >>>>> On Tue, Oct 13, 2009 at 11:12 AM, Taner Z. Sen >>>>> <taner@...> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> Is this bug fixed on CPAN? Or should I go ahead and make the >>>>>> changes >>>>>> Joan >>>>>> suggested? >>>>>> >>>>>> Taner >>>>>> >>>>>> At 12:58 PM 9/28/2009, Joan Pontius wrote: >>>>>> >>>>>> Hi Gmod Mailing List >>>>>> >>>>>> I am installing gbrowse on a new server, and found a problem and >>>>>> fix I >>>>>> want to share. >>>>>> >>>>>> The Bio::PrimerDesigner::primer3.pm that I installed has the >>>>>> sequence >>>>>> being saved as SEQUENCE. >>>>>> However, the new Primer3_core uses SEQUENCE_TEMPLATE for the >>>>>> sequence. >>>>>> >>>>>> So replacing SEQUENCE with SEQUENCE TEMPLATE in >>>>>> Bio::PrimerDesigner::primer3.pm seems to do the trick. >>>>>> >>>>>> >>>>>> >>>>>> Joan Pontius >>>>>> SAIC NCI Frederick >>>>>> >>>>>> Taner Z. Sen, Ph.D. >>>>>> Computational Biologist, USDA-ARS, MaizeGDB >>>>>> Collab. Assist. Prof., Dept. of Genetics, Development and Cell >>>>>> Biology >>>>>> Iowa State University >>>>>> 1025 Crop Genome Informatics Lab >>>>>> Ames, IA 50011 >>>>>> Phone: (515) 294-5326 >>>>>> Fax: (515) 294-8280 >>>>>> taner@iastate. edu >>>>>> http://www.public.iastate.edu/~taner/ >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> 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 >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Sheldon McKay, PhD >>>>> Cold Spring Harbor Laboratory >>>>> Office/Mobile: 516-367-6998 / 203-893-1682 >>>>> >>>>> Sent from Milford, Connecticut, United States >>>>> >>>>> Taner Z. Sen, Ph.D. >>>>> Computational Biologist, USDA-ARS, MaizeGDB >>>>> Collab. Assist. Prof., Dept. of Genetics, Development and Cell >>>>> Biology >>>>> Iowa State University >>>>> 1025 Crop Genome Informatics Lab >>>>> Ames, IA 50011 >>>>> Phone: (515) 294-5326 >>>>> Fax: (515) 294-8280 >>>>> taner@iastate. edu >>>>> http://www.public.iastate.edu/~taner/ >>>> >>>> >>>> >>>> -- >>>> Sheldon McKay, PhD >>>> Cold Spring Harbor Laboratory >>>> Office/Mobile: 516-367-6998 / 203-893-1682 >>>> >>>> Sent from Milford, Connecticut, United States >>>> >>> >>> >>> Taner Z. Sen, Ph.D. >>> Computational Biologist, USDA-ARS, MaizeGDB >>> Collab. Assist. Prof., Dept. of Genetics, Development and Cell >>> Biology >>> Iowa State University >>> 1025 Crop Genome Informatics Lab >>> Ames, IA 50011 >>> Phone: (515) 294-5326 >>> Fax: (515) 294-8280 >>> taner@iastate. edu >>> http://www.public.iastate.edu/~taner/ >>> >>> >>> >>> >>> >> >> >> >> -- >> Sheldon McKay, PhD >> Cold Spring Harbor Laboratory >> Office/Mobile: 516-367-6998 / 203-893-1682 >> > > > Taner Z. Sen, Ph.D. > Computational Biologist, USDA-ARS, MaizeGDB > Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology > Iowa State University > 1025 Crop Genome Informatics Lab > Ames, IA 50011 > Phone: (515) 294-5326 > Fax: (515) 294-8280 > taner@iastate. edu > http://www.public.iastate.edu/~taner/ > > > > > > ------------------------------------------------------------------------------ > 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 |
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