Problem in loading gff3 files using bp_seqfeature_load.pl
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Problem in loading gff3 files using bp_seqfeature_load.pl
by parimi rohit
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Hi All,
I am trying to load a GFF3 file into the MySQL database using the GBrowse tutorial in localhost. I am following the instructions given in the section 5.2. The MySQL Backend. I got the following error when i used the perl script to laod data into the created database "ctg2195split2". Can anyone let me know what the problem is and how to rectify it. Message on the shell prompt: [root@PP-4307-FPF01 ctg2195test]# /usr/bin/bp_seqfeature_load.pl -d ctg2195split2 -s Bio::DB::SeqFeature -a DBI::mysql -v -f -c -u root 5_GMHMMwheat.gff3 loading 5_GMHMMwheat.gff3... 173 features loaded in 0.08s Building object tree... 0.03s Loading bulk data into database...DBD::mysql::db do failed: The used command is not allowed with this MySQL version at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 530, <GEN0> line 174. -------------------- EXCEPTION -------------------- MSG: The used command is not allowed with this MySQL version STACK Bio::DB::SeqFeature::Store::DBI::mysql::_finish_bulk_update /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm:530 STACK Bio::DB::SeqFeature::Store::finish_bulk_update /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:1443 STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:324 STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:322 STACK Bio::DB::SeqFeature::Store::Loader::load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:219 STACK toplevel /usr/bin/bp_seqfeature_load.pl:102 My MySQL version is : Server version: 5.1.36-log Source distribution Regards, Rohit ------------------------------------------------------------------------------ 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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Problem in loading gff3 files using bp_seqfeature_load.pl
by parimi rohit
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Hi All, I am trying to load a GFF3 file into the MySQL database using the GBrowse tutorial in localhost. I am following the instructions given in the section 5.2. The MySQL Backend. I got the following error when I used the perl script to laod data into the created database "ctg2195split2". Can anyone let me know what the problem is and how to rectify it. Message on the shell prompt: [root@PP-4307-FPF01 ctg2195test]# /usr/bin/bp_seqfeature_load.pl -d ctg2195split2 -s Bio::DB::SeqFeature -a DBI::mysql -v -f -c -u root 5_GMHMMwheat.gff3 loading 5_GMHMMwheat.gff3... 173 features loaded in 0.08s Building object tree... 0.03s Loading bulk data into database...DBD::mysql::db do failed: The used command is not allowed with this MySQL version at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 530, <GEN0> line 174. -------------------- EXCEPTION -------------------- MSG: The used command is not allowed with this MySQL version STACK Bio::DB::SeqFeature::Store::DBI::mysql::_finish_bulk_update /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm:530 STACK Bio::DB::SeqFeature::Store::finish_bulk_update /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:1443 STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:324 STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:322 STACK Bio::DB::SeqFeature::Store::Loader::load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:219 STACK toplevel /usr/bin/bp_seqfeature_load.pl:102 My MySQL version is : Server version: 5.1.36-log Source distribution Regards, Rohit ------------------------------------------------------------------------------ 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: Problem in loading gff3 files using bp_seqfeature_load.pl
by Scott Cain-4
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Hi Rohit,
Can you tell us what version of BioPerl you are using? In the version I have, line 530 of mysql.pm doesn't correspond to a mysql command. If you are using a checkout from svn, please copy the first two lines of mysql.pm. They should look something like this: package Bio::DB::SeqFeature::Store::DBI::mysql; # $Id: mysql.pm 16229 2009-10-02 15:31:29Z lstein $ As for the specific problem, I can only assume that your version of mysql either wasn't compiled or configured to do something that the SeqFeature::Store adaptor needs to do, but without the command itself, it's hard to say what the problem might be. Scott On Mon, Oct 5, 2009 at 6:09 PM, parimi rohit <rohit.parimi@...> wrote: > Hi All, > > I am trying to load a GFF3 file into the MySQL database using the GBrowse > tutorial in localhost. I am following the instructions given in the section > 5.2. The MySQL Backend. I got the following error when i used the perl > script to laod data into the created database "ctg2195split2". > > Can anyone let me know what the problem is and how to rectify it. > > > Message on the shell prompt: > > [root@PP-4307-FPF01 ctg2195test]# /usr/bin/bp_seqfeature_load.pl -d > ctg2195split2 -s Bio::DB::SeqFeature -a DBI::mysql -v -f -c -u root > 5_GMHMMwheat.gff3 > > loading 5_GMHMMwheat.gff3... > > 173 features loaded in > 0.08s > Building object tree... 0.03s > > Loading bulk data into database...DBD::mysql::db do failed: The used command > is not allowed with this MySQL version at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line > 530, <GEN0> line 174. > > -------------------- EXCEPTION -------------------- > MSG: The used command is not allowed with this MySQL version > STACK Bio::DB::SeqFeature::Store::DBI::mysql::_finish_bulk_update > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm:530 > STACK Bio::DB::SeqFeature::Store::finish_bulk_update > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:1443 > STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:324 > STACK Bio::DB::SeqFeature::Store::Loader::load_fh > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:322 > STACK Bio::DB::SeqFeature::Store::Loader::load > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:219 > STACK toplevel /usr/bin/bp_seqfeature_load.pl:102 > > My MySQL version is : > > Server version: 5.1.36-log Source distribution > > > Regards, > Rohit > > > ------------------------------------------------------------------------------ > 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 > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ 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: Problem in loading gff3 files using bp_seqfeature_load.pl
by parimi rohit
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Hi Scott,
I was using BioPerl 1.6.0 when I tried to load data using the bp_seqfeature_load.pl script before. I installed BioPerl 1.6.1 yesterday to check if that would help me to make any progress. I also installed perl 5.10.1. I used to have perl 5.8.8 before. Now I tried to use the command: bp_seqfeature_load.pl -c -f -d ctg2195split2 -u root ctg2195split2.fasta 5_GMHMMwheat.gff3 I had the following error message: install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC contains: /usr/local/lib/perl5/5.10.1/x86_64-linux /usr/local/lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.10.1 .) at (eval 45) line 3. Perhaps the DBD::mysql perl module hasn't been fully installed, or perhaps the capitalisation of 'mysql' isn't right. Available drivers: DBM, ExampleP, File, Gofer, Proxy, Sponge. at /usr/local/lib/perl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 212 I identified that the DBD::mysql module was missing and I downloaded it using CPAN and tried to install it. When I run perl Makefile.pl with the following options and later run the make command, I get the following error, command: [FP_Facility@PP-4307-FPF01 DBD-mysql-4.012]$ perl Makefile.PL --testdb=dbmysqltest --testuser=root --testhost=localhost [FP_Facility@PP-4307-FPF01 DBD-mysql-4.012]$ make cp lib/DBD/mysql.pm blib/lib/DBD/mysql.pm cp lib/DBD/mysql/GetInfo.pm blib/lib/DBD/mysql/GetInfo.pm cp lib/DBD/mysql/INSTALL.pod blib/lib/DBD/mysql/INSTALL.pod cp lib/Bundle/DBD/mysql.pm blib/lib/Bundle/DBD/mysql.pm cc -c -I/usr/local/lib/perl5/site_perl/5.10.1/x86_64-linux/auto/DBI -I/usr/include/mysql -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fwrapv -DDBD_MYSQL_WITH_SSL -DDBD_MYSQL_INSERT_ID_IS_GOOD -g -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"4.012\" -DXS_VERSION=\"4.012\" -fPIC "-I/usr/local/lib/perl5/5.10.1/x86_64-linux/CORE" dbdimp.c In file included from dbdimp.c:20: dbdimp.h:22:49: error: mysql.h: No such file or directory dbdimp.h:23:45: error: mysqld_error.h: No such file or directory dbdimp.h:25:49: error: errmsg.h: No such file or directory In file included from dbdimp.c:20: dbdimp.h:144: error: expected specifier-qualifier-list before ‘MYSQL’ dbdimp.h:236: error: expected specifier-qualifier-list before ‘MYSQL_RES’ In file included from dbdimp.c:20: dbdimp.h:293: error: expected ‘)’ before ‘*’ token dbdimp.h:296: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘mysql_st_internal_execute’ dbdimp.h:328: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token dbdimp.c:408: error: expected ‘)’ before ‘*’ token dbdimp.c:635: error: ‘FIELD_TYPE_VAR_STRING’ undeclared here (not in a function) dbdimp.c:645: error: ‘FIELD_TYPE_DECIMAL’ undeclared here (not in a function) dbdimp.c:655: error: ‘FIELD_TYPE_TINY’ undeclared here (not in a function) and so on........ I tried the install with version 4.013 but the error remained same. For your convinience I am attaching the entire console error in this mail. Please let me know the problmem in installing the DBD::mysql module. On Tue, Oct 6, 2009 at 8:53 AM, Scott Cain <scott@...> wrote: Hi Rohit, ------------------------------------------------------------------------------ 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: Problem in loading gff3 files using bp_seqfeature_load.pl
by Scott Cain-4
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Hi Rohit,
I don't have enough information to really answer, but it seems like the DBD::mysql installer couldn't find the appropriate header files to compile. It needs files from the mysql instance that you are running in order to compile and install. The easist solution to this is to use a prepackaged mysql server for your platform, and get the "dev" package to go with it. It is also possible that, if you have those files but they are in a "non-standard" place, that you could provide that information on the command line when you execute perl Makefile.PL, but I don't know enough about DBD::mysql to say for sure. Scott On Oct 8, 2009, at 6:35 PM, parimi rohit wrote: > Hi Scott, > > I was using BioPerl 1.6.0 when I tried to load data using the > bp_seqfeature_load.pl script before. I installed BioPerl 1.6.1 > yesterday to check if that would help me to make any progress. I > also installed perl 5.10.1. I used to have perl 5.8.8 before. > > Now I tried to use the command: bp_seqfeature_load.pl -c -f -d > ctg2195split2 -u root ctg2195split2.fasta 5_GMHMMwheat.gff3 > > I had the following error message: > > install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC > (@INC contains: /usr/local/lib/perl5/5.10.1/x86_64-linux /usr/local/ > lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/x86_64-linux / > usr/local/lib/perl5/site_perl/5.10.1 .) at (eval 45) line 3. > Perhaps the DBD::mysql perl module hasn't been fully installed, > or perhaps the capitalisation of 'mysql' isn't right. > Available drivers: DBM, ExampleP, File, Gofer, Proxy, Sponge. > at /usr/local/lib/perl5/site_perl/5.10.1/Bio/DB/SeqFeature/Store/ > DBI/mysql.pm line 212 > > I identified that the DBD::mysql module was missing and I downloaded > it using CPAN and tried to install it. When I run perl Makefile.pl > with the following options and later run the make command, I get the > following error, > > command: > [FP_Facility@PP-4307-FPF01 DBD-mysql-4.012]$ perl Makefile.PL -- > testdb=dbmysqltest --testuser=root --testhost=localhost > > [FP_Facility@PP-4307-FPF01 DBD-mysql-4.012]$ make > > cp lib/DBD/mysql.pm blib/lib/DBD/mysql.pm > cp lib/DBD/mysql/GetInfo.pm blib/lib/DBD/mysql/GetInfo.pm > cp lib/DBD/mysql/INSTALL.pod blib/lib/DBD/mysql/INSTALL.pod > cp lib/Bundle/DBD/mysql.pm blib/lib/Bundle/DBD/mysql.pm > cc -c -I/usr/local/lib/perl5/site_perl/5.10.1/x86_64-linux/auto/DBI > -I/usr/include/mysql -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions - > fstack-protector --param=ssp-buffer-size=4 -m64 -D_GNU_SOURCE - > D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing - > fwrapv -DDBD_MYSQL_WITH_SSL -DDBD_MYSQL_INSERT_ID_IS_GOOD -g -fno- > strict-aliasing -pipe -fstack-protector -I/usr/local/include - > D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"4.012\" - > DXS_VERSION=\"4.012\" -fPIC "-I/usr/local/lib/perl5/5.10.1/x86_64- > linux/CORE" dbdimp.c > In file included from dbdimp.c:20: > dbdimp.h:22:49: error: mysql.h: No such file or directory > dbdimp.h:23:45: error: mysqld_error.h: No such file or directory > dbdimp.h:25:49: error: errmsg.h: No such file or directory > In file included from dbdimp.c:20: > dbdimp.h:144: error: expected specifier-qualifier-list before ‘MYSQL’ > dbdimp.h:236: error: expected specifier-qualifier-list before > ‘MYSQL_RES’ > In file included from dbdimp.c:20: > dbdimp.h:293: error: expected ‘)’ before ‘*’ token > dbdimp.h:296: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or > ‘__attribute__’ before ‘mysql_st_internal_execute’ > dbdimp.h:328: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or > ‘__attribute__’ before ‘*’ token > dbdimp.c:408: error: expected ‘)’ before ‘*’ token > dbdimp.c:635: error: ‘FIELD_TYPE_VAR_STRING’ undeclared here (not in > a function) > dbdimp.c:645: error: ‘FIELD_TYPE_DECIMAL’ undeclared here (not in a > function) > dbdimp.c:655: error: ‘FIELD_TYPE_TINY’ undeclared here (not in a > function) > > and so on........ > > > I tried the install with version 4.013 but the error remained same. > > For your convinience I am attaching the entire console error in this > mail. Please let me know the problmem in installing the DBD::mysql > module. > > > On Tue, Oct 6, 2009 at 8:53 AM, Scott Cain <scott@...> > wrote: > Hi Rohit, > > Can you tell us what version of BioPerl you are using? In the version > I have, line 530 of mysql.pm doesn't correspond to a mysql command. > If you are using a checkout from svn, please copy the first two lines > of mysql.pm. They should look something like this: > > package Bio::DB::SeqFeature::Store::DBI::mysql; > # $Id: mysql.pm 16229 2009-10-02 15:31:29Z lstein $ > > As for the specific problem, I can only assume that your version of > mysql either wasn't compiled or configured to do something that the > SeqFeature::Store adaptor needs to do, but without the command itself, > it's hard to say what the problem might be. > > Scott > > ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ 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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Problem using bp_seqfeature_load.pl
by Arun Ramani
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Hello,
I am trying to load a gff file into a MySQL database as per the tutorial. When I try to run bp_seqfeature_load.pl I get the following error. Error Message: Undefined subroutine &Bio::DB::SeqFeature::Store::rearrange called at /Library/Perl/5.8.8/Bio/DB/SeqFeature/Store.pm line 351. I did not come across any other instances of any one having this error. It seems to be like the libraries have a conflict and I have reinstalled bio-perl. I am still having the same errors. Please let me know if there is anything I can do to fix this and thanks a lot for your help in this regard. |
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Re: Problem using bp_seqfeature_load.pl
by Scott Cain-4
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Hello,
The rearrange method is inherited from somewhere deep within BioPerl (like Bio::Root or the like, I don't remember off hand). If the SeqFeature::Store module can't find it, something is wrong with BioPerl. What version of BioPerl are you using? How did you install it? Could there be more than one instance of BioPerl installed on your system? Scott On Wed, Nov 4, 2009 at 9:13 AM, deepfloyd <arun.to2008@...> wrote: > > Hello, > I am trying to load a gff file into a MySQL database as per the tutorial. > When I try to run bp_seqfeature_load.pl I get the following error. > > > Error Message: > Undefined subroutine &Bio::DB::SeqFeature::Store::rearrange called at > /Library/Perl/5.8.8/Bio/DB/SeqFeature/Store.pm line 351. > > I did not come across any other instances of any one having this error. It > seems to be like the libraries have a conflict and I have reinstalled > bio-perl. I am still having the same errors. Please let me know if there is > anything I can do to fix this and thanks a lot for your help in this regard. > > > -- > View this message in context: http://old.nabble.com/Problem-in-loading-gff3-files-using-bp_seqfeature_load.pl-tp25761770p26196979.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > 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: Problem using bp_seqfeature_load.pl
by Arun Ramani
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Hi Scott,
I am using BioPerl 1.6.1 and I installed it using CPAN. There is only one instance of BioPerl on my machine. At least when I do sudo find / -name Store.pm, I get back a single instance of its occurrence. The bp_seqfeature_load.pl says "use Bio::DB::GFF::Util::Rearrange" and I find Rearrange.pm in this path. If this is the rearrange that it requires later, I guess it is looking for it in the right place. Would you suggest I delete the current version of BioPerl and reinstall? Thanks Arun
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Re: Problem using bp_seqfeature_load.pl
by Scott Cain-4
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Hi Arun,
I was thinking that SFStore was using the _rearrange method from Bio::RootI, but as you pointed out, SFStore is explicitly using the rearrange method from Bio::DB::GFF::Util::Rearrange (which exports the rearrange method), so the fact that it can't find it when the load script is running still indicates that there is a problem. I'll throw this back out to the entire list: does anybody know what the problem might be? I currently have a Mac and use SFStore with Postgres and it works fine (Arun appears to be use a Mac with MySQL). Generally "reinstall" isn't a solution like it would be with other operating systems, but it seems that something may have gone wrong here. Scott On Wed, Nov 4, 2009 at 10:18 AM, deepfloyd <arun.to2008@...> wrote: > > Hi Scott, > > I am using BioPerl 1.6.1 and I installed it using CPAN. There is only one > instance of BioPerl on my machine. At least when I do sudo find / -name > Store.pm, I get back a single instance of its occurrence. > > The bp_seqfeature_load.pl says "use Bio::DB::GFF::Util::Rearrange" and I > find Rearrange.pm in this path. If this is the rearrange that it requires > later, I guess it is looking for it in the right place. > > Would you suggest I delete the current version of BioPerl and reinstall? > > Thanks > Arun > > > Scott Cain-4 wrote: >> >> Hello, >> >> The rearrange method is inherited from somewhere deep within BioPerl >> (like Bio::Root or the like, I don't remember off hand). If the >> SeqFeature::Store module can't find it, something is wrong with >> BioPerl. What version of BioPerl are you using? How did you install >> it? Could there be more than one instance of BioPerl installed on >> your system? >> >> Scott >> >> >> >> On Wed, Nov 4, 2009 at 9:13 AM, deepfloyd <arun.to2008@...> wrote: >>> >>> Hello, >>> I am trying to load a gff file into a MySQL database as per the tutorial. >>> When I try to run bp_seqfeature_load.pl I get the following error. >>> >>> >>> Error Message: >>> Undefined subroutine &Bio::DB::SeqFeature::Store::rearrange called at >>> /Library/Perl/5.8.8/Bio/DB/SeqFeature/Store.pm line 351. >>> >>> I did not come across any other instances of any one having this error. >>> It >>> seems to be like the libraries have a conflict and I have reinstalled >>> bio-perl. I am still having the same errors. Please let me know if there >>> is >>> anything I can do to fix this and thanks a lot for your help in this >>> regard. >>> >>> >>> -- >>> View this message in context: >>> http://old.nabble.com/Problem-in-loading-gff3-files-using-bp_seqfeature_load.pl-tp25761770p26196979.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >> >> > > -- > View this message in context: http://old.nabble.com/Problem-in-loading-gff3-files-using-bp_seqfeature_load.pl-tp25761770p26198060.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > 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. 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Re: Problem using bp_seqfeature_load.pl
by Arun Ramani
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Hi,
I managed to get it working. I did a new clean install of BioPerl and DBD::mysql and that reset all the conflicts. It is now seeing all the libraries and modules and I had no issues loading a test database. Thanks for your time. Cheers Arun
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