[Gmod-gbrowse] Host IP in bp_seqfeature

Discussion:

[Gmod-gbrowse] Host IP in bp_seqfeature_load.pl

Samy Jeevan Karloss Antony

2014-12-18 12:33:33 UTC

I have to load GFF3 files into MySQL server using host ip address. How to mention the IP address in bp_seqfeature_load.pl?

Jeevan

Josh Goodman

2014-12-18 13:55:23 UTC

Permalink

Hi Jeevan,

bp_seqfeature_load.pl takes a data source name (dsn) string as one of its
options (-d or --dsn). That dsn string allows you to specify a hostname,
for MySQL see https://metacpan.org/pod/DBD::mysql#connect for the required
format.

Regards,
Josh

On Thu Dec 18 2014 at 7:34:14 AM Samy Jeevan Karloss Antony <

Post by Samy Jeevan Karloss Antony
I have to load GFF3 files into MySQL server using host ip address. How to
mention the IP address in bp_seqfeature_load.pl?
Jeevan
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Samy Jeevan Karloss Antony

2014-12-18 14:31:03 UTC

Permalink

Thanks, Josh.

When I tried these commands below,

bp_seqfeature_load.pl -d DBI:mysql:database=Test_161214;host=192.168.168.215' -f -c Test.gff3 Test_Chr_Unmasked.fasta

and

bp_seqfeature_load.pl -d DBI:mysql:database=Test_161214;host=192.168.168.215;port=3306' -f -c Test.gff3 Test_Chr_Unmasked.fasta

and

bp_seqfeature_load.pl -d "DBI:mysql:database=Test_161214;host=192.168.168.215;port=3306" -f -c Test.gff3 Test_Chr_Unmasked.fasta

I am getting this error below. Any idea where things go wrong?

#############################################################################################################################################
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 72, near "$dbname qw(IndexIt TopLevel Local2Global)"
Global symbol "$tmp" requires explicit package name at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 84.
Global symbol "%self" requires explicit package name at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 86.
Global symbol "%self" requires explicit package name at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 88.
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 89, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 96, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 103, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 109, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 116, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 123, near "}"
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm has too many errors.
Compilation failed in require at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
BEGIN failed--compilation aborted at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
Compilation failed in require at /local/genome/packages/perl/5.18.2/bin/bp_seqfeature_load.pl line 20.
BEGIN failed--compilation aborted at /local/genome/packages/perl/5.18.2/bin/bp_seqfeature_load.pl line 20.
#############################################################################################################################################

Jeevan

On 18 Dec 2014, at 14:55, Josh Goodman <***@indiana.edu<mailto:***@indiana.edu>> wrote:

Hi Jeevan,

bp_seqfeature_load.pl<http://bp_seqfeature_load.pl/> takes a data source name (dsn) string as one of its options (-d or --dsn). That dsn string allows you to specify a hostname, for MySQL see https://metacpan.org/pod/DBD::mysql#connect for the required format.

Regards,
Josh

On Thu Dec 18 2014 at 7:34:14 AM Samy Jeevan Karloss Antony <***@nmbu.no<mailto:***@nmbu.no>> wrote:
I have to load GFF3 files into MySQL server using host ip address. How to mention the IP address in bp_seqfeature_load.pl<http://bp_seqfeature_load.pl/>?

Jeevan

Josh Goodman

2014-12-18 14:55:50 UTC

Permalink

Those errors are fairly severe and fatal, perhaps your install is corrupted?

What does this show?

/local/genome/packages/perl/5.18.2/bin/perl -c
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_
64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm

If it does not say "LoadHelper.pm syntax OK" then I would reinstall. You
may need to adjust your library paths with the '-I' flag.

e.g.

perl -c -I /path/to/my/additional/library/directory
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_
64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm

Josh

On Thu Dec 18 2014 at 9:31:13 AM Samy Jeevan Karloss Antony <

Post by Samy Jeevan Karloss Antony
Thanks, Josh.
When I tried these commands below,
bp_seqfeature_load.pl -d
âDBI:mysql:database=Test_161214;host=192.168.168.215' -f -c Test.gff3
Test_Chr_Unmasked.fasta
and
bp_seqfeature_load.pl -d
âDBI:mysql:database=Test_161214;host=192.168.168.215;port=3306' -f -c
Test.gff3 Test_Chr_Unmasked.fasta
and
bp_seqfeature_load.pl -d
"DBI:mysql:database=Test_161214;host=192.168.168.215;port=3306" -f -c
Test.gff3 Test_Chr_Unmasked.fasta
I am getting this error below. Any idea where things go wrong?
#############################################################################################################################################
syntax error at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 72, near "$dbname qw(IndexIt TopLevel Local2Global)"
Global symbol "$tmp" requires explicit package name at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 84.
Global symbol "%self" requires explicit package name at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 86.
Global symbol "%self" requires explicit package name at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 88.
syntax error at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 89, near "}"
syntax error at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 96, near "}"
syntax error at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 103, near "}"
syntax error at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 109, near "}"
syntax error at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 116, near "}"
syntax error at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
line 123, near "}"
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm
has too many errors.
Compilation failed in require at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/GFF3Loader.pm
line 73.
BEGIN failed--compilation aborted at
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/GFF3Loader.pm
line 73.
Compilation failed in require at /local/genome/packages/perl/5.18.2/bin/
bp_seqfeature_load.pl line 20.
BEGIN failed--compilation aborted at
/local/genome/packages/perl/5.18.2/bin/bp_seqfeature_load.pl line 20.
#############################################################################################################################################
Jeevan
Hi Jeevan,
bp_seqfeature_load.pl takes a data source name (dsn) string as one of its
options (-d or --dsn). That dsn string allows you to specify a hostname,
for MySQL see https://metacpan.org/pod/DBD::mysql#connect for the
required format.
Regards,
Josh
On Thu Dec 18 2014 at 7:34:14 AM Samy Jeevan Karloss Antony <

Scott Cain

2014-12-18 14:57:21 UTC

Permalink

Hi Jeevan,

What version of BioPerl are you using? The line numbers in the error messages don't correspond to lines in the current version of that module.

Scott

Sent from my iPad

Post by Samy Jeevan Karloss Antony
Thanks, Josh.
When I tried these commands below,
bp_seqfeature_load.pl -d âDBI:mysql:database=Test_161214;host=192.168.168.215' -f -c Test.gff3 Test_Chr_Unmasked.fasta
and
bp_seqfeature_load.pl -d âDBI:mysql:database=Test_161214;host=192.168.168.215;port=3306' -f -c Test.gff3 Test_Chr_Unmasked.fasta
and
bp_seqfeature_load.pl -d "DBI:mysql:database=Test_161214;host=192.168.168.215;port=3306" -f -c Test.gff3 Test_Chr_Unmasked.fasta
I am getting this error below. Any idea where things go wrong?
#############################################################################################################################################
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 72, near "$dbname qw(IndexIt TopLevel Local2Global)"
Global symbol "$tmp" requires explicit package name at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 84.
Global symbol "%self" requires explicit package name at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 86.
Global symbol "%self" requires explicit package name at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 88.
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 89, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 96, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 103, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 109, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 116, near "}"
syntax error at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm line 123, near "}"
/local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/LoadHelper.pm has too many errors.
Compilation failed in require at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
BEGIN failed--compilation aborted at /local/genome/packages/perl/5.18.2/lib/site_perl/5.18.2/x86_64-linux/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
Compilation failed in require at /local/genome/packages/perl/5.18.2/bin/bp_seqfeature_load.pl line 20.
BEGIN failed--compilation aborted at /local/genome/packages/perl/5.18.2/bin/bp_seqfeature_load.pl line 20.
#############################################################################################################################################
Jeevan

Post by Josh Goodman
Hi Jeevan,
bp_seqfeature_load.pl takes a data source name (dsn) string as one of its options (-d or --dsn). That dsn string allows you to specify a hostname, for MySQL see https://metacpan.org/pod/DBD::mysql#connect for the required format.
Regards,
Josh

Post by Samy Jeevan Karloss Antony
I have to load GFF3 files into MySQL server using host ip address. How to mention the IP address in bp_seqfeature_load.pl?
Jeevan
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Get technology previously reserved for billion-dollar corporations, FREE
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