[Bioperl-l] New to BioPerl ... part II
Olivier BUHARD
Olivier.Buhard at inserm.fr
Mon Mar 24 12:51:01 UTC 2014
Hi,
thank you a lot Christopher, Francisco and Hilmar for your great help!
I followed all your propositions. Changed to Strawberry Perl (latest
version, and I uninstalled Activeperl before) and I can now have a
connection to the local mysql server on my computer.
I look a bit closer in the files generated during the build process (in
cpan utility) in the meanwhile and found as you mention below, a problem
with the DBD::mysql that didn't take into account the connection
parameters I pass through the Makefile.PL script. Looking further into
the code, I saw the script asked for both user AND password... and I
didn't have a password for that specific user accessing my biosql db...
there was a function called "win32_config" or something like this that
then generated the configuration for the tests with a default user
'ODBC' I don't use.
Well, this is just for the "little story".
Now I checked my DBI and mysql DBD, they work fine. I can retrieve data
from another mysql database I use frequently.
Then I installed BioPerl (1.6.923) and BioPerl-DB (1.006900). I had to
force install for both because I got many exceptions, and particularly
one in Bio::Root::IO i'm a bit worried about, I feel it's an important
piece of the module.
Once I finished install, I tried load_seqdatabase.pl on a truncated
version of the same gbpri1.seq from NCBI FTP. But again it doesn't work,
but for a different reason than before I think. I get a connection to my
biosql database, but there is some glitch, I can't find out what happens.
The script threw me a lot of warning messages, saying "failed to insert
or to be found by unique key".
As I forced the installation of BioPerl and BioPerl-DB, is there a
chance I missed some critical message? It seems the problem is in the
BioPerl-DB module but not related to the connection (when I enter a
wrong user, I get a denied access message, so it's OK for the connection
apparently).
I'll try on a Linux install soon to verify. But if you have any idea in
the meanwhile, I'll appreciate a lot!
Below is the output from the load_seqdatabase script I get:
Many thanks for your (really appreciated) help!
Best regards.
Olivier
-----------------------
C:\Perl Bio Scripts>perl load_seqdatabase.pl --dbname=biosql_hs
--dbuser=biodb_user gbTest.seq
Loading gbTest.seq ...
Subroutine new redefined at C:/strawberry/perl/site/lib/Bio\Species.pm
line 120, <GEN0> line 98.
Subroutine classification redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line 176, <GEN0> line 98.
Subroutine species redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line272, <GEN0> line 98.
Subroutine genus redefined at C:/strawberry/perl/site/lib/Bio\Species.pm
line 377, <GEN0> line 98.
Subroutine sub_species redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line 407, <GEN0> line 98.
Subroutine variant redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line455, <GEN0> line 98.
Subroutine binomial redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line 490, <GEN0> line 98.
Subroutine validate_species_name redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line 530, <GEN0> line 98.
Subroutine validate_name redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line 539, <GEN0> line 98.
.../...
Subroutine remove_Descendant redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line 604, <GEN0> line 98.
Subroutine name redefined at C:/strawberry/perl/site/lib/Bio\Species.pm
line 606, <GEN0> line 98.
Subroutine taxon redefined at C:/strawberry/perl/site/lib/Bio\Species.pm
line 619, <GEN0> line 98.
Subroutine tree redefined at C:/strawberry/perl/site/lib/Bio\Species.pm
line 639, <GEN0> line 98.
Subroutine DESTROY redefined at
C:/strawberry/perl/site/lib/Bio\Species.pm line649, <GEN0> line 98.
--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement
execution: Le champ 'term_id' ne peut Ûtre vide (null)
name: INSERT ASSOC [2]
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
values: FK[Bio::SeqFeature::Generic]:3,
FK[Bio::Annotation::SimpleValue]:, value:"mRNA", rank:"1"
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement
execution: Le champ 'term_id' ne peut Ûtre vide (null)
name: INSERT ASSOC [2]
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
values: FK[Bio::SeqFeature::Generic]:3,
FK[Bio::Annotation::SimpleValue]:, rank:"1", value:"Homo sapiens"
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement
execution: Le champ 'term_id' ne peut Ûtre vide (null)
name: INSERT ASSOC [2]
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
values: FK[Bio::SeqFeature::Generic]:4,
FK[Bio::Annotation::SimpleValue]:, value:"hepatocyte growth factor
activator inhibitor", rank:"1"
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement
execution: Le champ 'term_id' ne peut Ûtre vide (null)
name: INSERT ASSOC [2]
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
values: FK[Bio::SeqFeature::Generic]:4,
FK[Bio::Annotation::SimpleValue]:, value:"BAA25014.1", rank:"1"
---------------------------------------------------
Could not store AB000099:
------------- EXCEPTION -------------
MSG: create: object (Bio::Species) failed to insert or to be found by
unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219
STACK Bio::DB::Persistent::PersistentObject::create
C:/strawberry/perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:257
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
STACK Bio::DB::Persistent::PersistentObject::store
C:/strawberry/perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:284
STACK (eval) load_seqdatabase.pl:630
STACK toplevel load_seqdatabase.pl:612
-------------------------------------
at load_seqdatabase.pl line 643, <GEN0> line 162.
Le 21/03/2014 05:59, Fields, Christopher J a écrit :
> Agree with Francisco, Strawberry Perl is definitely the way to go. You can do it with ActivePerl but IIRC the PPM installs were always a pain.
>
> chris
>
> On Mar 20, 2014, at 10:54 PM, Francisco J. Ossandón <fossandonc at hotmail.com> wrote:
>
>> Hi Olivier,
>> Currently there is no PPM package from the latest version, the last one is
>> like 4 years old, so is better to download the latest version from CPAN
>> (1.6.923).
>> I have one recommendation though... unless you are very attached to
>> ActivePerl, uninstall it and install Strawberry Perl instead
>> (http://strawberryperl.com/).
>>
>> When I started to learn Bioperl several years ago I used ActivePerl too, but
>> it always gave me trouble installing new modules from CPAN. I switched to
>> Strawberry a few years ago and is much better because it includes by default
>> additional libraries and compiling tools (gcc, mingw, dmake, etc) that makes
>> easier the installation of CPAN modules (including some Bioperl
>> dependencies)... Since the installation instructions at the wiki only
>> considered ActivePerl, I updated the wiki a few days ago to include
>> Strawberry Perl as an additional option
>> (http://www.bioperl.org/wiki/Special:RecentChanges).
>>
>> By the way... something odd among the errors you are getting is that it says
>> that " perl514.dll cannot be found", but if you installed 5.18 you should
>> have perl518.dll instead... did you install 5.18 above 5.14?? Because I can
>> tell that overwriting it can produce obscure and mysterious bugs, is better
>> to uninstall the old one first, then delete the whole folder, and then make
>> a clean install of the new one.
>>
>> Cheers and good luck,
>>
>> Francisco J. Ossandon
>>
>> -----Mensaje original-----
>> De: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Hilmar Lapp
>> Enviado el: jueves, 20 de marzo de 2014 20:49
>> Para: Olivier BUHARD
>> CC: BioPerl List
>> Asunto: Re: [Bioperl-l] New to BioPerl ... part II
>>
>> I think the exception message appears due to the actual problem you're
>> already describing. Bioperl-db will catch the failure and then print the
>> error message. Since it doesn't seem to say anything about failing to
>> connect to the database, it's either failing before or past that point for
>> an unexpected reason. My suspicion is that it fails to load the DBD driver
>> for Perl DBI.
>>
>> You can test that by writing a small script (not using Bioperl or
>> Bioperl-DB) that simply opens a connection to the database. If that fails,
>> that's where the problem is.
>>
>> You can also try that with Bioperl-db:
>>
>> $conn = $dbadp->dbcontext()->dbi()->new_connection();
>>
>> This should give you an open DBI-compliant connection.
>>
>> If that part works, then the problem is somewhere with the dynamic
>> auto-loading code.
>>
>> -hilmar
>>
>>
>>
>> On Wed, Mar 19, 2014 at 6:46 PM, Olivier BUHARD
>> <Olivier.Buhard at inserm.fr>wrote:
>>
>>> Hi,
>>>
>>> thank you all for your answers. I had the (wrong) notion that windows
>>> did ignore the shebang...
>>>
>>> I am using Bioperl 1.6.1... I'll try to install 1.6.923 but I can't
>>> find it with ActivePerl ppm (I switched to 5.18), so I'll have to try
>>> with command line ppm. I'm running windows XP... perhaps also have to
>>> try with Linux.
>>>
>>> I'm getting in the doc and tutos I can find about Bioperl-db and I'm
>>> beginning to understand how it deals with parsing and organizing the data.
>>> However, my first attempts to load sequences in my BioSQL db are
>>> unsuccessful. From the gbpri1.seq I downloaded from NCBI FTP,
>>> load_seqdatabase.pl crashes at the moment it tries to INSERT in the
>>> db, telling me perl514.dll cannot be found, and sending a bunch of
>>> error messages in a last breath:
>>>
>>> C:\tmp>perl load_seqdatabase.pl -dbname biosql_hs -dbuser biodb_user
>>> -dbpass ******** gbpri1.seq Loading gbpri1.seq ...
>>> UNIVERSAL->import is deprecated and will be removed in a future perl
>>> UNIVERSAL->at
>>> C:/Perl/site/lib/Bio/Tree/TreeFunctionsI.pm line 94.
>>> UNIVERSAL->import is deprecated and will be removed in a future perl
>>> UNIVERSAL->at
>>> C:/Perl/site/lib/Bio\Tree\TreeFunctionsI.pm line 94.
>>>
>>> ------------- EXCEPTION -------------
>>> MSG: failed to open connection:
>>> STACK Bio::DB::DBI::base::new_connection
>>> C:/Perl/site/lib/Bio/DB/DBI/ba
>>> se.pm:267
>>> STACK Bio::DB::DBI::base::get_connection
>>> C:/Perl/site/lib/Bio/DB/DBI/ba
>>> se.pm:227
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh
>>> C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1498
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::rollback
>>> C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1417
>>> STACK toplevel load_seqdatabase.pl:636
>>> -------------------------------------
>>>
>>> I think I'm doing something wrong, but I can't find what. The mySQL
>>> server (version 4.1.9) is on, I've installed the DBI and DBD::mySQL. I
>>> checked the user for its privileges and password, so what can be wrong?
>>>
>>> I've tried writing a shorter script to get in the command that breaks
>>> the process (below) and I found it was when it tries to ->create():
>>>
>>> #!perl
>>>
>>> use strict;
>>> use Bio::DB::BioDB;
>>> use Bio::SeqIO;
>>>
>>> my $seq_file = shift or die("GB_crawler.pl - Usage : perl
>>> GB_crawler.pl <SEQ_FILE>\n\n");
>>>
>>> my $dbadp = Bio::DB::BioDB->new( -database => 'biosql',
>>> -host => 'localhost',
>>> -user => 'biodb_user',
>>> -pass => 'THE_PASSWORD_HERE',
>>> -dbname => 'biosql_hs',
>>> -driver => 'mysql'
>>> );
>>> $dbadp->verbose(1);
>>>
>>> my $seqio_obj = Bio::SeqIO->new(-file => "<$seq_file", -format =>
>>> 'genbank' ); while (my $seq_obj = $seqio_obj->next_seq()){
>>> print $seq_obj->display_id(),"\n";
>>> my $species = $seq_obj->species();
>>> my $seq_spec = $species->binomial();
>>> if ($seq_spec eq 'Homo sapiens') { # I'm just interested in Hs seq
>>> my $p_seq = $dbadp->create_persistent($seq_obj);
>>> $p_seq->create();
>>> }
>>> }
>>>
>>> The output is: (I can't put all here, it' too long...)
>>>
>>> C:\tmp>perl GB_crawler.pl gbpri1.seq
>>>
>>> UNIVERSAL->import is deprecated and will be removed in a future perl
>>> UNIVERSAL->at
>>> C:/Perl/site/lib/Bio/Tree/TreeFunctionsI.pm line 94.
>>> AB000095
>>> attempting to load adaptor class for Bio::Seq::RichSeq
>>> attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
>>> attempting to load adaptor class for Bio::Seq
>>> attempting to load module Bio::DB::BioSQL::SeqAdaptor
>>> instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
>>>
>>> .../...
>>>
>>> attempting to load adaptor class for Bio::Tree::TreeFunctionsI
>>> attempting to load module Bio::DB::BioSQL::TreeFunctionsIAdaptor
>>> attempting to load module
>>> Bio::DB::BioSQL::TreeFunctionsAdaptor
>>> UNIVERSAL->import is deprecated and will be removed in a future perl
>>> UNIVERSAL->at
>>> C:/Perl/site/lib/Bio\Tree\TreeFunctionsI.pm line 94.
>>> no adaptor found for class Bio::Tree::Tree no adaptor found for class
>>> Bio::Annotation::TypeManager no adaptor found for class
>>> Bio::DB::Taxonomy::list no adaptor found for class Bio::Tree::Tree
>>> attempting to load adaptor class for BioNamespace
>>> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor
>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor
>>> no adaptor found for class Bio::Annotation::TypeManager no adaptor
>>> found for class Bio::DB::Taxonomy::list no adaptor found for class
>>> Bio::Tree::Tree attempting to load driver for adaptor class
>>> Bio::DB::BioSQL::
>>> BioNamespaceAdaptor
>>>
>>> attempting to load driver for adaptor class Bio::DB::BioSQL::
>>> BasePersistenceAdaptor
>>> Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
>>> peer for Bio::DB::BioSQL::BioNamespaceAdaptor
>>>
>>> ------------- EXCEPTION -------------
>>> MSG: failed to open connection:
>>> STACK Bio::DB::DBI::base::new_connection
>>> C:/Perl/site/lib/Bio/DB/DBI/ba
>>> se.pm:267
>>>
>>> STACK Bio::DB::DBI::base::get_connection
>>> C:/Perl/site/lib/Bio/DB/DBI/ba
>>> se.pm:227
>>>
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh
>>> C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1498
>>> STACK Bio::DB::BioSQL::BaseDriver::insert_object
>>> C:/Perl/site/lib/Bio/DB/
>>> BioSQL/BaseDriver.pm:970
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>> C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:212
>>> STACK Bio::DB::Persistent::PersistentObject::create
>>> C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:257
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>> C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
>>> STACK Bio::DB::Persistent::PersistentObject::create
>>> C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:257
>>> STACK toplevel GB_crawler.pl:52
>>> -------------------------------------
>>>
>>> Again, the script halts asking for Perl514.dll, then the EXCEPTION MSG
>>> appears...
>>> Is there a chance ActivePerl 5.18 couldn't work with Bioperl-DB (I
>>> have
>>> 1.006000 version)?
>>>
>>> Thanks for any answer !
>>>
>>> Best regards
>>>
>>> Olivier
>>>
--
--------------------
BUHARD Olivier
"Instabilité de microsatellites et cancer"
Centre de Recherche Saint Antoine
équipe 11/INSERM UMRS 938
Bâtiment Kourilsky,
Hôpital Saint Antoine
34 rue Crozatier
75012 PARIS
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