[Bioperl-l] New to BioPerl ... part II
Francisco J. Ossandón
fossandonc at hotmail.com
Fri Mar 21 03:54:33 UTC 2014
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
>
> Le 06/03/2014 21:04, Smithies, Russell a écrit :
>
>> BioPerl-1.6.923.tar.gz installed OK for me and I can run your script
>> on that gbk file from Windows with ActivePerl 5.16.1 and I get no
>> warnings at all.
>>
>> --Russell
>>
>> -----Original Message-----
>> From:bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces@
>> lists.open-bio.org] On Behalf Of Smithies, Russell
>> Sent: Friday, 7 March 2014 8:03 a.m.
>> To: Olivier BUHARD;bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] New to BioPerl - A little presentation...
>> and a question about GenBank and Bioperl
>>
>> Hi,
>> -w on the shebang line is for displaying warnings, so naturally if
>> you leave it off you won't get warnings.
>> A slightly better method is to 'use warnings' instead - but be aware
>> it gives you slightly different results Eg.
>>
>> #!perl
>>
>> use strict;
>> use warnings;
>> use Bio::SeqIO;
>>
>> And on Windows systems you can shorten the shebang line to #!perl as
>> obviously the usual path of #!/usr/bin/perl isn't relevant.
>>
>> When I run your code on the exact same file I get the required output
>> and no warnings - though admittedly that's on a Linux system.
>> Is it possible you're running an older version of BioPerl?
>> I'll update my Windows BioPerl (to CJFIELDS/BioPerl-1.6.923.tar.gz)
>> install and give it a go.
>>
>> --Russell
>>
>>
>>
>> -----Original Message-----
>> From:bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces@
>> lists.open-bio.org] On Behalf Of Olivier BUHARD
>> Sent: Friday, 7 March 2014 12:06 a.m.
>> To:bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] New to BioPerl - A little presentation... and a
>> question about GenBank and Bioperl
>>
>> Hello,
>>
>>
>> I'm new to BioPerl and would like to ask you for a few advice about
>> the use of Bioperl.
>>
>> I am a molecular biologist and I frequently use Perl to write scripts
>> to prepare or analyse files I get from various databases, so I'm
>> familiar enough with Perl.
>> We work in my lab on a particular type of tumorigenic process called
>> MSI, for MicroSatellite Instability. I'll not go through all the
>> story but a hallmark of the associated cancers is that the size of
>> their genomic repeated DNA sequences spread throughout the genome, is
altered.
>> Up to now, we got a list of those sequences from a collaboration who
>> could make that for us. But now the list we have is old and we have
>> to get this information by our own means and naturally I started
>> looking at Bioperl.
>> And before I go through learning all I need (which I guess, will take
>> some time), I will really appreciate if someone could tell me if I
>> Bioperl can help from start to end.
>>
>> In summary, I plan to search all the short repetitive sequences (I'm
>> just interested in human genome at the moment) I can find in the
>> Genbank flat file provided by the NCBI FTP site. The idea is to
>> create a BioSQL database (I already installed using a schema for
>> mySQL) that I could query using an appropriate algorithm.
>> I saw Bioperl is made to read those files with multiple entries. So
>> building the BioSQL database would not be a problem. My first
>> question is about how I will crawl through the genomic sequences to
>> detect short repeat tandem sequences of defined size and patterns
>> (some are mononucleotides repeats, like (A)27, other could be
>> dinucleotides redpeats like (CA)12, etc.). BLAST is not design for
>> such a job... Are there some tools already available in Bioperl to
>> deal with low complexity DNA in general and short tandem repeats in
>> particular, something like repeatmasker or windowmasker but with a
>> different kind of output? I'm interested in retrieving some of the
>> features provided with the genbank format (find repeats in coding or
>> non-coding regions, get their position in the genes or the transcripts
with respect to exon position, intron-exon proximity...).
>>
>> I also have a more direct and "practical" question. I just tried a
>> few sample codes provided in the beginners' toturials on the Bioperl
>> site. I just ran the following on the gbpri1.seq provided on the NCBI
>> FTP but I got some errors and warnings for many (but not all) sequences.
>>
>> #!/usr/bin/perl -w
>>
>> use strict;
>> use Bio::SeqIO;
>>
>> 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"; }
>>
>> This is what I get for AB000095 locus:
>>
>> Replacement list is longer than search list at
>> C:/Perl/site/lib/Bio/Range.pm lin e 251.
>> UNIVERSAL->import is deprecated and will be removed in a future perl
>> UNIVERSAL->at
>> C:/Perl/
>> site/lib/Bio/Tree/TreeFunctionsI.pm line 94 Subroutine new redefined
>> at C:/Perl/site/lib/Bio\Location\Simple.pm line 93, <GE
>> N0> line 41.
>> Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Simple.pm
>> line 115,
>> <GEN0> line 41.
>> Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm
>> line 144, <G
>> EN0> line 41.
>> Subroutine length redefined at
>> C:/Perl/site/lib/Bio\Location\Simple.pm
>> line 190,
>> <GEN0> line 41.
>> Subroutine location_type redefined at
>> C:/Perl/site/lib/Bio\Location\Simple.pm li ne 281, <GEN0> line 41.
>> Subroutine to_FTstring redefined at
>> C:/Perl/site/lib/Bio\Location\Simple.pm line
>> 328, <GEN0> line 41.
>> Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location\Simple.pm
>> line 370,
>> <GEN0> line 41.
>> AB000095
>>
>> But when I remove the shebang option -w... the warnings disappear.
>> (I use ActivePerl 5.14.2 on a Windows XP computer. I had the idea
>> that shebang was not used under Windows, but it seems tat's wrong here...
>> Is that due to some problem about my Perl installation, or is it
>> Bio::SeqIO code related?
>>
>> Thank in advance for any answer.
>>
>> Kind regards
>>
>>
> --
>
> --------------------
>
> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
--
Hilmar Lapp -:- lappland.io
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