Perl Forum for Beginners

Hello there

Jul 6, 2009 10:19 pm
Emanuele Osimo

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Hello there,
I'm a biologist and I'm trying to start using bioperl for bioinformatic
purposese but I've never programmed.
Could you suggest me something to read to start from 0 level?

In the meantime, I installed bioperl and I'm doing some little trials to get
to know something: I would like to create a script that reads a series of
NM_... codes (RefSeq for cDNA) and creates a multifasta file that contains
all the genomic sequences of the related genes.
I found this article:
http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences
I'm trying the part "Using the Perl API at ENSEMBL"

But when I just paste it in a file and run it into perl, it says:

> Can't locate Bio/EnsEMBL/DBSQL/DBAdaptor.pm in @INC (@INC contains:
> /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8
> /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin
> /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level
> /Library/Perl/Updates/5.8.8
> /System/Library/Perl/5.8.8/darwin-thread-multi-2level
> /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level
> /Library/Perl/5.8.8 /Library/Perl
> /Network/Library/Perl/5.8.8/darwin-thread-multi-2level
> /Network/Library/Perl/5.8.8 /Network/Library/Perl
> /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .)
> at getgenomseq line 7.
> BEGIN failed--compilation aborted at getgenomseq line 7.
>

I thought I have to install the Ensembl API, and I did that, but it
continues to give me the same error.
What am I doing wrong?
Thanks
Emanuele

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Jul 7, 2009 1:33 am
Jim Gibson
Re: Hello there

On 7/6/09 Mon Jul 6, 2009 3:19 PM, "Emanuele Osimo" <e.osimo@gmail.com>
scribbled:

> Hello there,
> I'm a biologist and I'm trying to start using bioperl for bioinformatic
> purposese but I've never programmed.
> Could you suggest me something to read to start from 0 level?

See the FAQ 2 for Perl. Try this at a command line:

perldoc perlfaq2

for information on Perl or this extract:

perldoc -q books

for some good books. I would recommend starting by reading the book
"Learning Perl", by Schwartz, et. al. There is some material for beginners
included with the built-in Perl documentation. See "perldoc perl" for an
index of what is available.

>
> In the meantime, I installed bioperl and I'm doing some little trials to get
> to know something: I would like to create a script that reads a series of
> NM_... codes (RefSeq for cDNA) and creates a multifasta file that contains
> all the genomic sequences of the related genes.
> I found this article:
> http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences
> I'm trying the part "Using the Perl API at ENSEMBL"
>
> But when I just paste it in a file and run it into perl, it says:
>
>> Can't locate Bio/EnsEMBL/DBSQL/DBAdaptor.pm in @INC (@INC contains:
>> /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8
>> /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin
>> /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level
>> /Library/Perl/Updates/5.8.8
>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level
>> /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level
>> /Library/Perl/5.8.8 /Library/Perl
>> /Network/Library/Perl/5.8.8/darwin-thread-multi-2level
>> /Network/Library/Perl/5.8.8 /Network/Library/Perl
>> /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
>> /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .)
>> at getgenomseq line 7.
>> BEGIN failed--compilation aborted at getgenomseq line 7.
>>
>
> I thought I have to install the Ensembl API, and I did that, but it
> continues to give me the same error.
> What am I doing wrong?

You are missing the module Bio::EnsEMBL::DBSQL::DBAdaptor
Try to install it again and check the logs.
That is about all I can help with that problem.




Jul 7, 2009 1:25 am
Dave Tang
Re: Hello there

On Tue, 07 Jul 2009 08:19:50 +1000, Emanuele Osimo <e.osimo@gmail.com>
wrote:

> Hello there,
> I'm a biologist and I'm trying to start using bioperl for bioinformatic
> purposese but I've never programmed.
> Could you suggest me something to read to start from 0 level?

Have you looked at Beginning Perl for Bioinformatics
(http://oreilly.com/catalog/9780596000806/)? It is written for biologists
who wish to learn Perl. There is also a chapter on using bioperl.

Dave

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