[Bioperl-l] Running into problems

Juan Jovel jovel_juan at hotmail.com
Tue Jan 31 10:54:33 EST 2012


Those are not BioPerl problems, but basic Perl errors. I suggest you consolidate your Perl background before moving into BioPerl, it would make things much easier (try to understand how modules work as well, so you will be able to profit from BioPerl modules at maximum).



> Date: Tue, 31 Jan 2012 06:50:29 -0800
> From: joel.klein at wur.nl
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Running into problems
> 
> 
> I update my script with your recommendations however it still gives me the
> following errors when I run it with the following command:
> 
> $ perl blast1.pl
> "my" variable $writer masks earlier declaration in same scope at blast1.pl
> line 50.
> Global symbol "$fac" requires explicit package name at blast1.pl line 15.
> Global symbol "$seqio_obj" requires explicit package name at blast1.pl line
> 24.
> Global symbol "$seq_obj" requires explicit package name at blast1.pl line
> 25.
> Global symbol "$seqio_obj" requires explicit package name at blast1.pl line
> 25.
> Global symbol "$result" requires explicit package name at blast1.pl line 29.
> Global symbol "$fac" requires explicit package name at blast1.pl line 29.
> Global symbol "$file" requires explicit package name at blast1.pl line 33.
> Global symbol "$fac" requires explicit package name at blast1.pl line 33.
> Global symbol "$fac" requires explicit package name at blast1.pl line 35.
> Execution of blast1.pl aborted due to compilation errors.
> 
> Apparently, I did something wrong but I dont know how to resolve this, any
> suggestion?
> Thanks for your help so far.
>  
> 
> Joel 
> 
> 
> Smithies, Russell wrote:
> > 
> > I'd probably cheat a bit and optimise my blast parameters so there's less
> > output to process.
> > Also, are you sure an e-value of 100 is what you're after? I'd be aiming
> > much lower - probably 1e-6.
> > It also pays to mask repeats if you're blasting against a whole genome to
> > cut down on the number of rubbish hits.
> > 
> > --Russell
> > 
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
> >> Sent: Tuesday, 31 January 2012 12:21 a.m.
> >> To: Bioperl-l at lists.open-bio.org
> >> Subject: [Bioperl-l] Running into problems
> >> 
> >> 
> >> HI all,
> >> 
> >> I'm quite new to bioperl and tried to write a script that creates a
> >> database
> >> from a newly sequenced genome and then preforms a tblastn against a
> >> multiple protein fasta file and then creates a blast report were only the
> >> results that only preservers identity scores above 98%. However my script
> >> keeps returning numerous errors and problems and since I have only a
> >> little
> >> experience I cannot determine were I went wrong. I include the code that
> >> I
> >> got so far in the attachment. Hope someone can help.
> >> Regards Joel
> >> 
> >> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
> >> --
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> >> 
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