[Bioperl-l] Running into problems

Rutger Vos rutgeraldo at gmail.com
Tue Jan 31 10:27:53 EST 2012


Here's a pretty good page that describes the topic of scoping:
http://perl.plover.com/FAQs/Namespaces.html

On Tue, Jan 31, 2012 at 4:24 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Joel,
>
> This is a fundamental perl thing: when you "use strict" (which is a
> very good thing to do to help you catch other, more difficult to
> detect problems), you need to identify all of the variables you use
> either as coming from a package you used, or when you first declare
> them in your script, with "my" in front of it.  That is what all of
> the "Global symbol" things are about.  I'd suggest getting the
> "Learning Perl" book, which is quite good for beginners.
>
> Scott
>
>
> On Tue, Jan 31, 2012 at 9:50 AM, Bradyjoel <joel.klein at wur.nl> wrote:
> >
> > 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 "$seqio_obj" requires explicit package name at blast1.plline
> > 24.
> > Global symbol "$seq_obj" requires explicit package name at blast1.plline
> > 25.
> > Global symbol "$seqio_obj" requires explicit package name at blast1.plline
> > 25.
> > Global symbol "$result" requires explicit package name at blast1.plline 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
> >>> --
> >>> View this message in context: http://old.nabble.com/Running-into-
> >>> problems-tp33228400p33228400.html
> >>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >>>
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> > View this message in context:
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> >
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>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
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>



-- 
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com


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