[Bioperl-l] Running into problems

Scott Cain scott at scottcain.net
Tue Jan 31 10:24:20 EST 2012


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 "$seqio_obj" requires explicit package name at blast1.pl line
> 24.
> Global symbol "$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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-- 
------------------------------------------------------------------------
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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