[Bioperl-l] Running into problems

[Bradyjoel]

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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