[Bioperl-l] Running into problems

Fields, Christopher J cjfields at illinois.edu
Wed Feb 1 10:37:06 EST 2012


That looks like a bug to me, but it's hard to say w/o having more information, such as the actual code you are using, the version of BioPerl, etc.  See the BioPerl FAQ to get the version number.

chris

On Feb 1, 2012, at 8:33 AM, Bradyjoel wrote:

> 
> Thank you for your help! I think I'm almost there, but I still get 1 more
> error when I run the script:
> 
> $ perl blast2.pl
> Searching gi|146341649|ref|YP_001206697.1|
> Undefined subroutine &main::hsp_filter called at
> /usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
> line 71.
> 
> 
> 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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