[Bioperl-l] Running into problems

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Feb 1 16:31:49 EST 2012


Sorry, typo.
Make sure you have your hsp_filter sub in there somewhere.

--Rusell

> -----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: Thursday, 2 February 2012 3:34 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Running into problems
> 
> 
> 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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> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
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> problems-tp33228400p33243496.html
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