[Bioperl-l] Running into problems

Bradyjoel joel.klein at wur.nl
Thu Feb 2 05:29:11 EST 2012


That did the trick, its working now thank you all very much!



Smithies, Russell wrote:
> 
> 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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>> >> problems-tp33228400p33228400.html
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>> >>
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