[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.
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.
>>> -----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
>>> 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
>>> experience I cannot determine were I went wrong. I include the code that
>>> 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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