[Bioperl-l] Running into problems
joel.klein at wur.nl
Wed Feb 1 09:33:33 EST 2012
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
Undefined subroutine &main::hsp_filter called at
/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
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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