[Bioperl-l] Running into problems

Fields, Christopher J cjfields at illinois.edu
Wed Feb 1 11:55:11 EST 2012


It's possible the attachment was scrubbed, can you send this to me directly?

chris

On Feb 1, 2012, at 10:47 AM, Bradyjoel wrote:

> 
> the bioperl version that I have found with this command is:
> $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> 1.006901
> $  perl -MBio::Root::Version -e 'printf "%vd\n",
> $Bio::Root::Version::VERSION'
> 49.46.48.48.54.57.48.49
> 
> And I put the perl code that I'm currently using in the attachment. 
> 
> 
> 
> Fields, Christopher J wrote:
>> 
>> 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
>>>>> --
>>>>> View this message in context: http://old.nabble.com/Running-into-
>>>>> problems-tp33228400p33228400.html
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>>>>> 
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>>> 
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> 
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