[Bioperl-l] Running into problems

Bradyjoel joel.klein at wur.nl
Wed Feb 1 11:47:14 EST 2012


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
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