[Bioperl-l] Fwd: megablast using bioperl

[Xiujing Gu]

Thanks for the links!
But, they only talk about the regular blastall program, not the megablast.

I am not sure how can I switch from blastall to megablast. I tried to just call megablast, but I got a very differenct report.

$VAR1 = bless( {
                 'primary_seq' => bless( {
                                           'display_id' => 'test',
                                           '_seq_length' => undef,
                                           '_root_verbose' => 0,
                                           'seq' =>
 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTCTGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCACAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCTAGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTATCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCCTTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGCTTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGCCTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATTTATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAGCAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACTTGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGCAGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGTTAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTAGCCA
GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAGATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTGTGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGACCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCAGTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATACTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTTTACCAAGAATG',
                                           'alphabet' => 'dna'
                                         }, 'Bio::PrimarySeq' ),
                 '_root_verbose' => 0
               }, 'Bio::Seq' );
Can't locate object method "nextSbjct" via package "Bio::Seq" 



Thanks,
Xiujing Gu


--- On Mon, 2/1/10, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:

From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
Date: Monday, February 1, 2010, 3:12 PM

Have you read the docs? It's very well documented:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm

Have you searched the BioPerl wiki? Again, well documented with examples:
http://www.bioperl.org/wiki/HOWTO:StandAloneBlast

And if that doesn't help, perhaps you need to improve your Google skills:
http://www.google.com/support/websearch/?ctx=web

--Russell



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Jason Stajich
> Sent: Tuesday, 2 February 2010 8:48 a.m.
> To: BioPerl List
> Cc: xiujingg at yahoo.com
> Subject: [Bioperl-l] Fwd: megablast using bioperl
> 
> Xiujing -
> Your message is best asked on the mailing list.
> 
> Begin forwarded message:
> 
> > From: Xiujing Gu <xiujingg at yahoo.com>
> > Date: February 1, 2010 7:58:55 AM PST
> > To: jason at bioperl.org
> > Subject: megablast using bioperl
> >
> > Hello Jason:
> >
> > After numerous googling, I found you might be the only person who
> > knows about this subject. Would you so kindly show me an example of
> > setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
> >
> > Thanks a lot!
> >
> > Best regards,
> > Xiujing
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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