[Bioperl-l] Running into problems

Bradyjoel joel.klein at wur.nl
Wed Feb 1 09:32:19 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
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
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/Running-into-problems-tp33228400p33243492.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



More information about the Bioperl-l mailing list