[Bioperl-l] error

Chris Fields cjfields at uiuc.edu
Mon Mar 27 14:36:52 EST 2006


Please reply to the mailing list as well.  Don't use attachments either,
especially Word-like doc files b/c they might not get through.  Copy and
paste any text into the email.

As for your attached script, I get everything to work fine; below is a
sampling of the returned info.  Your bioperl version is WAY too old (v1.0.1
is from June 2002; there have been many updates since then, esp. to BLAST
and RemoteBlast), so that's likely the issue.  Update to the latest from CVS
(my recommendation if you use RemoteBlast).  

Oh, and a bit of advice: don't use 'package Bio::Perl' in a script like
this:

#Code for :Running Remote Blast Program
package Bio::Perl;
use Bio::Perl;
use Bio::Tools::Run::RemoteBlast;
...

It didn't do any harm here AFAIK but it will likely cause havoc in your code
down the line.  You normally don't use this declaration unless you are
coding a perl module (class), so by using this statement here you
essentially change the default package prefix from main to Bio::Perl here
(not good).  Any declared variables, methods, etc. are therefore in
Bio::Perl's namespace and not main which could interfere with vars, methods,
etc. declared as class members/methods in Bio::Perl.  That apparently didn't
happen though, but I would highly recommend not doing it again in the
future, JIC.

Here's the output:
--------------------------------------------------
result db is Non-redundant SwissProt sequences
sp|P49895|IOD1_HUMAN    Type I iodothyronine deiodinase (Type-I
5'deiodinase) (DIOI) (Type 1 DI) (5DI)          290     9e-79

sp|P24389|IOD1_RAT      Type I iodothyronine deiodinase (Type-I
5'deiodinase) (DIOI) (Type 1 DI) (5DI)          240     1e-63

sp|Q61153|IOD1_MOUSE    Type I iodothyronine deiodinase (Type-I
5'deiodinase) (DIOI) (Type 1 DI) (5DI)          236     2e-62

sp|P49894|IOD1_CANFA    Type I iodothyronine deiodinase (Type-I
5'deiodinase) (DIOI) (Type 1 DI) (5DI)          232     3e-61

sp|Q95N00|IOD1_SUNMU    Type I iodothyronine deiodinase (Type-I
5'deiodinase) (DIOI) (Type 1 DI) (5DI)          214     8e-56

......

sp|Q9Z1Y9|IOD2_MOUSE    Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              134
2e-31
sp|P70551|IOD2_RAT      Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              134
2e-31
sp|Q6QN12|IOD2_PIG      Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              132
4e-31
sp|Q92813|IOD2_HUMAN    Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              131
1e-30
sp|Q5I3B2|IOD2_BOVIN    Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              130
2e-30
sp|P49898|IOD3_RANCA    Type III iodothyronine deiodinase (Type-III
5'deiodinase) (DIOIII) (Type 3 DI) (5DIII)          130
3e-30
sp|Q9IAX2|IOD2_CHICK    Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              128
1e-29
sp|P49896|IOD2_RANCA    Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              125
7e-29
sp|P79747|IOD2_FUNHE    Type II iodothyronine deiodinase (Type-II
5'deiodinase) (DIOII) (Type 2 DI) (5DII)              120
2e-27

--------------------------------------------------

Good luck!

Chris

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: sonmitra mondal [mailto:sonmitra4u at yahoo.co.in]
> Sent: Monday, March 27, 2006 3:32 AM
> To: Chris Fields
> Subject: Re: [Bioperl-l] error
> 
> Respected Sir,
> I am sending all the details as asked by you .
> 
> Script : attached file
> I am writing & saving the script using vi editor of
> Linux .
> O.S.        : Linux
> Perl Version: v5.8.0
> BioPerl     : perl-bioperl1-1.0-1.i386.rpm
> I/P file    : seqs.fasta
>             : the details of the i/p file is
>               given in the attached file .
> 
> I am just hanging on this single error :Invalid RID
> for more than 1 n 1/2 week . Please help me as soon as
> possible for you .
> 
> with regards,
> Sonmitra
> 
> --- Chris Fields <cjfields at uiuc.edu> wrote:
> 
> > Which script?  I'm guessing one from the Beginner's
> > HOWTO or one
> > using Bio::Perl.  An RID is usually from a NCBI
> > BLAST run.
> >
> > We need more information (OS, perl version, bioperl
> > version, script,
> > input, etc) to actually help you; otherwise we're
> > just shooting in
> > the dark.
> >
> > Chris
> >
> > On Mar 24, 2006, at 6:06 AM, sonmitra mondal wrote:
> >
> > > while running the script in unix i am facing one
> > > problem , everytime during execution it's showing
> > 1
> > > error message : Invalid RID .
> > > Please help me
> > >
> > > With regards
> > > Sonmitra
> > > student of M.Sc. Bioinformatics
> > >
> > >
> > >
> > >
> >
> __________________________________________________________
> > > Yahoo! India Matrimony: Find your partner now. Go
> > to http://
> > > yahoo.shaadi.com
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > >
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> 
> 
> 
> 
> __________________________________________________________
> Yahoo! India Matrimony: Find your partner now. Go to
> http://yahoo.shaadi.com



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