[Bioperl-l] error

Chris Fields cjfields at uiuc.edu
Tue Mar 28 09:48:34 EST 2006


Sonmitra,

I tried the script from your attachment last time and it worked fine (I had
no problems, got results from a BLAST hit), and I'm running bioperl updated
from CVS.  The CVS repository has recently changed, so I'll point out the
browsable version for now.   Note that this is bleeding-edge code, though
it's probably more stable than most CVS code.

Go here:

http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/

At the bottom of the web page is a link to download the contents of the
repository as a tarball.  Click this link to download bioperl-live,
decompress everything, then change into the bioperl-live folder.  Type the
following, waiting between each until it is finished.

perl Makefile.PL
make  
make test
make install

You will get a number of prompts after 'perl Makefile.PL' asking about
script installation, etc (not a bad idea to install the scripts).  'make
test' is optional and will probably not pass all tests (rarely does), but
it's a good idea to run it to make sure most things work properly.  If
nothing works with 'make test' you're in trouble.

Okay, so here's where I rant a bit:

Most of your questions are answered in the FAQ, the installation pages (and
links), and the HOWTO's (particularly the Beginner's HOWTO).  Googling the
mail-list also helps.  All of this is available through the Bioperl wiki,
which is a rich (and updated) source of information:

http://www.bioperl.org/wiki/Main_Page
http://www.bioperl.org/wiki/FAQ
http://www.bioperl.org/wiki/Installing_BioPerl
http://www.bioperl.org/wiki/HOWTOs
http://www.bioperl.org/wiki/Mailing_lists

Make sure to read my previous response to you very carefully.  There were a
few things I mentioned to you that are very important.  Also, when I
mentioned responding to the mailing list, I meant it (note that I added the
mailing list to this response).  I will not respond to you again unless it's
directly through or copied to the list in some way.

Remember, Bioperl is essentially a volunteer effort.  We really don't mind
helping out with user problems when we know the answer or can help out in
some way (or fix the problem/bug if there is one), but there needs to be a
record of the responses here so that people can search through the archives
to find answers to questions, problems, etc.  Responding to every
'bioperl-module x doesn't work, why?' query quickly gets redundant when the
potential answer is in the mail-list archives, wiki, etc.  Again, if someone
knows the answer, we will generally respond, but don't expect us to drop
everything we're doing in order to help you out. Everybody here has their
own priorities, agendas, and so on; don't be surprised if you don't get an
immediate answer to your questions.  

Also, your chances of getting a response to a question are much greater by
emailing the list than through me directly (you might get an answer from
somebody using bioperl on Linux, for instance).  This is a community effort.
I would say, by far, a large percentage of the questions posted here get
some response.  

My 2c

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: Tuesday, March 28, 2006 12:28 AM
> To: Chris Fields
> Subject: RE: [Bioperl-l] error
> 
> I am sending you my script & input as asked by you .
> Tell me one thing more precisely that which bioperl
> version  i will install .
> 
> 
> #Code for :Running Remote Blast Program
> package Bio::Perl;
> use Bio::Perl;
> use Bio::Tools::Run::RemoteBlast;
> my (@params, $remote_blast_object, $blast_file, $r,
> $rc, $database);
> my $sleep_time = 2;
> $database = 'swissprot';
> @params = (-prog=>'blastp', -data=>'swissprot',
> -expect=>'1e-10');
> $remote_blast_object =
> Bio::Tools::Run::RemoteBlast->new(@params);
> $blast_file = Bio::Root::IO->catfile("seqs.fasta");
> $r = $remote_blast_object->submit_blast( $blast_file);
> while ( my @rids = $remote_blast_object->each_rid ) {
> foreach my $rid ( @rids ) {
> my$rc = $remote_blast_object->retrieve_blast($rid);
> if(!ref($rc) ) { # $rc not a reference => error or job
> not yet finished
> if( $rc < 0 ) {
> $remote_blast_object->remove_rid($rid);
> print "Error return code for BlastID code $rid ...
> \n";}
> sleep $sleep_time; if ($sleep_time < 120) {$sleep_time
> *= 2;}
> } else {
> 
> $sleep_time = 2;
> $remote_blast_object->remove_rid($rid);
> my $count = 0;
> while( my $res = $rc->next_result ) {
> $count++;
> print "result db is ", $res->database_name(), "\n";
> while( my $hit = $res->next_hit()) {
> print $hit->name(),"\t",$hit->description()," \t";
> while( my $hsp = $hit->next_hsp ) {
> print "\t",$hsp->bits,"\t",$hsp->evalue;
> }
> print "\n";
> }
> }
> }
> }
> }
> 
> 
> 
> Input file :
> Seqs.fasta
> >seq1
> MGLPQPGLWLKRLWVLLEVAVHVVVGKVLLILFPDRVKRNILAM
> 
> GEKTGMTRNPHFSHDNWIPTFFSTQYFWFVLKVRWQRLEDTTELGGLAPNCPVVRLSG
> 
> QRCNIWEFMQGNRPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSIADFLVIYIEEAHASG
> 
> >seq2
> MGLPQPGLWLKRLWVLLEVAVHVVVGKVLLILFPDRVKRNILAM
> 
> GEKTGNRPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSIADFLVIYIEEAHASDGWAFK
> 
> NNMDIRNHQNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQLYAALPERLYIIQEGRI
>                      LYKGKSGPWNYNPEEVRAVLEKLHS
> >seq3
> MGLPQPGLWLKRLWVLLEVAVHVVVGKVLLILFPDRVKRNILAM
> 
> GEKTGMTRNPHFSHDNWIPTFFSTQYFWFVLKVRWQRLEDTTELGGLAPNCPVVRLSG
> 
> QRCNIWEFMQDGWAFKNNMDIRNHQNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQL
> 
> YAALPERLYIIQEGRILYKGKSGPWNYNPEEVRAVLEKLHS
> 
> 
> 
> Or even if I give a file with single sequence that
> time also it's not working & generating the same error
> .:Invaid RID
> Another file : roa1.fasta
> >ROA1_HUMAN Heterogeneous nuclear ribonucleoprotein A1
> (Helix-destabilizing prot
> ein) (Single-strand RNA-binding protein) (hnRNP core
> protein A1).
> SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT
> YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL
> RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL
> SKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSG
> DGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGG
> SGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSS
> SSSSYGSGRRF
> 
> 
> 
> 
> 
> --- Chris Fields <cjfields at uiuc.edu> wrote:
> 
> > 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
> >
> === message truncated ===
> 
> 
> 
> 
> __________________________________________________________
> Yahoo! India Matrimony: Find your partner now. Go to
> http://yahoo.shaadi.com



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