[Bioperl-l] Problems when retrieve sequences from GenBank

Caio Freire freire at ime.usp.br
Wed Oct 24 12:01:05 EDT 2012


Dear Chris,

Tx for your rapid answer.
We're anxious to see the next Bioperl update. It's an useful tool.
I agree that 'strict pragma' is important, but sometimes we have hurry...

Caio






2012/10/23 Fields, Christopher J <cjfields at illinois.edu>

> The 'Bad Gateway' error may very well be a server-side issue (see the HTML
> output, which gives a NCBI email).  The other issue with the BioProject
> should be addressed in the latest bipoperl code.
>
> However, I'm really not sure how you managed to get the script working
> correctly to begin with; are you sure this script is complete?  I gave up
> testing just b/c there are too many fundamental problems I was correcting
> (my limit is usually 2-3 corrections, I went past that in this case):
>
> 1) Missing variables, arrays, hashes ($seq, @names, %hash)
> 2) Possibly mislabeled variable, $cont1 -> $cont?
> 3) No localization
>
> I want to point out (and I hate to be the grammar police) but adding 'use
> strict; use warnings;' would have caught pretty much all of these issues.
>
> chris
>
> On Oct 23, 2012, at 6:33 AM, Caio Freire <freire at ime.usp.br> wrote:
>
> > Hi BioPerl users,
> >
> > A couple of year ago, I wrote a script to retrieve sequences from
> GenBank,
> > using Bio::DB::GenBank module and it worked very well in my machine on
> > Ubuntu 10.04. Now, I'm having some problems to do this job on Ubuntu
> 12.04,
> > since my script returns a warning like this "MSG: Unrecognized DBSOURCE
> > data: BioProject: PRJNA37833". I don't find an obvious solution in
> Google..
> > Could anyone help me? My script is in the bottom of this mail.
> >
> >
> >
> > Sometimes the message is:
> >
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: WebDBSeqI Request Error:
> > HTTP/1.1 502 Bad Gateway
> > Connection: close
> > Date: Tue, 23 Oct 2012 11:08:47 GMT
> > Accept-Ranges: bytes
> > Server: Apache
> > Vary: accept-language,accept-charset
> > Content-Language: en
> > Content-Type: text/html; charset=iso-8859-1
> > Client-Date: Tue, 23 Oct 2012 11:09:25 GMT
> > Client-Peer: 165.112.7.20:80
> > Client-Response-Num: 1
> > Client-Transfer-Encoding: chunked
> > Link: <mailto:info at ncbi.nlm.nih.gov>; rev="made"
> > Title: Bad Gateway!
> >
> > <?xml version="1.0" encoding="ISO-8859-1"?>
> > <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
> >  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
> > <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
> > <head>
> > <title>Bad Gateway!</title>
> > <link rev="made" href="mailto:info at ncbi.nlm.nih.gov" />
> > <style type="text/css"><!--/*--><![CDATA[/*><!--*/
> >    body { color: #000000; background-color: #FFFFFF; }
> >    a:link { color: #0000CC; }
> >    p, address {margin-left: 3em;}
> >    span {font-size: smaller;}
> > /*]]>*/--></style>
> > </head>
> >
> > <body>
> > <h1>Bad Gateway!</h1>
> > <p>
> >
> >
> >    The proxy server received an invalid
> >    response from an upstream server.
> >
> >
> >    </p>
> > <p>
> >
> >    The proxy server could not handle the request <em><a
> >
> href="/entrez/eutils/efetch.fcgi">GET&nbsp;/entrez/eutils/efetch.fcgi</a></em>.<p>
> > Reason: <strong>Error reading from remote server</strong></p>
> >
> >
> > </p>
> > <p>
> > If you think this is a server error, please contact
> > the <a href="mailto:info at ncbi.nlm.nih.gov">webmaster</a>.
> >
> > </p>
> >
> > <h2>Error 502</h2>
> > <address>
> >  <a href="/">eutils.ncbi.nlm.nih.gov</a><br />
> >
> >  <span>Tue Oct 23 07:08:47 2012<br />
> >  Apache</span>
> > </address>
> > </body>
> > </html>
> >
> >
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> > STACK: Bio::DB::WebDBSeqI::_stream_request
> > /usr/share/perl5/Bio/DB/WebDBSeqI.pm:773
> > STACK: Bio::DB::WebDBSeqI::get_seq_stream
> > /usr/share/perl5/Bio/DB/WebDBSeqI.pm:467
> > STACK: Bio::DB::WebDBSeqI::get_Stream_by_id
> > /usr/share/perl5/Bio/DB/WebDBSeqI.pm:288
> > STACK: Bio::DB::WebDBSeqI::get_Seq_by_id
> > /usr/share/perl5/Bio/DB/WebDBSeqI.pm:158
> > STACK: check.pl:28
> > -----------------------------------------------------------
> >
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: id does not exist
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> > STACK: Bio::DB::WebDBSeqI::get_Seq_by_id
> > /usr/share/perl5/Bio/DB/WebDBSeqI.pm:167
> > STACK: check.pl:28
> > -----------------------------------------------------------
> >
> >
> >
> >
> > My script:
> >
> > #!/usr/bin/perl -w
> >
> > use Bio::DB::GenBank;
> >
> > $file = shift @ARGV;
> > open FH, "<$file";
> > @content = <FH>;
> > $cont1=0;
> > foreach $line (@content){
> > if ($line =~ /^>.+/g){
> > $name = $line;
> > $name =~ s/>//g;
> > push (@names, $name);
> > $seq = '';
> > $cont++;
> > }#close if
> > elsif($line !~ /^>/){
> > $seq .= $line;
> > $seq =~ s/\s//g;
> > $seq = uc($seq);
> > }#close elsif
> > $hash1{$name} = $seq;
> > }
> >
> > ######################################################
> > $db_obj = Bio::DB::GenBank->new;
> > foreach $name(@names){
> > @split = split (/_/, $name);
> > $ident = $split[-1];
> > $Bio::Seq::seq_obj = $db_obj->get_Seq_by_id($ident);
> > $GBsequencia = $Bio::Seq::seq_obj->seq();
> > $GBsequencia =~ s/\n+//g;
> > $seq = $hash1{$name};
> > if ($GBsequencia ne $seq){
> > $cont1++;
> > print "Problems: $name\n"
> > }
> > }
> > print "Total: $cont\tProblems: $cont1\n";
> >
> >
> >
> >
> >
> > Best,
> > ===============================================================
> > Caio César de Melo Freire, BSc Biomedicine
> >
> > PhD candidate - Bioinformatics
> >
> > Laboratory of Molecular Evolution and Bioinformatics
> > Institute of Biomedical Sciences - II
> >
> > University of Sao Paulo
> > +551130918453
> > Av. Prof. Lineu Prestes, 1374 - Cidade Universitária "Armando Salles
> > Oliveira", Butantã - São Paulo - SP - CEP 05508-900
> > ================================================================
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



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