[Bioperl-l] get cds from genbank record

Pedro Antonio Reche reche at research.dfci.harvard.edu
Fri Jan 16 10:39:31 EST 2004


Dear Heikki,
thanks for your replay. Actually I have tried to use that before and  
still does not work. The program still quits with the same error  
message.
Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm line  
3327.
[Fri Jan 16 10:29:50 2004] bio_get_cds.pl: Filehandle  
Bio::Tools::GuessSeqFormat::$fh opened only for output at  
/usr/local/share/perl/5.6.1/Bio/Tools/GuessSeqFormat.pm line 472.
Content-type: text/html

Content-Type: text/html; charset=ISO-8859-1

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html
         PUBLIC "-//W3C//DTD XHTML Basic 1.0//EN"
         "http://www.w3.org/TR/xhtml-basic/xhtml-basic10.dtd">
<html xmlns="http://www.w3.org/1999/xhtml"  
lang="en-US"><head><title>Error</title>
</head><body><h1>Error</h1><p>Sorry, the following error has occurred:  
</p><p><i>Can't locate object method &quot;throw&quot; via package  
&quot;Bio::Root::Exception&quot; (perhaps you forgot to load  
&quot;Bio::Root::Exception&quot;?) at  
/usr/local/share/perl/5.6.1/Bio/Root/Root.pm line 328.

by the way every time I execute one of the bioperl working scripts I  
get the annoying message of the first line:
Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm line  
3327.
Do you know why is that.

One more thing, following my first post I got an email from from  
quarantine at maxstrengthmail.com on behalf of the bioperl mailing list  
saying that my e-mail was in quarantine, and asking me press a link to  
get the message deliver. Oddly, I could see the message already posted  
and therefore I wonder if this was a legitimate e-mail or some type so  
scang.  Please advice. Here it follows the message I got.
Dear Pedro Antonio Reche <reche at research.dfci.harvard.edu>:

I am an automated email sentry designed to protect against unwanted  
email.

You recently sent an email titled '[Bioperl-l] get cds from genbank  
record' to 'bioperl-l'.

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On Jan 16, 2004, at 2:50 AM, Heikki Lehvaslaiho wrote:

> Perdo,
>
> It should work again if you spesify the sequence format for the output:
>
>   my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format =>  
> 'fasta');
>
> It should have been spesified even before 1.4, I an surprised that it  
> worked
> without it.
>
> 	-Heikki
>
>
> On Thursday 15 Jan 2004 20:35, Pedro Antonio Reche wrote:
>> !/usr/sbin/perl -w
>> #use strict;
>> use Bio::SeqIO;
>> use Bio::Seq;
>>
>>
>> my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank');
>> my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa");
>>
>> while( my $seq = $in->next_seq ) {
>>
>>     foreach my $f ( grep { $_->primary_tag eq 'CDS' }
>>        $seq->top_SeqFeatures ) {
>>     my ($gname);
>>     if( $f->has_tag('gene') ) {
>>         ($gname) = $f->each_tag_value('gene');
>>     } elsif( $f->has_tag('product') ) {
>>         ($gname) = $f->each_tag_value('product');
>>     }
>>
>>     my ($ref) = $f->has_tag('protein_id') &&
>> $f->each_tag_value('protein_id');
>>     my ($gi)  = $f->has_tag('db_xref') &&  
>> $f->each_tag_value('db_xref');
>>
>>     my ($translation) = $f->has_tag('translation') &&
>>                           $f->each_tag_value('translation');
>>
>>     unless( $gi && $ref && $gname && $translation ) {
>>       print STDERR "not fully annotated CDS ($gi,$ref,$gname),
>> skipping...\n";
>>       next;
>>     }
>>     my $outseq = Bio::PrimarySeq->new(-seq => $translation,
>>                                       -display_id =>
>>             sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref));
>>     $out->write_seq($outseq);
>>   }
>
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
======================================================================== 
======
Pedro A Reche, PhD
MIF Bioinformatics Group Head
Dana-Farber Cancer Institute  (D1510A)                                   
                                             TL: 617 632 3824
Harvard Medical School                                                   
                                                          FX: 617 632  
3351
44 Binney Street ,                                                       
                             EM: reche at research.dfci.harvard.edu
Boston, MA 02115, USA                                                    
                                        W3: www.mifoundation.org			

							




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