[Bioperl-l] possible bug printing GenBank feature qualfiers

[Scott Markel]

Chris,

Looks like I made my test case too simple.  In our application,
which calls BioPerl, I'm creating the feature with the zero-
valued qualifier.  It's not being read in from a file, so
my only issue is with writing GenBank files.  The real feature
is one for a primer binding site.  The qualifier contains the
number of mismatches.  The one line change of

     $value = $value->{"value"}

definitely fixes our problem and causes no regression
failures in our application.

Scott

Chris Fields wrote:

> I tried this on WinXP (I'm using bioperl-live) and got a warning: 
> 
> -------------------- WARNING ---------------------
> MSG: Unexpected error in feature table for  Skipping feature, attempting to
> recover
> ---------------------------------------------------
> 
> Running using debugging shows that no feature key was found in
> _read_FTHelper_GenBank.  So I'm getting an error, but on input not output.
> In fact, turning on -verbose in the SeqIO input object gives the below extra
> output, whereas turning -verbose on only in the output object just gives the
> warning above.
> 
> ====================================
> C:\Perl\Scripts\gb_test>test.pl
> no feature key!
> 
> -------------------- WARNING ---------------------
> MSG: Unexpected error in feature table for  Skipping feature, attempting to
> recover
> STACK Bio::SeqIO::genbank::next_seq
> C:\Perl\src\bioperl\core/Bio\SeqIO\genbank.pm:583
> STACK toplevel C:\Perl\Scripts\gb_test\test.pl:18
> sequence length is 10
> ====================================
> 
> The sequence came back w/o any features in the feature table, which is what
> I would expect from this error:
> ====================================
> LOCUS       MY_LOCUS                  10 aa            linear   linear 
> DEFINITION  my description.
> ACCESSION   12345
> KEYWORDS    .
> FEATURES             Location/Qualifiers
> ORIGIN      
>         1 atggagaact
> //
> ====================================
> 
> Adding the extra line before the s/// didn't help any (warning still pops
> up, no change in output).  Anybody out there with any ideas?  
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign 
> 
> 
> 
>>-----Original Message-----
>>From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>bounces at lists.open-bio.org] On Behalf Of Scott Markel
>>Sent: Thursday, March 30, 2006 7:18 PM
>>To: bioperl-l at lists.open-bio.org
>>Subject: [Bioperl-l] possible bug printing GenBank feature qualfiers
>>
>>In our upgrade from BioPerl 1.4 to 1.5.1 we tripped over the
>>following.
>>
>>Annotation tags used by Bio::SeqIO::FTHelper were strings and
>>are now Bio::Annotation::SimpleValue.  In the _print_GenBank_FTHelper
>>subroutine of Bio::SeqIO::genbank the following code still
>>assumes that tags are strings.
>>
>>    foreach my $tag ( keys %{$fth->field} ) {
>>        foreach my $value ( @{$fth->field->{$tag}} ) {
>>        $value =~ s/\"/\"\"/g;
>>
>>If the tag value was a zero, an empty string is written.
>>
>>We think that
>>
>>            $value = $value->{"value"};
>>
>>should be added before the s/// call.
>>
>>Here's our test case.  Note that the qualifier value for "foo"
>>is changed to an empty string.
>>
>>Input file
>>
>>====================================
>>LOCUS       MY_LOCUS                  10 aa            linear   UNK
>>DEFINITION  my description.
>>ACCESSION   12345
>>FEATURES             Location/Qualifiers
>>      misc_feature    1..10
>>                      /foo="0"
>>ORIGIN
>>         1 atggagaact
>>//
>>====================================
>>
>>Perl code
>>====================================
>>use strict;
>>use warnings;
>>
>>use Bio::SeqIO;
>>
>>my $inputFilename = "input.gbff";
>>my $outputFilename = "output.gbff";
>>
>>my $in  = Bio::SeqIO->new(-file   => $inputFilename,
>>                           -format => "genbank");
>>my $out = Bio::SeqIO->new(-file => ">$outputFilename",
>>                           -format => "genbank");
>>
>>my $sequence = $in->next_seq();
>>$out->write_seq($sequence);
>>====================================
>>
>>Output file
>>====================================
>>LOCUS       MY_LOCUS                  10 aa            linear   linear
>>DEFINITION  my description.
>>ACCESSION   12345
>>KEYWORDS    .
>>FEATURES             Location/Qualifiers
>>      misc_feature    1..10
>>                      /foo=""
>>ORIGIN
>>         1 atggagaact
>>//
>>====================================
>>
>>I'll add this to bugzilla, but first I want to make sure
>>I'm not missing something obvious.
>>
>>Scott

-- 
Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
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