[Bioperl-l] problem with trunc_with_features (SeqUtils.pm)

Heath O'Brien heath.obrien at gmail.com
Mon Apr 9 17:37:56 EDT 2012


Hi Frank,

I just tried it with the latest version from bioperl-live, and it  
worked the way I described in my email.

all good things,
Heath


On 9-Apr-12, at 5:21 PM, Frank Schwach wrote:

> Hi Heath,
>
> I have recently worked a bit on that module and contributed the code  
> to bioperl-live. I think this behaviour may already have changed but  
> I'm not 100% sure at the moment. When I have some time I will review  
> the code to confirm. In the meantime, you could give it a go with  
> the bioperl-live version if that's an option for you?
>
> Cheers,
>
> Frank
>
>
> On 03/04/12 17:56, Heath O'Brien wrote:
>> Hi All,
>>
>> I've encountered a bug in the trunc_with_features function in  
>> SeqUtils.pm, or at
>> least behavior that was unexpected to me:
>>
>> Features with fuzzy coordinates in the original sequence are  
>> converted to exact
>> coordinates in the truncated sequence. For example, the script  
>> below changes the
>> coordinates for the feature from<1..5 to 1..5.
>>
>> I have modified the code to change this behavior on my system, but  
>> I thought I'd
>> post something here in case others encounter the same problem.
>>
>> all good things,
>>  Heath
>>
>>
>>
>> #!/usr/bin/perl -w
>>
>> use strict;
>> use warnings;
>> use Bio::SeqIO;
>> use Bio::SeqUtils;
>>
>> my $infile= shift;
>>
>> my $inIO = Bio::SeqIO->new('-file' =>  $infile,
>>          '-format' =>  'genbank') or die "could not open seq file  
>> $infile\n";
>>
>> my $outfile = $infile . '_out.gbk';
>>
>> my $outIO = Bio::SeqIO->new('-file' =>  ">$outfile",
>>          '-format' =>  'genbank') or die "could not open seq file  
>> $outfile\n";
>>
>> my $in_seq = $inIO->next_seq;
>> my $out_seq = Bio::SeqUtils->trunc_with_features($in_seq, 1, 5);
>> $outIO->write_seq($out_seq);
>> exit;
>>
>>
>> LOCUS       test_sequence        57303 bp    DNA     linear   UNA
>> DEFINITION  Sequence to demonstrate unexpected behavior of  
>> trunc_with_features
>> ACCESSION   unknown
>> KEYWORDS    .
>> FEATURES             Location/Qualifiers
>>      source          1..10
>>                      /mol_type="genomic DNA"
>>      gene<1..5
>>                      /gene="test"
>>      CDS<1..5
>>                      /product="hypothetical protein"
>> ORIGIN
>>         1 caagattaaa
>> //
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research  
> Limited, a charity registered in England with number 1021457 and a  
> company registered in England with number 2742969, whose registered  
> office is 215 Euston Road, London, NW1 2BE.



More information about the Bioperl-l mailing list