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

Frank Schwach fs5 at sanger.ac.uk
Tue Apr 10 04:42:54 EDT 2012


Hi Heath,

Yes, I just had a look too and it's true that it would currently ignore 
the original type. I had added some new methods (delete, insert, ligate) 
and with those the location type is preserved but not with the already 
existing methods like trunc_with_features. I will look into it when I 
have some time and make some changes.

Cheers,

Frank


On 09/04/12 22:37, Heath O'Brien wrote:
> 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.
>


-- 
 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. 


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