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

Roy Chaudhuri roy.chaudhuri at gmail.com
Tue Apr 10 07:10:36 EDT 2012


Hi Heath, Frank,

This was probably my fault back in the mists of time. Looks like an easy 
fix though, I've reported the issue on Redmine and submitted a patch:
https://redmine.open-bio.org/issues/3339

We should probably also add Heath's example as a test case.

Cheers,
Roy.

On 10/04/2012 09:42, Frank Schwach wrote:
> 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.
>>
>
>



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