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

Heath O'Brien heath.obrien at gmail.com
Tue Apr 10 11:34:59 EDT 2012


Works perfect for me. Thanks!

all good things,
  Heath

On 10-Apr-12, at 10:45 AM, Roy Chaudhuri wrote:

> Turns out I spoke too soon, I added in some new tests and they  
> highlighted problems with both trunc_with_features and  
> revcom_with_features. I think I have resolved all the issues in the  
> most recent Redmine patch - Frank, Heath, please could you check  
> that it works for you?
>
> Cheers,
> Roy.
>
> On 10/04/2012 12:52, Frank Schwach wrote:
>> Brilliant, thanks Roy!
>> Frank
>>
>>
>> On 10/04/12 12:10, Roy Chaudhuri wrote:
>>> 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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