Re: problem with trunc_with_features (SeqUtils.pm)

> 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
>>>>>>>> //
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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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