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

Fields, Christopher J cjfields at illinois.edu
Tue Apr 10 13:08:45 EDT 2012


I have committed these to bioperl-live, they passed tests for me.  I have left the bug report open, however, in case more work needs to be done.  Roy, did you want to close that when you are ready?

chris

On Apr 10, 2012, at 10:34 AM, Heath O'Brien wrote:

> 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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