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

Roy Chaudhuri roy.chaudhuri at gmail.com
Wed Apr 11 06:55:49 EDT 2012


Hi Chris,

I think it should be fine to close, but my account doesn't have 
permission to do so.

Cheers,
Roy.

On 10/04/2012 18:08, Fields, Christopher J wrote:
> 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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