Heath O'Brien | 3 Apr 18:56 2012
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problem with trunc_with_features (SeqUtils.pm)

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",
(Continue reading)

Frank Schwach | 9 Apr 23:21 2012
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Re: problem with trunc_with_features (SeqUtils.pm)

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
>
>
>
(Continue reading)

Heath O'Brien | 9 Apr 23:37 2012
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Re: problem with trunc_with_features (SeqUtils.pm)

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:
>>
(Continue reading)

Frank Schwach | 10 Apr 10:42 2012
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Re: problem with trunc_with_features (SeqUtils.pm)

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
(Continue reading)

Roy Chaudhuri | 10 Apr 13:10 2012
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Re: problem with trunc_with_features (SeqUtils.pm)

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.
(Continue reading)


Gmane