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

Frank Schwach fs5 at sanger.ac.uk
Mon Apr 9 17:21:31 EDT 2012


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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