[Bioperl-l] How to get coil prediction out of Bio::Tools::Run::Coil modules

[Jason Stajich]

The sequence isn't part of the report - or at least isn't parsed but  
you can just do this (pseudo-y-code here).
my $seqout =Bio::SeqIO->new(-format => 'fasta');


for my $feature ( @features )
  my $featseq = $seqin->subseq($feature->start, $feature->end);
  $seqout->write_seq($featseq);
}


On May 8, 2009, at 9:19 AM, Raul Mendez Giraldez wrote:

> Hi,
>
> I'm trying to get coiled-coiled prediction in protein sequences using
> Bob Russell's program ncoils, through the bioperl interface
> Bio::Tools::Run::Coil, but the only thing I can get from any element  
> on
> the features list is just the sequence name, and few more not so  
> useful
> atributes.
>
> I'm running the following script:
>
>
> #!/home/rmendez/bin/perl -w
>
> use strict;
> use FileHandle;
> use Data::Dumper;
>
> use Bio::Tools::Run::Coil;
>
> my $seqin=filein.fasta
> my $factory=Bio::Tools::Run::Coil->new('-c');			
> my @features=$factory->run($seqin);
>
> print "Printing content of features[0]\n";
> print Dumper $features[0];
>
> ----
>
> And the output is (the content of the first element of the features
> array) is :
>                 '_gsf_tag_hash' => {
>                                      'percent_id' => [
>                                                        'NULL'
>                                                      ],
>                                      'hid' => [
>                                                 'ncoils'
>                                               ],
>                                      'evalue' => [
>                                                    0
>                                                  ]
>                                    },
>                 '_location' => bless( {
>                                         '_location_type' => 'EXACT',
>                                         '_start' => 138,
>                                         '_end' => 172
>                                       }, 'Bio::Location::Simple' ),
>                 '_gsf_seq_id' => 'ENSDARP00000084927',
>                 '_parse_h' => {},
>                 '_root_cleanup_methods' => [
>                                              sub { "DUMMY" }
>                                            ],
>                 '_source_tag' => 'Coils',
>                 '_primary_tag' => 'ncoils',
>                 '_root_verbose' => 0
>               }, 'Bio::SeqFeature::Generic' );
>
> Then how could I get the sequence itself with the coil annotation  
> 'xxx'?
>
> Thanks,
>
> Raul
>
>
>
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Jason Stajich
jason at bioperl.org