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

[Raul Mendez Giraldez]

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