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

[Raul Mendez Giraldez]

Hi Jason,

Thank you so much for your suggestion, although it was 

my $featseq = $seqin->trunc($feature->start, $feature->end);

sice the subseq method just give you an string with the sequence, trunc
outputs a seqobj as it is needed to be passed to write_seq.

Cheers,
Raul

El vie, 08-05-2009 a las 13:04 -0700, Jason Stajich escribió:
> 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
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> Jason Stajich
> jason at bioperl.org
> 
> 
> 
> 
> 
> 
> 
>