[Bioperl-l] How to get coil prediction out of Bio::Tools::Run::Coil modules
Jason Stajich
jason at bioperl.org
Fri May 8 20:04:06 UTC 2009
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
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