[Bioperl-l] How to get coil prediction out of Bio::Tools::Run::Coil modules
Raul Mendez Giraldez
raulmendez at cbm.uam.es
Fri May 8 16:19:40 UTC 2009
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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