| Bio::Cluster::SequenceFamily(3pm) | User Contributed Perl Documentation | Bio::Cluster::SequenceFamily(3pm) |
Bio::Cluster::SequenceFamily - Sequence Family object
use Bio::SeqIO;
use Bio::Cluster::SequenceFamily;
use File::Spec;
my $file = File::Spec->catfile('t','data','swiss.dat');
my $seqio= Bio::SeqIO->new(-format => 'swiss',
-file => $file);
my @mem;
while(my $seq = $seqio->next_seq){
push @mem, $seq;
}
#create the family
my $family = Bio::Cluster::SequenceFamily->new(
-family_id=>"Family_1",
-description=>"Family Description Here",
-annotation_score=>"100",
-members=>\@mem);
#access the family
foreach my $mem ($family->get_members){
print $mem->display_id."\t".$mem->desc."\n";
}
#select members if members have a Bio::Species Object
my @mem = $family->get_members(-binomial=>"Homo sapiens");
@mem = $family->get_members(-ncbi_taxid => 9606);
@mem = $family->get_members(-common_name=>"Human");
@mem = $family->get_members(-species=>"sapiens");
@mem = $family->get_members(-genus=>"Homo");
This is a simple Family object that may hold any group of object. For more specific families, one should derive from FamilyI.
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User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
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Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
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Email shawnh@fugu-sg.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
Title : new
Usage : my $family = Bio::Cluster::SequenceFamily->new(
-family_id=>"Family_1",
-description=>"Family Description Here",
-annotation_score=>"100",
-members=>\@mem);
Function: Constructor for SequenceFamily object
Returns : Bio::Cluster::SequenceFamily object
See Bio::Cluster::SequenceFamily.
Title : version
Usage : $family->version("1.0");
Function: get/set for version
Returns : a string version of the family generated.
Title : annotation_score Usage : $family->annotation_score(100); Function: get/set for annotation_score which represent the confidence in which the consensus description has been assigned to the family. Returns : Bio::SimpleAlign
See Bio::SimpleAlign
Title : alignment
Usage : $family->alignment($align);
Function: get/set for an alignment object representing
the multiple alignment of the members of the family.
Returns : Bio::SimpleAlign
See Bio::SimpleAlign
Title : tree
Usage : $family->tree($tree);
Function: get/set for an tree object representing
the phylogenetic tree of the family.
Returns : Bio::Tree
See Bio::Tree
Title : family_score Usage : Bio::Cluster::FamilyI->family_score(95); Function: get/set for the score of algorithm used to generate the family if present This is aliased to cluster_score(). Returns : the score Args : the score
Title : family_id
Usage : $family->family_id("Family_1");
Function: get/set for family id
This is aliased to display_id().
Returns : a string specifying identifier of the family
Title : display_id Usage : Function: Get/set the display name or identifier for the cluster Returns : a string Args : optional, on set the display ID ( a string)
Title : description
Usage : $fam->description("POLYUBIQUITIN")
Function: get/set for the consensus description of the cluster
Returns : the description string
Args : Optional the description string
Title : get_members
Usage : Valid criteria:
-common_name
-binomial
-ncbi_taxid
-organelle
-genus
$family->get_members(-common_name =>"human");
$family->get_members(-species =>"homo sapiens");
$family->get_members(-ncbi_taxid => 9606);
For now, multiple critieria are ORed.
Will return all members if no criteria are provided.
Function: get members using methods from L<Bio::Species>
the phylogenetic tree of the family.
Returns : an array of objects that are member of this family.
Title : size
Usage : $fam->size();
Function: get/set for the size of the family,
calculated from the number of members
Returns : the size of the family
Args :
Title : cluster_score Usage : $fam->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number
These are mostly for adding/removing/changing.
Title : add_members Usage : $fam->add_member([$seq1,$seq1]); Function: add members to a family Returns : Args : the member(s) to add, as an array or arrayref
Title : remove_members Usage : $fam->remove_members(); Function: remove all members from a family Returns : the previous array of members Args : none
Title : members Usage : $members = $fam->members([$seq1,$seq1]); Function: Deprecated. Use add_members() or get_members() instead
| 2020-10-24 | perl v5.30.3 |