GenomeAnnotation
$return = $obj->genomeTO_to_reconstructionTO($genomeTO)
$genomeTO is a genomeTO $return is a reconstructionTO genomeTO is a reference to a hash where the following keys are defined: id has a value which is a genome_id scientific_name has a value which is a string domain has a value which is a string genetic_code has a value which is an int source has a value which is a string source_id has a value which is a string close_genomes has a value which is a reference to a list where each element is a reference to a list containing 2 items: 0: a genome_id 1: a float DNA_kmer_data has a value which is a reference to a list where each element is a reference to a list containing 5 items: 0: a string 1: an int 2: an int 3: an int 4: a string contigs has a value which is a reference to a list where each element is a contig features has a value which is a reference to a list where each element is a feature genome_id is a string contig is a reference to a hash where the following keys are defined: id has a value which is a contig_id dna has a value which is a string contig_id is a string feature is a reference to a hash where the following keys are defined: id has a value which is a feature_id location has a value which is a location type has a value which is a feature_type function has a value which is a string protein_translation has a value which is a string aliases has a value which is a reference to a list where each element is a string annotations has a value which is a reference to a list where each element is an annotation feature_id is a string location is a reference to a list where each element is a region_of_dna region_of_dna is a reference to a list containing 4 items: 0: a contig_id 1: an int 2: a string 3: an int feature_type is a string annotation is a reference to a list containing 3 items: 0: a string 1: a string 2: an int reconstructionTO is a reference to a hash where the following keys are defined: subsystems has a value which is a variant_subsystem_pairs bindings has a value which is a fid_role_pairs assignments has a value which is a fid_function_pairs variant_subsystem_pairs is a reference to a list where each element is a variant_of_subsystem variant_of_subsystem is a reference to a list containing 2 items: 0: a subsystem 1: a variant subsystem is a string variant is a string fid_role_pairs is a reference to a list where each element is a fid_role_pair fid_role_pair is a reference to a list containing 2 items: 0: a fid 1: a role fid is a string role is a string fid_function_pairs is a reference to a list where each element is a fid_function_pair fid_function_pair is a reference to a list containing 2 items: 0: a fid 1: a function function is a string
$return = $obj->genomeTO_to_feature_data($genomeTO)
$genomeTO is a genomeTO $return is a fid_data_tuples genomeTO is a reference to a hash where the following keys are defined: id has a value which is a genome_id scientific_name has a value which is a string domain has a value which is a string genetic_code has a value which is an int source has a value which is a string source_id has a value which is a string close_genomes has a value which is a reference to a list where each element is a reference to a list containing 2 items: 0: a genome_id 1: a float DNA_kmer_data has a value which is a reference to a list where each element is a reference to a list containing 5 items: 0: a string 1: an int 2: an int 3: an int 4: a string contigs has a value which is a reference to a list where each element is a contig features has a value which is a reference to a list where each element is a feature genome_id is a string contig is a reference to a hash where the following keys are defined: id has a value which is a contig_id dna has a value which is a string contig_id is a string feature is a reference to a hash where the following keys are defined: id has a value which is a feature_id location has a value which is a location type has a value which is a feature_type function has a value which is a string protein_translation has a value which is a string aliases has a value which is a reference to a list where each element is a string annotations has a value which is a reference to a list where each element is an annotation feature_id is a string location is a reference to a list where each element is a region_of_dna region_of_dna is a reference to a list containing 4 items: 0: a contig_id 1: an int 2: a string 3: an int feature_type is a string annotation is a reference to a list containing 3 items: 0: a string 1: a string 2: an int fid_data_tuples is a reference to a list where each element is a fid_data_tuple fid_data_tuple is a reference to a list containing 4 items: 0: a fid 1: a md5 2: a location 3: a function fid is a string md5 is a string function is a string
$return = $obj->reconstructionTO_to_roles($reconstructionTO)
$reconstructionTO is a reconstructionTO $return is a reference to a list where each element is a role reconstructionTO is a reference to a hash where the following keys are defined: subsystems has a value which is a variant_subsystem_pairs bindings has a value which is a fid_role_pairs assignments has a value which is a fid_function_pairs variant_subsystem_pairs is a reference to a list where each element is a variant_of_subsystem variant_of_subsystem is a reference to a list containing 2 items: 0: a subsystem 1: a variant subsystem is a string variant is a string fid_role_pairs is a reference to a list where each element is a fid_role_pair fid_role_pair is a reference to a list containing 2 items: 0: a fid 1: a role fid is a string role is a string fid_function_pairs is a reference to a list where each element is a fid_function_pair fid_function_pair is a reference to a list containing 2 items: 0: a fid 1: a function function is a string
$return = $obj->reconstructionTO_to_subsystems($reconstructionTO)
$reconstructionTO is a reconstructionTO $return is a variant_subsystem_pairs reconstructionTO is a reference to a hash where the following keys are defined: subsystems has a value which is a variant_subsystem_pairs bindings has a value which is a fid_role_pairs assignments has a value which is a fid_function_pairs variant_subsystem_pairs is a reference to a list where each element is a variant_of_subsystem variant_of_subsystem is a reference to a list containing 2 items: 0: a subsystem 1: a variant subsystem is a string variant is a string fid_role_pairs is a reference to a list where each element is a fid_role_pair fid_role_pair is a reference to a list containing 2 items: 0: a fid 1: a role fid is a string role is a string fid_function_pairs is a reference to a list where each element is a fid_function_pair fid_function_pair is a reference to a list containing 2 items: 0: a fid 1: a function function is a string
$return = $obj->annotate_genome($genomeTO)
$genomeTO is a genomeTO $return is a genomeTO genomeTO is a reference to a hash where the following keys are defined: id has a value which is a genome_id scientific_name has a value which is a string domain has a value which is a string genetic_code has a value which is an int source has a value which is a string source_id has a value which is a string close_genomes has a value which is a reference to a list where each element is a reference to a list containing 2 items: 0: a genome_id 1: a float DNA_kmer_data has a value which is a reference to a list where each element is a reference to a list containing 5 items: 0: a string 1: an int 2: an int 3: an int 4: a string contigs has a value which is a reference to a list where each element is a contig features has a value which is a reference to a list where each element is a feature genome_id is a string contig is a reference to a hash where the following keys are defined: id has a value which is a contig_id dna has a value which is a string contig_id is a string feature is a reference to a hash where the following keys are defined: id has a value which is a feature_id location has a value which is a location type has a value which is a feature_type function has a value which is a string protein_translation has a value which is a string aliases has a value which is a reference to a list where each element is a string annotations has a value which is a reference to a list where each element is an annotation feature_id is a string location is a reference to a list where each element is a region_of_dna region_of_dna is a reference to a list containing 4 items: 0: a contig_id 1: an int 2: a string 3: an int feature_type is a string annotation is a reference to a list containing 3 items: 0: a string 1: a string 2: an int
Given a genome object populated with contig data, perform gene calling and functional annotation and return the annotated genome. NOTE: Many of these "transformations" modify the input hash and copy the pointer. Be warned.
$return = $obj->call_selenoproteins($genomeTO)
$return = $obj->call_pyrrolysoproteins($genomeTO)
$return = $obj->call_RNAs($genomeTO)
$return = $obj->call_CDSs($genomeTO)
$return = $obj->find_close_neighbors($genomeTO)
$return = $obj->assign_functions_to_CDSs($genomeTO)
$return = $obj->annotate_proteins($genomeTO)
Given a genome object populated with feature data, reannotate the features that have protein translations. Return the updated genome object.
$return = $obj->call_CDSs_by_projection($genomeTO)
a string
a reference to a list where each element is a md5
A region of DNA is maintained as a tuple of four components:
the contig the beginning position (from 1) the strand the length We often speak of "a region". By "location", we mean a sequence of regions from the same genome (perhaps from distinct contigs).
a reference to a list containing 4 items: 0: a contig_id 1: an int 2: a string 3: an int
a "location" refers to a sequence of regions
a reference to a list where each element is a region_of_dna
a reference to a list containing 3 items: 0: a string 1: a string 2: an int
a reference to a hash where the following keys are defined: id has a value which is a feature_id location has a value which is a location type has a value which is a feature_type function has a value which is a string protein_translation has a value which is a string aliases has a value which is a reference to a list where each element is a string annotations has a value which is a reference to a list where each element is an annotation
a reference to a hash where the following keys are defined: id has a value which is a contig_id dna has a value which is a string
a reference to a hash where the following keys are defined: id has a value which is a genome_id scientific_name has a value which is a string domain has a value which is a string genetic_code has a value which is an int source has a value which is a string source_id has a value which is a string close_genomes has a value which is a reference to a list where each element is a reference to a list containing 2 items: 0: a genome_id 1: a float DNA_kmer_data has a value which is a reference to a list where each element is a reference to a list containing 5 items: 0: a string 1: an int 2: an int 3: an int 4: a string contigs has a value which is a reference to a list where each element is a contig features has a value which is a reference to a list where each element is a feature
a reference to a list containing 2 items: 0: a subsystem 1: a variant
a reference to a list where each element is a variant_of_subsystem
a reference to a list containing 2 items: 0: a fid 1: a role
a reference to a list where each element is a fid_role_pair
a reference to a list containing 2 items: 0: a fid 1: a function
a reference to a list where each element is a fid_function_pair
a reference to a hash where the following keys are defined: subsystems has a value which is a variant_subsystem_pairs bindings has a value which is a fid_role_pairs assignments has a value which is a fid_function_pairs
a reference to a list containing 4 items: 0: a fid 1: a md5 2: a location 3: a function
a reference to a list where each element is a fid_data_tuple
To install Bio::KBase, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::KBase
CPAN shell
perl -MCPAN -e shell install Bio::KBase
For more information on module installation, please visit the detailed CPAN module installation guide.