Bio::Palantir::Parser::Gene - BiosynML DTD-derived internal class
version 0.211420
# TODO
ArrayRef of Bio::Palantir::Parser::Domain
ArrayRef of Bio::Palantir::Parser::Motif
ArrayRef of Bio::Palantir::Parser::Qualifier
Bio::Palantir::Parser::Location composed object
Returns the number of Domains of the Gene.
# $gene is a Bio::Palantir::Parser::Gene my $count = $gene->count_domains;
This method does not accept any arguments.
Returns all the Domains of the Gene (not an array reference).
# $gene is a Bio::Palantir::Parser::Gene my @domains = $gene->all_domains;
Returns one Domain of the Gene by its index. You can also use negative index numbers, just as with Perl's core array handling. If the specified Domain does not exist, this method will return undef.
undef
# $gene is a Bio::Palantir::Parser::Gene my $domain = $gene->get_domain($index); croak "Domain $index not found!" unless defined $domain;
This method accepts just one argument (and not an array slice).
Shifts the first Domain of the array off and returns it, shortening the array by 1 and moving everything down. If there are no more Domains in the array, returns undef.
# $gene is a Bio::Palantir::Parser::Gene while (my $domain = $gene->next_domain) { # process $domain # ... }
Returns the number of Motifs of the Gene.
# $gene is a Bio::Palantir::Parser::Gene my $count = $gene->count_orphan_motifs;
Returns all the Motifs of the Gene (not an array reference).
# $gene is a Bio::Palantir::Parser::Gene my @orphan_motifs = $gene->all_orphan_motifs;
Returns one Motif of the Gene by its index. You can also use negative index numbers, just as with Perl's core array handling. If the specified Motif does not exist, this method will return undef.
# $gene is a Bio::Palantir::Parser::Gene my $orphan_motif = $gene->get_orphan_motif($index); croak "Motif $index not found!" unless defined $orphan_motif;
Shifts the first Motif of the array off and returns it, shortening the array by 1 and moving everything down. If there are no more Motifs in the array, returns undef.
# $gene is a Bio::Palantir::Parser::Gene while (my $orphan_motif = $gene->next_orphan_motif) { # process $orphan_motif # ... }
Returns the number of Qualifiers of the Gene.
# $gene is a Bio::Palantir::Parser::Gene my $count = $gene->count_qualifiers;
Returns all the Qualifiers of the Gene (not an array reference).
# $gene is a Bio::Palantir::Parser::Gene my @qualifiers = $gene->all_qualifiers;
Returns one Qualifier of the Gene by its index. You can also use negative index numbers, just as with Perl's core array handling. If the specified Qualifier does not exist, this method will return undef.
# $gene is a Bio::Palantir::Parser::Gene my $qualifier = $gene->get_qualifier($index); croak "Qualifier $index not found!" unless defined $qualifier;
Shifts the first Qualifier of the array off and returns it, shortening the array by 1 and moving everything down. If there are no more Qualifiers in the array, returns undef.
# $gene is a Bio::Palantir::Parser::Gene while (my $qualifier = $gene->next_qualifier) { # process $qualifier # ... }
Returns the value of the element <gene_name>.
<gene_name
# $gene is a Bio::Palantir::Parser::Gene my $name = $gene->name;
Returns the value of the element <sequence>.
<sequence
# $gene is a Bio::Palantir::Parser::Gene my $sequence = $gene->sequence;
Returns the value of the element <operon>.
<operon
# $gene is a Bio::Palantir::Parser::Gene my $operon = $gene->operon;
Returns the value of the element <transcript_id>.
<transcript_id
# $gene is a Bio::FastParsers::Biosynml::Gene my $transcript_id = $gene->transcript_id;
Returns the value of the element <protein_sequence>.
<protein_sequence
# $gene is a Bio::FastParsers::Biosynml::Gene my $protein_sequence = $gene->protein_sequence;
Returns the value of the element <gene_id>.
<gene_id
# $gene is a Bio::FastParsers::Biosynml::Gene my $gene_id = $gene->gene_id;
Returns the value of the element <protein_id>.
<protein_id
# $gene is a Bio::FastParsers::Biosynml::Gene my $protein_id = $gene->protein_id;
Returns the value of the element <product_id>.
<product_id
# $gene is a Bio::FastParsers::Biosynml::Gene my $product_id = $gene->product_id;
Returns the value of the element <locus_tag>.
<locus_tag
# $gene is a Bio::FastParsers::Biosynml::Gene my $locus_tag = $gene->locus_tag;
Returns the value of the element <smcog>.
<smcog
# $gene is a Bio::FastParsers::Biosynml::Gene my $smcog = $gene->smcog;
Returns the value of the element <uniprot_id>.
<uniprot_id
# $gene is a Bio::FastParsers::Biosynml::Gene my $uniprot_id = $gene->uniprot_id;
Returns the values of the elements <go_ids>.
<go_ids
# $gene is a Bio::FastParsers::Biosynml::Gene my @go_ids = $gene->go_ids;
Returns the value of the element <uniparc_id>.
<uniparc_id
# $gene is a Bio::FastParsers::Biosynml::Gene my $uniparc_id = $gene->uniparc_id;
Returns the value of the element <type>.
<type
# $gene is a Bio::FastParsers::Biosynml::Gene my $type = $gene->type;
Returns the value of the element <domains_detail>.
<domains_detail
# $gene is a Bio::FastParsers::Biosynml::Gene my $domains_detail = $gene->domains_detail;
Returns the value of the element <kind>.
<kind
# $gene is a Bio::FastParsers::Biosynml::Gene my $kind = $gene->kind;
Returns the value of the element <subtype>.
<subtype
# $gene is a Bio::FastParsers::Biosynml::Gene my $subtype = $gene->subtype;
Returns the values of the elements <bgc_domains>.
<bgc_domains
# $gene is a Bio::FastParsers::Biosynml::Gene my @bgc_domains = $gene->bgc_domains;
Returns the values of the elements <monomers>.
<monomers
# $gene is a Bio::FastParsers::Biosynml::Gene my @monomers = $gene->monomers;
Returns the values of the elements <nrpspredictor_monomers>.
<nrpspredictor_monomers
# $gene is a Bio::FastParsers::Biosynml::Gene my @nrpspredictor_monomers = $gene->nrpspredictor_monomers;
Returns the values of the elements <stachelhaus_monomers>.
<stachelhaus_monomers
# $gene is a Bio::FastParsers::Biosynml::Gene my @stachelhaus_monomers = $gene->stachelhaus_monomers;
Returns the values of the elements <minowa_monomers>.
<minowa_monomers
# $gene is a Bio::FastParsers::Biosynml::Gene my @minowa_monomers = $gene->minowa_monomers;
Loic MEUNIER <lmeunier@uliege.be>
This software is copyright (c) 2019 by University of Liege / Unit of Eukaryotic Phylogenomics / Loic MEUNIER and Denis BAURAIN.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install Bio::Palantir, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Palantir
CPAN shell
perl -MCPAN -e shell install Bio::Palantir
For more information on module installation, please visit the detailed CPAN module installation guide.