Bio-KBase

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er_scripts/get_relationship_IsLocatedIn  view on Meta::CPAN

use Data::Dumper;
use Carp;

#
# This is a SAS Component
#


=head1 get_relationship_IsLocatedIn

A feature is a set of DNA sequence fragments. Most features
are a single contiquous fragment, so they are located in only one
DNA sequence; however, fragments have a maximum length, so even a
single contiguous feature may participate in this relationship
multiple times. A few features belong to multiple DNA sequences. In
that case, however, all the DNA sequences belong to the same genome.
A DNA sequence itself will frequently have thousands of features
connected to it.

Example:

    get_relationship_IsLocatedIn -a < ids > table.with.fields.added

er_scripts/get_relationship_IsLocusFor  view on Meta::CPAN

use Data::Dumper;
use Carp;

#
# This is a SAS Component
#


=head1 get_relationship_IsLocusFor

A feature is a set of DNA sequence fragments. Most features
are a single contiquous fragment, so they are located in only one
DNA sequence; however, fragments have a maximum length, so even a
single contiguous feature may participate in this relationship
multiple times. A few features belong to multiple DNA sequences. In
that case, however, all the DNA sequences belong to the same genome.
A DNA sequence itself will frequently have thousands of features
connected to it.

Example:

    get_relationship_IsLocusFor -a < ids > table.with.fields.added

lib/Bio/KBase/CDMI/CDMILoader.pm  view on Meta::CPAN

sub ReadFastaRecord {
    # Get the parameters. Note we allow for both static and object-oriented
    # calls.
    shift if UNIVERSAL::isa($_[0],__PACKAGE__);
    my ($ih) = @_;
    # Declare the return variables for the ID and comment. When we read a
    # header record, we'll set the next-ID variable and that will stop the
    # read loop.
    my ($nextID, $nextComment);
    # This will hold the sequence fragments.
    my @lines;
    # Loop until we've read the whole sequence.
    while (! eof $ih && ! defined $nextID) {
        # Read the next line.
        my $line = <$ih>;
        chomp $line;
        # Check for a header.
        if (substr($line,0,1) eq '>') {
            # This is a header line. Save the ID and comment.
            ($nextID, $nextComment) = split /\s+/, substr($line, 1), 2;

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN

	id has a value which is a string
	source_id has a value which is a string


=end text



=item Description

A feature is a set of DNA sequence fragments. Most features
are a single contiquous fragment, so they are located in only one
DNA sequence; however, fragments have a maximum length, so even a
single contiguous feature may participate in this relationship
multiple times. A few features belong to multiple DNA sequences. In
that case, however, all the DNA sequences belong to the same genome.
A DNA sequence itself will frequently have thousands of features
connected to it.
It has the following fields:

=over 4

lib/Bio/KBase/CDMI/Client.pm  view on Meta::CPAN

					    status_line => $self->{client}->status_line,
					    method_name => 'get_relationship_IsInstanceOf',
				       );
    }
}



=head2 $result = get_relationship_IsLocatedIn(ids, from_fields, rel_fields, to_fields)

A feature is a set of DNA sequence fragments. Most features
are a single contiquous fragment, so they are located in only one
DNA sequence; however, fragments have a maximum length, so even a
single contiguous feature may participate in this relationship
multiple times. A few features belong to multiple DNA sequences. In
that case, however, all the DNA sequences belong to the same genome.
A DNA sequence itself will frequently have thousands of features
connected to it.
It has the following fields:

=over 4