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#!perl
use strict;
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

would read in a file of ids and add a column for each field in the relationship.

The standard input should be a tab-separated table (i.e., each line
is a tab-separated set of fields).  Normally, the last field in each
line would contain the id. If some other column contains the id,
use

    -c N

where N is the column (from 1) that contains the id.

This is a pipe command. The input is taken from the standard input, and the
output is to the standard output.

=head2 Command-Line Options

=over 4

=item -c Column

This is used only if the column containing id is not the last.

=item -from field-list

Choose a set of fields from the Feature entity to return. Field-list is a comma-separated list of 
strings. The following fields are available:

=over 4

=item id

=item feature_type

=item source_id

=item sequence_length

=item function

=item alias

=back    

=item -rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of 
strings. The following fields are available:

=over 4