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#!perl
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
HideShow 109 lines of Pod
=head1 all_entities_Feature
Return all instances of the Feature entity.
A feature (sometimes also called a gene) is a part of a
genome that is of special interest. Features may be spread across
multiple DNA sequences (contigs) of a genome, but never across more
than one genome. Each feature in the database has a unique
ID that functions as its ID in this table.
Normally a Feature is just a single contigous region on a contig.
Features have types, and an appropriate choice of available types
allows the support of protein-encoding genes, exons, RNA genes,
binding sites, pathogenicity islands, or whatever.
Example:
    all_entities_Feature -a 
would retrieve all entities of type Feature and include all fields
in the entities in the output.
=head2 Related entities
The Feature entity has the following relationship links:
=over 4
     
=item Controls CoregulatedSet
=item Encompasses Feature
=item HasCoregulationWith Feature
=item HasFunctional Role
=item HasIndicatedSignalFrom Experiment
=item HasLevelsFrom ProbeSet
=item IsAnnotatedBy Annotation
=item IsContainedIn SSCell
=item IsCoregulatedWith Feature
=item IsEncompassedIn Feature
=item IsExemplarOf Role
=item IsFormedInto AtomicRegulon
=item IsInPair Pairing
=item IsLocatedIn Contig
=item IsMemberOf Family
=item IsOwnedBy Genome
=item IsRegulatedIn CoregulatedSet
=item Produces ProteinSequence
=back
=head2 Command-Line Options
=over 4
=item -a
Return all fields.
=item -h
Display a list of the fields available for use.
=item -fields field-list
Choose a set of fields to return. Field-list is a comma-separated list of 
strings. The following fields are available:
=over 4
=item feature_type
=item source_id
=item sequence_length
=item function
=item alias
=back    
    
=back
=head2 Output Format
The standard output is a tab-delimited file. It consists of the input
file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  
=cut
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;
#Default fields
my @all_fields = ( 'feature_type', 'source_id', 'sequence_length', 'function', 'alias' );
my %all_fields = map { $_ => 1 } @all_fields;
my $usage = "usage: all_entities_Feature [-show-fields] [-a | -f field list] > entity.data";
my $a;
my $f;
my @fields;
my $show_fields;
my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script("a"                => \$a,
                                                                  "show-fields" => \$show_fields,
                                                                  "h"           => \$show_fields,
                                                                  "fields=s"    => \$f);
if ($show_fields)
{
    print STDERR "Available fields: @all_fields\n";
    exit 0;
}
if (@ARGV != 0 || ($a && $f))
{
    print STDERR $usage, "\n";
    exit 1;
}
if ($a)
{
    @fields = @all_fields;
}
elsif ($f) {
    my @err;
    for my $field (split(",", $f))
    {
        if (!$all_fields{$field})
        {
            push(@err, $field);
        }
        else
        {
            push(@fields, $field);
        }
    }
    if (@err)
    {
        print STDERR "all_entities_Feature: unknown fields @err. Valid fields are: @all_fields\n";
        exit 1;
    }
}
my $start = 0;
my $count = 1_000_000;
my $h = $geO->all_entities_Feature($start, $count, \@fields );
while (%$h)
{
    while (my($k, $v) = each %$h)
    {
        print join("\t", $k, map { ref($_) eq 'ARRAY' ? join(",", @$_) : $_ } @$v{@fields}), "\n";
    }
    $start += $count;
    $h = $geO->all_entities_Feature($start, $count, \@fields);
}