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#!perl
use strict;
use Data::Dumper;
use Bio::KBase::Utilities::ScriptThing;
use Carp;
#
# This is a SAS Component
#
HideShow 76 lines of Pod
=head1 get_entity_ContigChunk
ContigChunks are strings of DNA thought of as being a string in a 4-character alphabet
with an associated ID.  We allow a broader alphabet that includes U (for RNA) and
the standard ambiguity characters.
The notion of ContigChunk was introduced to avoid transferring/manipulating
huge contigs to access small substrings.  A ContigSequence is formed by
concatenating a set of one or more ContigChunks.  Thus, ContigChunks are the
basic units moved from the database to memory.  Their existence should be
hidden from users in most circumstances (users are expected to request
substrings of ContigSequences, and the Kbase software locates the appropriate
ContigChunks).
Example:
    get_entity_ContigChunk -a < ids > table.with.fields.added
would read in a file of ids and add a column for each filed in the entity.
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 Related entities
The ContigChunk entity has the following relationship links:
=over 4
     
=item IsSectionOf ContigSequence
=back
=head2 Command-Line Options
=over 4
=item -c Column
Use the specified column to define the id of the entity to retrieve.
=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 sequence
=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 = ( 'sequence' );
my %all_fields = map { $_ => 1 } @all_fields;
my $usage = "usage: get_entity_ContigChunk [-h] [-c column] [-a | -f field list] < ids > extended.by.a.column(s)";
my $column;
my $a;
my $f;
my $i = "-";
my @fields;
my $show_fields;
my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script('c=i'              => \$column,
                                                                  "a"           => \$a,
                                                                  "h"           => \$show_fields,
                                                                  "show-fields" => \$show_fields,
                                                                  "fields=s"    => \$f,
                                                                  'i=s'         => \$i);
if ($show_fields)
{
    print STDERR "Available fields: @all_fields\n";
    exit 0;
}
if ($a && $f) { print STDERR $usage; exit 1 }
if ($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 "get_entity_ContigChunk: unknown fields @err. Valid fields are: @all_fields\n";
        exit 1;
    }
} else {
    print STDERR $usage;
    exit 1;
}
my $ih;
if ($i eq '-')
{
    $ih = \*STDIN;
}
else
{
    open($ih, "<", $i) or die "Cannot open input file $i: $!\n";
}
while (my @tuples = Bio::KBase::Utilities::ScriptThing::GetBatch($ih, undef, $column)) {
    my @h = map { $_->[0] } @tuples;
    my $h = $geO->get_entity_ContigChunk(\@h, \@fields);
    for my $tuple (@tuples) {
        my @values;
        my ($id, $line) = @$tuple;
        my $v = $h->{$id};
        if (! defined($v))
        {
            #nothing found for this id
            print STDERR $line,"\n";
        } else {
            foreach $_ (@fields) {
                my $val = $v->{$_};
                push (@values, ref($val) eq 'ARRAY' ? join(",", @$val) : $val);
            }
            my $tail = join("\t", @values);
            print "$line\t$tail\n";
        }
    }
}