RDO / Bio-KBase-0.06 / scripts / roles_to_protein_families 

            

              
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#!perl
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
=head1 roles_to_protein_families
roles_to_protein_families can be used to locate the protein families containing
features that have assigned functions implying that they implement designated roles.
Note that for any input role (given as a role description), you may have a set
of distinct protein_families returned.
Example:
    roles_to_protein_families [arguments] < input > output
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 identifer. If another column contains the identifier
use
    -c N
where N is the column (from 1) that contains the subsystem.
This is a pipe command. The input is taken from the standard input, and the
output is to the standard output.
=head2 Documentation for underlying call
This script is a wrapper for the CDMI-API call roles_to_protein_families. It is documented as follows:
  $return = $obj->roles_to_protein_families($roles)
=over 4
=item Parameter and return types
=begin html
<pre>
$roles is a roles
$return is a reference to a hash where the key is a role and the value is a protein_families
roles is a reference to a list where each element is a role
role is a string
protein_families is a reference to a list where each element is a protein_family
protein_family is a string
</pre>
=end html
=begin text
$roles is a roles
$return is a reference to a hash where the key is a role and the value is a protein_families
roles is a reference to a list where each element is a role
role is a string
protein_families is a reference to a list where each element is a protein_family
protein_family is a string
=end text
=back
=head2 Command-Line Options
=over 4
=item -c Column
This is used only if the column containing the subsystem is not the last column.
=item -i InputFile    [ use InputFile, rather than stdin ]
=back
=head2 Output Format
The standard output is a tab-delimited file. It consists of the input
file with extra columns added.
Input lines that cannot be extended are written to stderr.
=cut
my $usage = "usage: roles_to_protein_families [-c column] < input > output";
use Bio::KBase::CDMI::CDMIClient;
use Bio::KBase::Utilities::ScriptThing;
my $column;
my $input_file;
my $kbO = Bio::KBase::CDMI::CDMIClient->new_for_script('c=i' => \$column,
                                      'i=s' => \$input_file);
if (! $kbO) { print STDERR $usage; exit }
my $ih;
if ($input_file)
{
    open $ih, "<", $input_file or die "Cannot open input file $input_file: $!";
}
else
{
    $ih = \*STDIN;
}
while (my @tuples = Bio::KBase::Utilities::ScriptThing::GetBatch($ih, undef, $column)) {
    my @h = map { $_->[0] } @tuples;
    my $h = $kbO->roles_to_protein_families(\@h);
    for my $tuple (@tuples) {
        #
        # Process output here and print.
        #
        my ($id, $line) = @$tuple;
        my $v = $h->{$id};
        if (! defined($v))
        {
            print STDERR $line,"\n";
        }
        elsif (ref($v) eq 'ARRAY')
        {
            foreach $_ (@$v)
            {
                print "$line\t$_\n";
            }
        }
        else
        {
            print "$line\t$v\n";
        }
    }
}