RDO / Bio-KBase-0.06 / scripts / complexes_to_roles 

            

              
1
2
3
4
5
6
7
8
—
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149

              
#!perl
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
=head1 complexes_to_roles
Complexes catalyze reactions and are made up of one or more roles.  The roles
that make up a complex can be "optional", or not.
This command takes as input a table with a column composed of complex ids and
adds one column (containing a role that is part of the complex).  The "optional" field
is not returned, so you do not get back a field indicating whether or not the role is optional.  
If you need that information, we recommend that you use
    get_relationship_IsTriggeredBy -rel optional -to id
This would tack on both the optional flag and the role.
Example:
    complexes_to_roles [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 complexes_to_roles. It is documented as follows:
  $return = $obj->complexes_to_roles($complexes)
=over 4
=item Parameter and return types
=begin html
<pre>
$complexes is a complexes
$return is a reference to a hash where the key is a complexes and the value is a roles
complexes is a reference to a list where each element is a complex
complex is a string
roles is a reference to a list where each element is a role
role is a string
</pre>
=end html
=begin text
$complexes is a complexes
$return is a reference to a hash where the key is a complexes and the value is a roles
complexes is a reference to a list where each element is a complex
complex is a string
roles is a reference to a list where each element is a role
role 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: complexes_to_roles [-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->complexes_to_roles(\@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";
        }
    }
}