From Code to Community: Sponsoring The Perl and Raku Conference 2025 Learn more

SENDU / bioperl-run-1.5.2_005-RC / Bio / Tools / Run / AbstractRunner.pm 

            

              
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

              
package Bio::Tools::Run::AbstractRunner;
use strict;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Run::WrapperBase;
our @ISA=qw(Bio::Root::Root Bio::Root::IO Bio::Tools::Run::WrapperBase);
use Bio::Root::AccessorMaker ('$'=>[qw(input_file output_file)]);
sub new {
    my ($class, @args)=@_;
    my $self=$class->SUPER::new(@args);
    $self->_initialize(@args);
    return $self;
}
sub _initialize {
    my ($self, @args)=@_;
    my ($program_name, $program_dir)=$self->_rearrange(
        [qw(program_name program_dir)], @args);
    defined $program_name and $self->program_name($program_name);
    defined $program_dir and $self->program_dir($program_dir);
}
sub _run_program {
    my $self=shift;
    my $program = shift;
    $program ||= $self->program_path; # See WrapperBase
    my $cmd = "$program ". $self->final_param ;
    print STDERR "$cmd\n";
    my $ret = system($cmd);
    $ret==0 or $self->throw("CMD: $cmd\nNot working properly\n$?");
}
sub run {
    my $self=shift;
    $self->_find_files(shift);
    $self->_create_input_files;
    $self->run_file;
    $self->_parse_output_files;
     
}
no strict 'refs';
for my $method (qw(final_param _find_files _create_input_files _parse_output_files aaaa)){
    *{__PACKAGE__ . $method} = sub {shift->throw_not_implemented;};
}
1;
__END__
=pod
=head1 NAME
Bio::Tools::Run::AbstractRunner
=head1 SYNOPSIS
*** Give standard usage here
=head1 DESCRIPTION
=head2 Objective
The problems of bioperl-run wrapper before the time this module is made are:
=over 3
=item *
There are a lot of duplicate code among bioperl-run modules
=item *
It seems only to support object-in-object-out process, while sometimes
people just need file-in-file-out one, which has been actually
implemented but not exposed as a public method.
=item *
the different implementations, which should be similar and easy,
confuse the new developers who wants to make wrappers for their own
programs but did not know how. So it is better to review bioperl-run
and make the simple things as they should be.
=back
=head2 Temp file issues
    $runner->add_tmp_file($tmp_file);
    $runner->remove_tmp_files;
=head2 Unimplemented
Since it is an abstract module where there are methods to be implemented in
the concrete modules
=over 4
=item * final_param
=item * _find_files
=item * _create_input_files
=item * _parse_output_files
=back
=head1 AUTHOR
Juguang Xiao, juguang at tll.org.sg
=head1 COPYRIGHT
This module is a free software.
You may copy or redistribute it under the same terms as Perl itself.
=cut