File Coverage

blib/lib/Bio/Tools/Run/Coil.pm
Criterion Covered Total %
statement 31 89 34.8
branch 1 26 3.8
condition 0 6 0.0
subroutine 11 17 64.7
pod 5 5 100.0
total 48 143 33.5


line stmt bran cond sub pod time code
1             # Wrapper module for Coil Bio::Tools::Run::Coil
2             #
3             # Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
4             # originally written by Marc Sohrmann (ms2@sanger.ac.uk)
5             # Written in BioPipe by Balamurugan Kumarasamy
6             # Please direct questions and support issues to
7             #
8             # Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
9              
10             # You may distribute this module under the same terms as perl itself
11             #
12             # POD documentation - main docs before the code
13              
14             =head1 NAME
15              
16             Bio::Tools::Run::Coil - wrapper for ncoils program
17              
18             =head1 SYNOPSIS
19              
20             # Build a Coil factory
21             my $factory = Bio::Tools::Run::Coil->new($params);
22              
23             # Pass the factory a Bio::Seq object
24             # @feats is an array of Bio::SeqFeature::Generic objects
25             my @feats = $factory->run($seq);
26              
27             =head1 DESCRIPTION
28              
29             This module is a wrapper for the B program available via
30             L for predicting
31             coiled coils in protein sequences.
32              
33             By default it looks for an executable called I and data/parameter files
34             in the directory specified by the I environmental variable.
35              
36             =head1 REFERENCES
37              
38             Lupas, van Dyke & Stock,
39             I,
40             Science B<252>:1162-1164, 1991.
41              
42             Lupas, A.,
43             I,
44             Meth. Enzymology B<266>:513-525, 1996.
45              
46             =head1 FEEDBACK
47              
48             =head2 Mailing Lists
49              
50             User feedback is an integral part of the evolution of this and other
51             Bioperl modules. Send your comments and suggestions preferably to one
52             of the Bioperl mailing lists. Your participation is much appreciated.
53              
54             bioperl-l@bioperl.org - General discussion
55             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
56              
57             =head2 Support
58              
59             Please direct usage questions or support issues to the mailing list:
60              
61             I
62              
63             rather than to the module maintainer directly. Many experienced and
64             reponsive experts will be able look at the problem and quickly
65             address it. Please include a thorough description of the problem
66             with code and data examples if at all possible.
67              
68             =head2 Reporting Bugs
69              
70             Report bugs to the Bioperl bug tracking system to help us keep track
71             the bugs and their resolution. Bug reports can be submitted via the
72             web:
73              
74             http://redmine.open-bio.org/projects/bioperl/
75              
76             =head1 AUTHORS
77              
78             Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
79             originally written by Marc Sohrmann (ms2@sanger.ac.uk)
80              
81             Written in BioPipe by Balamurugan Kumarasamy
82              
83             # Please direct questions and support issues to
84             #
85             Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
86              
87             =head1 APPENDIX
88              
89             The rest of the documentation details each of the object
90             methods. Internal methods are usually preceded with a _
91              
92             =cut
93              
94             package Bio::Tools::Run::Coil;
95              
96 1         62 use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR
97 1     1   100003 $PROGRAMNAME @COIL_PARAMS %OK_FIELD);
  1         1  
98 1     1   4 use strict;
  1         1  
  1         15  
99 1     1   515 use Bio::SeqIO;
  1         38628  
  1         28  
100 1     1   6 use Bio::Root::Root;
  1         1  
  1         13  
101 1     1   3 use Bio::Root::IO;
  1         1  
  1         13  
102 1     1   432 use Bio::Tools::Coil;
  1         42933  
  1         31  
103 1     1   379 use Bio::Tools::Run::WrapperBase;
  1         2  
  1         46  
104              
105             @ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
106              
107             BEGIN {
108 1     1   2 @COIL_PARAMS=qw(PROGRAM VERBOSE QUIET SILENT);
109 1         2 foreach my $attr ( @COIL_PARAMS)
110 4         619 { $OK_FIELD{$attr}++; }
111             }
112              
113             sub AUTOLOAD {
114 0     0   0 my $self = shift;
115 0         0 my $attr = $AUTOLOAD;
116 0         0 $attr =~ s/.*:://;
117 0         0 $attr = uc $attr;
118 0 0       0 $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
119 0 0       0 $self->{$attr} = shift if @_;
120 0         0 return $self->{$attr};
121             }
122              
123             =head2 program_name
124              
125             Title : program_name
126             Usage : $factory>program_name()
127             Function: holds the program name
128             Returns: string
129             Args : None
130              
131             =cut
132              
133             sub program_name {
134 6     6 1 22 return 'ncoils';
135             }
136              
137             =head2 program_dir
138              
139             Title : program_dir
140             Usage : $factory->program_dir(@params)
141             Function: returns the program directory, obtained from ENV variable.
142             Returns: string
143             Args :
144              
145             =cut
146              
147             sub program_dir {
148 3 50   3 1 11 return Bio::Root::IO->catfile($ENV{COILSDIR}) if $ENV{COILSDIR};
149             }
150              
151             =head2 new
152              
153             Title : new
154             Usage : $coil->new(@params)
155             Function: creates a new Coil factory
156             Returns: Bio::Tools::Run::Coil
157             Args :
158              
159             =cut
160              
161             sub new {
162 1     1 1 72 my ($class,@args) = @_;
163 1         13 my $self = $class->SUPER::new(@args);
164 1         13 my ($attr, $value);
165 1         4 while (@args) {
166 0         0 $attr = shift @args;
167 0         0 $value = shift @args;
168 0 0       0 next if( $attr =~ /^-/ ); # don't want named parameters
169 0 0       0 if ($attr =~/PROGRAM/i) {
170 0         0 $self->executable($value);
171 0         0 next;
172             }
173 0         0 $self->$attr($value);
174             }
175 1         4 return $self;
176             }
177              
178             =head2 predict_protein_features
179              
180             Title : predict_protein_features()
181             Usage : DEPRECATED. Use $obj->run instead.
182             Function: Runs Coil and creates an array of featrues
183             Returns : An array of Bio::SeqFeature::Generic objects
184             Args : A Bio::PrimarySeqI
185              
186             =cut
187              
188             sub predict_protein_features{
189 0     0 1   return shift->run(@_);
190             }
191              
192             =head2 run
193              
194             Title : run
195             Usage : $obj->run($seq)
196             Function: Runs Coil and creates an array of featrues
197             Returns : An array of Bio::SeqFeature::Generic objects
198             Args : A Bio::PrimarySeqI, or a Fasta filename.
199              
200             =cut
201              
202             sub run{
203 0     0 1   my ($self,$seq) = @_;
204 0           my @feats;
205            
206 0 0         if (ref($seq) ) { # it is an object
207 0 0         if (ref($seq) =~ /GLOB/) {
208 0           $self->throw("cannot use filehandle");
209             }
210            
211 0           my $infile1 = $self->_writeSeqFile($seq);
212            
213 0           $self->_input($infile1);
214            
215 0           @feats = $self->_run();
216 0           unlink $infile1;
217             }
218             else {
219             #The argument is not a seq object but a sequence in a fasta file.
220             #Perhaps should check here or before if this file is fasta format...if not die
221             #Here the file does not need to be created or deleted. Its already written and may be used by other runnables.
222              
223 0           $self->_input($seq);
224              
225 0           @feats = $self->_run();
226            
227             }
228            
229 0           return @feats;
230              
231             }
232              
233             =head2 _input
234              
235             Title : _input
236             Usage : obj->_input($seqFile)
237             Function: Internal(not to be used directly)
238             Returns :
239             Args :
240              
241             =cut
242              
243             sub _input() {
244 0     0     my ($self,$infile1) = @_;
245 0 0         if(defined $infile1){
246            
247 0           $self->{'input'}=$infile1;
248             }
249 0           return $self->{'input'};
250              
251             }
252              
253             =head2 _run
254              
255             Title : _run
256             Usage : $obj->_run()
257             Function: Internal(not to be used directly)
258             Returns : An array of Bio::SeqFeature::Generic objects
259             Args :
260              
261             =cut
262              
263             sub _run {
264 0     0     my ($self)= @_;
265            
266 0           my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
267 0           my $str =$self->executable." -f < ".$self->{'input'}." > ".$outfile;
268 0 0 0       if($self->quiet || $self->verbose <=0 || $self->silent){
      0        
269 0 0         my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
270 0           $str.=" 2>$null";
271             }
272 0           my $status = system($str);
273 0 0         $self->throw( "Coil call ($str) crashed: $? \n") unless $status==0;
274            
275 0           my $coil_parser = Bio::Tools::Coil->new();
276 0           my $filehandle;
277 0 0         if (ref ($outfile) !~ /GLOB/) {
278 0 0         open (COIL, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
279 0           $filehandle = \*COIL;
280             }
281             else {
282 0           $filehandle = $outfile;
283             }
284              
285 0           my @coil_feat;
286            
287 0           while(my $coil_feat = $coil_parser->next_result($filehandle)){
288              
289 0           push @coil_feat, $coil_feat;
290             }
291            
292 0           $self->cleanup();
293 0           close($tfh1);
294 0           undef $tfh1;
295              
296 0           unlink $outfile;
297 0           return @coil_feat;
298              
299             }
300              
301             =head2 _writeSeqFile
302              
303             Title : _writeSeqFile
304             Usage : obj->_writeSeqFile($seq)
305             Function: Internal(not to be used directly)
306             Returns :
307             Args :
308              
309             =cut
310              
311             sub _writeSeqFile{
312 0     0     my ($self,$seq) = @_;
313 0           my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir());
314 0           my $in = Bio::SeqIO->new(-fh => $tfh , '-format' => 'Fasta');
315 0           $in->write_seq($seq);
316              
317 0           return $inputfile;
318              
319             }
320             1;