1Bio::Tools::Run::RNAMotUisfe(r3)Contributed Perl DocumenBtiaot:i:oTnools::Run::RNAMotif(3)
2
6 Bio::Tools::Run::RNAMotif - Wrapper for local execution of rnamotif,
7 rm2ct, rmfmt, rmprune
8
10 #run rnamotif|rmfmt|rm2ct
11 my @params = (
13 descr => 'pyrR.descr',
14 fmt => 'gb',
15 setvar => 'ctx_maxlen=20',
16 context => 1,
17 sh => 1,
18 );
19 my $factory = Bio::Tools::Run::RNAMotif->new(-program =>'rnamotif',
21 -prune => 1,
22 @params);
23 # Pass the factory a Bio::Seq object or a file name
25 # Returns a Bio::SearchIO object
26 #my $searchio = $factory->run("B_sub.gb");
28 my $searchio = $factory->run($seq);
29 while (my $result = $searchio->next_result){
30 while(my $hit = $result->next_hit){
31 while (my $hsp = $hit->next_hsp){
32 print join("\t", ( $r->query_name,
33 $hit->name,
34 $hsp->hit->start,
35 $hsp->hit->end,
36 $hsp->meta,
37 $hsp->score,
38 )), "\n";
39 }
40 }
41 }
42 # Pass a finished report through rmfmt (-a format only)
44 # Returns Bio::AlignIO object
45 my $aio = Bio::AlignIO->new(-file=>"rna.msf",-format=>'msf');
47 my $factory = Bio::Tools::Run::RNAMotif->new('program'=>'rmfmt',
48 'a' => 1);
49 my $alnin = $factory->run('trna.rnamotif');
50 my $aln = $alnin->next_aln;
52 $aio->write_aln($aln);
54
56 Wrapper module for Tom Macke and David Cases's RNAMotif suite of
57 programs. This allows running of rnamotif, rmprune, rm2ct, and rmfmt.
58 Binaries are available at
59 http://www.scripps.edu/mb/case/casegr-sh-3.5.html.
60 This wrapper allows for one to save output to an optional named file or
62 tempfile using the '-outfile_name' or '-tempfile' parameters; this is
63 primarily for saving output from the rm2ct program, which currently
64 does not have a parser available. If both a named output file and
65 tempfile flag are set, the output file name is used. The default
66 setting is piping output into a filehandle for parsing (or output to
67 STDERR, for rm2ct which requires '-verbose' set to 1).
68 WARNING: At this time, there is very little checking of parameter
70 settings, so one could have an error if setting the worng parameter for
71 a program. Future versions will likely add some error checking.
72
74 All program parameters are currently supported. Of note, the 'D'
75 parameter, used for setting the value of a variable to a value, is
76 changed to 'set_var' to avoid name collisions with 'd' (used for
77 dumping internal data structures).
78
80 Mailing Lists
81 User feedback is an integral part of the evolution of this and other
82 Bioperl modules. Send your comments and suggestions preferably to one
83 of the Bioperl mailing lists. Your participation is much appreciated.
84 bioperl-l@bioperl.org - General discussion
86 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
87 Support
89 Please direct usage questions or support issues to the mailing list:
90 bioperl-l@bioperl.org
92 rather than to the module maintainer directly. Many experienced and
94 reponsive experts will be able look at the problem and quickly address
95 it. Please include a thorough description of the problem with code and
96 data examples if at all possible.
97 Reporting Bugs
99 Report bugs to the Bioperl bug tracking system to help us keep track
100 the bugs and their resolution. Bug reports can be submitted via the
101 web:
102 http://bugzilla.open-bio.org/
104
106 Email: cjfields-at-uiuc-dot-edu
107
109 cjfields-at-uiuc-dot-edu
110
112 The rest of the documentation details each of the object methods.
113 Internal methods are usually preceded with a _
114 new
116 Title : new
117 Usage : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
118 Function: creates a new RNAMotif factory
119 Returns: Bio::Tools::Run::RNAMotif
120 Args : list of parameters
121 -tempfile => set tempfile flag (default 0)
122 -outfile_name => set file to send output to (default none)
123 -prune => set rmprune postprocess flag (default 0)
124 program_name
126 Title : program_name
127 Usage : $factory>program_name()
128 Function: holds the program name
129 Returns: string
130 Args : None
131 program_dir
133 Title : program_dir
134 Usage : $factory->program_dir(@params)
135 Function: returns the program directory, obtained from ENV variable.
136 Returns: string
137 Args :
138 version
140 Title : version
141 Usage : $v = $prog->version();
142 Function: Determine the version number of the program
143 Example :
144 Returns : float or undef
145 Args : none
146 run
148 Title : run
149 Usage : $obj->run($seqFile)
150 Function: Runs RNAMotif programs, returns Bio::SearchIO/Bio::AlignIO
151 Returns : Depends on program:
152 'rnamotif' - returns Bio::SearchIO
153 'rmfmt -a' - returns Bio::AlignIO
154 all others - sends output to outfile, tempfile, STDERR
155 Use search() (for Bio::SearchIO stream) or get_AlignIO() (for
157 Bio::AlignIO stream) for a uniform Bioperl object interface.
158 Args : A Bio::PrimarySeqI or file name
160 Note : This runs any RNAMotif program set via program()
161 search
163 Title : search
164 Usage : $searchio = $obj->search($seqFile)
165 Function: Runs 'rnamotif' on seqs, returns Bio::SearchIO
166 Returns : A Bio::SearchIO
167 Args : A Bio::PrimarySeqI or file name
168 Note : Runs 'rnamotif' only, regardless of program setting; all other
169 parameters loaded
170 get_AlignIO
172 Title : get_AlignIO
173 Usage : $aln = $obj->get_AlignIO($seqFile)
174 Function: Runs 'rmfmt -a' on file, returns Bio::AlignIO
175 Returns : A Bio::AlignIO
176 Args : File name
177 Note : Runs 'rmfmt -a' only, regardless of program setting; only file
178 name and outfile (if any) are set
179 tempfile
181 Title : tempfile
182 Usage : $obj->tempfile(1)
183 Function: Set tempfile flag. When set, writes output to a tempfile; this
184 is overridden by outfile_name() if set
185 Returns : Boolean setting (or undef if not set)
186 Args : [OPTIONAL] Boolean
187 prune
189 Title : prune
190 Usage : $obj->prune(1)
191 Function: Set rmprune flag. When set, follows any searches with a call to
192 rmprune (this deletes some redundant sequence hits)
193 Returns : Boolean setting (or undef if not set)
194 Args : [OPTIONAL] Boolean
195 _run
197 Title : _run
198 Usage : $obj->_run()
199 Function: Internal(not to be used directly)
200 Returns :
201 Args :
202 _setparams
204 Title : _setparams
205 Usage : Internal function, not to be called directly
206 Function: creates a string of params to be used in the command string
207 Example :
208 Returns : string of params
209 Args :
210 _writeSeqFile
212 Title : _writeSeqFile
213 Usage : obj->_writeSeqFile($seq)
214 Function: Internal(not to be used directly)
215 Returns : writes passed Seq objects to tempfile, to be used as input
216 for program
217 Args :
218perl v5.12.0 2010-04-29 Bio::Tools::Run::RNAMotif(3)