| Bio::Tools::Run::ERPIN(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::ERPIN(3pm) |
Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of programs.
#run
my @params = (
trset => 'BL.erpin',
region => [1, 10],
# Set up search strategy this way...
strategy => [ 'umask' => [1, 2],
'umask' => [1, 2, 3, 4],
'umask' => [1, 2, 3, 4, 5, 6],
'nomask',
'cutoff' => [0, 10, 15, 20]
]
# or use a simple string...
#strategy => '-umask 4 -add 5 -nomask -cutoff 0 10 15',
pcw => 100
);
my $factory = Bio::Tools::Run::ERPIN->new(-program =>'erpin',
@params);
# Pass the factory a Bio::Seq object or a file name
# Returns a Bio::SearchIO object
#my $search = $factory->run("B_sub.fas");
my $search = $factory->run($seq);
my @feat;
while (my $result = $searchio->next_result){
while(my $hit = $result->next_hit){
while (my $hsp = $hit->next_hsp){
print join("\t", ( $r->query_name,
$hit->name,
$hsp->hit->start,
$hsp->hit->end,
$hsp->meta,
$hsp->score,
)), "\n";
}
}
}
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/
Email: cjfields-at-uiuc-dot-edu
cjfields-at-uiuc-dot-edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
Function: creates a new RNAMotif factory
Returns: Bio::Tools::Run::RNAMotif
Args : list of parameters
-tempfile => set tempfile flag (default 0)
-outfile_name => set file to send output to (default none)
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : version Usage : $v = $prog->version(); Function: Determine the version number of the program Example : Returns : float or undef Args : none
Title : run Usage : $obj->run($seqFile) Function: Runs ERPIN programs and returns Bio::SearchIO Returns : Args : Must pass Bio::PrimarySeqI's or file names
Title : tempfile Usage : $obj->tempfile(1) Function: Set tempfile flag. When set, writes output to a tempfile; this is overridden by outfile_name() if set Returns : Boolean setting (or undef if not set) Args : [OPTIONAL] Boolean
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : Args :
Title : _setparams Usage : Internal function, not to be called directly Function: creates a string of params to be used in the command string Example : Returns : string of params Args :
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : writes passed Seq objects to tempfile, to be used as input
for program
Args :
| 2023-01-22 | perl v5.36.0 |